Literature

N4-hydroxycytidine (NHC) has been recently reported to have promising antiviral activity against SARS-CoV-2. To join worldwide efforts in identifying potential drug targets against this pandemic, the target landscape of NHC was defined by extracting all known targets of its chemical neighborhood, including drugs, analogues, and metabolites, and by performing target predictions from two independent platforms, following the recent Public Health Assessment via Structural Evaluation (PHASE) protocol. The analysis provides a list of over 30 protein targets that could be useful in future design activities of new COVID-19 antivirals. The relevance for existing drugs within the same chemical space, such as remdesivir, is also discussed.

Targeted contact-tracing through mobile phone apps has been proposed as an instrument to help contain the spread of COVID-19 and manage the lifting of nation-wide lock-downs currently in place in USA and Europe. However, there is an ongoing debate on its potential efficacy, especially in light of region-specific demographics. We built an expanded SIR model of COVID-19 epidemics that accounts for region-specific population densities, and we used it to test the impact of a contact-tracing app in a number of scenarios. Using demographic and mobility data from Italy and Spain, we used the model to simulate scenarios that vary in baseline contact rates, population densities, and fraction of app users in the population. Our results show that, in support of efficient isolation of symptomatic cases, app-mediated contact-tracing can successfully mitigate the epidemic even with a relatively small fraction of users, and even suppress altogether with a larger fraction of users. However, when regional differences in population density are taken into consideration, the epidemic can be significantly harder to contain in higher density areas, highlighting potential limitations of this intervention in specific contexts. This work corroborates previous results in favor of app-mediated contact-tracing as mitigation measure for COVID-19, and draws attention on the importance of region-specific demographic and mobility factors to achieve maximum efficacy in containment policies.

We combine sequence analysis, molecular dynamics and hybrid quantum mechanics/molecular mechanics simulations to obtain the first description of the mechanism of reaction of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and of the inhibition of the enzyme by Remdesivir. Despite its evolutionary youth, the enzyme is highly optimized to have good fidelity in nucleotide incorporation and a good catalytic efficiency. Our simulations strongly suggest that Remdesivir triphosphate (the active form of drug) is incorporated into the nascent RNA replacing ATP, leading to a duplex RNA which is structurally very similar to an unmodified one. We did not detect any reason to explain the inhibitory activity of Remdesivir at the active site. Displacement of the nascent Remdesivir-containing RNA duplex along the exit channel of the enzyme can occur without evident steric clashes which would justify delayed inhibition. However, after the incorporation of three more nucleotides we found a hydrated Serine which is placed in a perfect arrangement to react through a Pinner’s reaction with the nitrile group of Remdesivir. Kinetic barriers for crosslinking and polymerization are similar suggesting a competition between polymerization and inhibition. Analysis of SARS-CoV-2 mutational landscape and structural analysis of polymerases across different species support the proposed mechanism and suggest that virus has not explored yet resistance to Remdesivir inhibition.

The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplification. As such, it is virtually capable of detecting any given RNA modification present in the molecule that is being sequenced, as well as provide polyA tail length estimations at the level of individual RNA molecules. Although this technology has been publicly available since 2017, the complexity of the raw Nanopore data, together with the lack of systematic and reproducible pipelines, have greatly hindered the access of this technology to the general user. Here we address this problem by providing a fully benchmarked workflow for the analysis of direct RNA sequencing reads, termed MasterOfPores. The pipeline starts with a pre-processing module, which converts raw current intensities into multiple types of processed data including FASTQ and BAM, providing metrics of the quality of the run, quality-filtering, demultiplexing, base-calling and mapping. In a second step, the pipeline performs downstream analyses of the mapped reads, including prediction of RNA modifications and estimation of polyA tail lengths. Four direct RNA MinION sequencing runs can be fully processed and analyzed in 10 h on 100 CPUs. The pipeline can also be executed in GPU locally or in the cloud, decreasing the run time fourfold. The software is written using the NextFlow framework for parallelization and portability, and relies on Linux containers such as Docker and Singularity for achieving better reproducibility. The MasterOfPores workflow can be executed on any Unix-compatible OS on a computer, cluster or cloud without the need of installing any additional software or dependencies, and is freely available in Github (https://github.com/biocorecrg/master_of_pores). This workflow simplifies direct RNA sequencing data analyses, facilitating the study of the (epi)transcriptome at single molecule resolution.

Covid-19, caused by the SARS-CoV-2 virus, has reached the category of a worldwide pandemic. Even though intensive efforts, no effective treatments or a vaccine are available. Molecular characterization of the transcriptional response in Covid-19 patients could be helpful to identify therapeutic targets. In this study, RNAseq data from peripheral blood mononuclear cell samples from Covid-19 patients and healthy controls was analyzed from a functional point of view using probabilistic graphical models. Two networks were built: one based on genes differentially expressed between healthy and infected individuals and another one based on the 2,000 most variable genes in terms of expression in order to make a functional characterization. In the network based on differentially expressed genes, two inflammatory response nodes with different tendencies were identified, one related to cytokines and chemokines, and another one related to bacterial infections. In addition, differences in metabolism, which were studied in depth using Flux Balance Analysis, were identified. SARS-CoV2-infection caused alterations in glutamate, methionine and cysteine, and tetrahydrobiopterin metabolism. In the network based on 2,000 most variable genes, also two inflammatory nodes with different tendencies between healthy individuals and patients were identified. Similar to the other network, one was related to cytokines and chemokines. However, the other one, lower in Covid-19 patients, was related to allergic processes and self-regulation of the immune response. Also, we identified a decrease in T cell node activity and an increase in cell division node activity. In the current absence of treatments for these patients, functional characterization of the transcriptional response to SARS-CoV-2 infection could be helpful to define targetable processes. Therefore, these results may be relevant to propose new treatments.

The coronavirus disease 2019 (COVID-19) pandemic has caused an unprecedented global health crisis, with several countries imposing lockdowns to control the coronavirus spread. Important research efforts are focused on evaluating the association of environmental factors with the survival and spread of the virus and different works have been published, with contradictory results in some cases. Data with spatial and temporal information is a key factor to get reliable results and, although there are some data repositories for monitoring the disease both globally and locally, an application that integrates and aggregates data from meteorological and air quality variables with COVID-19 information has not been described so far to the best of our knowledge. Here, we present DatAC (Data Against COVID-19), a data fusion project with an interactive web frontend that integrates COVID-19 and environmental data in Spain. DatAC is provided with powerful data analysis and statistical capabilities that allow users to explore and analyze individual trends and associations among the provided data. Using the application, we have evaluated the impact of the Spanish lockdown on the air quality, observing that NO2, CO, PM2.5, PM10 and SO2 levels decreased drastically in the entire territory, while O3 levels increased. We observed similar trends in urban and rural areas, although the impact has been more important in the former. Moreover, the application allowed us to analyze correlations among climate factors, such as ambient temperature, and the incidence of COVID-19 in Spain. Our results indicate that temperature is not the driving factor and without effective control actions, outbreaks will appear and warm weather will not substantially limit the growth of the pandemic. DatAC is available at https://covid19.genyo.es.

There is limited information describing features and outcomes of patients requiring hospitalization for COVID19 disease and still no treatments have clearly demonstrated efficacy. Demographics and clinical variables on admission, as well as laboratory markers and therapeutic interventions were extracted from electronic Clinical Records (eCR) in 4712 SARS-CoV2 infected patients attending 4 public Hospitals in Madrid. Patients were stratified according to age and stage of severity. Using multivariate logistic regression analysis, cut-off points that best discriminated mortality were obtained for each of the studied variables. Principal components analysis and a neural network (NN) algorithm were applied. A high mortality incidence associated to age >70, comorbidities (hypertension, neurological disorders and diabetes), altered vitals such as fever, heart rhythm disturbances or elevated systolic blood pressure, and alterations in several laboratory tests. Remarkably, analysis of therapeutic options either taken individually or in combination drew a universal relationship between the use of Cyclosporine A and better outcomes as also a benefit of tocilizumab and/or corticosteroids in critically ill patients. We present a large Spanish population-based study addressing factors influencing survival in current SARS CoV2 pandemic, with particular emphasis on the effectivity of treatments. In addition, we have generated an NN capable of identifying severity predictors of SARS CoV2. A rapid extraction and management of data protocol from eCR and artificial intelligence in-house implementations allowed us to perform almost real time monitoring of the outbreak evolution.

The recent emergence of the novel SARS-CoV-2 in China and its rapid spread in the human population has led to a public health crisis worldwide. Like in SARS-CoV, horseshoe bats currently represent the most likely candidate animal source for SARS-CoV-2. Yet, the specific mechanisms of cross-species transmission and adaptation to the human host remain unknown. Here we show that the unsupervised analysis of conservation patterns across the β-CoV spike protein family, using sequence information alone, can provide valuable insights on the molecular basis of the specificity of β-CoVs to different host cell receptors. More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). Furthermore, by integrating structural data, in silico mutagenesis and coevolution analysis we could elucidate the role of SDPs in mediating ACE2 binding across the Sarbecovirus lineage, either by engaging the receptor through direct intermolecular interactions or by affecting the local environment of the receptor binding motif. Finally, by the analysis of coevolving mutations across a paired MSA we were able to identify key intermolecular contacts occurring at the spike-ACE2 interface. These results show that effective mining of the evolutionary records held in the sequence of the spike protein family can help tracing the molecular mechanisms behind the evolution and host-receptor adaptation of circulating and future novel β-CoVs.

INTRODUCTION: Healthcare workers are vulnerable to adverse mental health impacts of the COVID-19 pandemic. We assessed prevalence of mental disorders and associated factors during the first wave of the pandemic among healthcare professionals in Spain. METHODS: All workers in 18 healthcare institutions (6 AACC) in Spain were invited to web-based surveys assessing individual characteristics, COVID-19 infection status and exposure, and mental health status (May 5 - September 7, 2020). We report: probable current mental disorders (Major Depressive Disorder-MDD- [PHQ-8≥10], Generalized Anxiety Disorder-GAD- [GAD-7≥10], Panic attacks, Posttraumatic Stress Disorder -PTSD- [PCL-5≥7]; and Substance Use Disorder -SUD-[CAGE-AID≥2]. Severe disability assessed by the Sheehan Disability Scale was used to identify probable "disabling" current mental disorders. RESULTS: 9,138 healthcare workers participated. Prevalence of screen-positive disorder: 28.1% MDD; 22.5% GAD, 24.0% Panic; 22.2% PTSD; and 6.2% SUD. Overall 45.7% presented any current and 14.5% any disabling current mental disorder. Workers with pre-pandemic lifetime mental disorders had almost twice the prevalence than those without. Adjusting for all other variables, odds of any disabling mental disorder were: prior lifetime disorders (TUS: OR=5.74; 95%CI 2.53-13.03; Mood: OR=3.23; 95%CI:2.27-4.60; Anxiety: OR=3.03; 95%CI:2.53-3.62); age category 18-29 years (OR=1.36; 95%CI:1.02-1.82), caring "all of the time" for COVID-19 patients (OR=5.19; 95%CI: 3.61-7.46), female gender (OR=1.58; 95%CI: 1.27-1.96) and having being in quarantine or isolated (OR= 1.60; 95CI:1.31-1.95). CONCLUSIONS: One in seven Spanish healthcare workers screened positive for a disabling mental disorder during the first wave of the COVID-19 pandemic. Workers reporting pre-pandemic lifetime mental disorders, those frequently exposed to COVID-19 patients, infected or quarantined/isolated, female workers, and auxiliary nurses should be considered groups in need of mental health monitoring and support.

We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.

COVID-19 presents a wide range of symptoms, including gastrointestinal manifestations such as diarrhea, nausea, and abdominal pain. Lactobacillus acidophilus has been proposed as a potential adjunct therapy to alleviate these symptoms due to its probiotic properties, which help restore gut microbiota balance and modulate immune responses. This review systematically analyzed studies assessing the effects of L. acidophilus in COVID-19 patients with gastrointestinal symptoms. The literature search was conducted through PubMed and the WHO COVID-19 database using keywords such as "Lactobacillus acidophilus", "COVID-19", "gastrointestinal symptoms", and "inflammation markers". The search covered studies published until February 2025. Inclusion criteria: observational and clinical trials with L. acidophilus for symptom relief. Exclusion: animal studies and non-ethical approvals. The findings suggest that L. acidophilus supplementation may contribute to faster resolution of diarrhea, improved gut microbiota balance, and reduced inflammatory markers. However, some studies have found no significant impact on hospitalization rates or disease progression. The probiotic's mechanisms of action appear to involve microbiota modulation, intestinal barrier reinforcement, and anti-inflammatory effects rather than direct viral inhibition in COVID-19 after progression. Some L. acidophilus strains show promise, and clinical validation should follow careful preclinical studies (in vitro, cell lines, and animal models), especially in vulnerable populations such as immunocompromised individuals. Understanding the gut-lung axis and its role in immune response regulation, together with the need for a thorough characterization of the specific strains, including biochemical, genomic, and functional properties, before testing in humans, may provide deeper insights into the therapeutic potential of probiotics in viral infections.

Background/Objectives: People with HIV (PWH) often have a suboptimal response to vaccines, raising concerns regarding the efficacy of coronavirus disease 2019 (COVID-19) vaccines in this population. We aimed to evaluate the humoral immune response to the B.1 lineage and Omicron variant in PWH on antiretroviral therapy (ART) following COVID-19 vaccination. Methods: We conducted a prospective study of 19 PWH on ART who received a two-dose series of the COVID-19 mRNA vaccine and a booster six months later. Participants without HIV infection (n = 25) were included as a healthy control (HC) group. The humoral response to the COVID-19 vaccine (anti-SARS-CoV-2 S IgG levels and ability to block ACE2-S interaction) against both the original B.1 lineage and the Omicron variant was assessed using immunoassays. Results: The humoral response in PWH was very strong (geometric mean fold rise, GMFR > 8) after the second dose and strong (GMFR > 4) after the booster dose for both the B.1 lineage and the Omicron variant. We found comparable humoral responses to the B.1 lineage and Omicron variant between PWH and HC groups after the second and booster doses (q-value > 0.05). The COVID-19 vaccine generated a significantly weaker humoral response against the Omicron variant compared to the B.1 lineage in both groups (q-value < 0.05). However, this response improved after the booster dose, although it remained weaker in PWH. Conclusions: PWH showed a strong humoral response to the COVID-19 vaccine against B.1 and Omicron, though the Omicron response was weaker than B.1. Booster doses in PWH improved the Omicron response, but it stayed lower than B.1. Findings confirm vaccine effectiveness in PWH, stressing the critical role of boosters and potential need for updated vaccines for variants like Omicron.

SUMMARYThe mechanisms by which viruses enter host cells are crucial for their ability to infect and cause disease, serving as major targets for both host immune responses and therapeutic strategies. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry process is primarily driven by the binding of the viral spike (S) protein to the angiotensin-converting enzyme 2 (ACE2) receptor, in conjunction with the activity of endosomal cathepsin L and the serine protease transmembrane protease serine 2 (TMPRSS2). Nevertheless, recent scientific advances have expanded our understanding of SARS-CoV-2 entry mechanisms, uncovering alternative receptors and novel cofactors that may enhance viral tropism and adaptability. Given the critical role of the SARS-CoV-2 S protein in mediating host cell entry, it has become a primary target for prevention and therapeutic strategies. However, the continuous spread of SARS-CoV-2 has led to the emergence of S protein variants that may potentially confer a fitness advantage or modify key aspects of SARS-CoV-2 biology, such as transmissibility, infectivity, antigenicity, and/or pathogenicity, posing significant challenges to the efficacy of current interventions. In this review, we provide an updated and comprehensive overview of the latest advances in SARS-CoV-2 entry pathways and molecular mechanisms, exploring their implications for antiviral drug discovery, vaccine design, and the development of other biomedical strategies while addressing the challenges posed by the ongoing evolution of the virus.

Background

This study assesses the cerebrospinal fluid (CSF) levels of the viral receptor angiotensin-converting enzyme 2 (ACE2) and of the serine protease TMPRSS2 fragments in patients with SARS-CoV-2 infection presenting encephalitis (CoV-Enceph).

Methods

The study included biobanked CSF from 18 CoV-Enceph, 4 subjects with COVID-19 without encephalitis (CoV), 21 with non-COVID-19-related encephalitis (Enceph), and 21 neurologically healthy controls. Participants underwent a standardized assessment for encephalitis. A large subset of samples underwent analysis for an extended panel of CSF neuronal, glial, and inflammatory biomarkers. ACE2 and TMPRSS2 species were determined in the CSF by western blotting.

Results

ACE2 was present in CSF as several species, full-length forms and 2 cleaved fragments of 80 and 85 kDa. CoV-Enceph patients displayed increased CSF levels of full-length species, as well as the 80 kDa fragment, but not the alternative 85 kDa fragment, compared with controls and Enceph patients, characterized by increases of both fragments. Furthermore, TMPRSS2 was increased in the CSF of Enceph patients compared with controls, but not in CoV-Enceph patients. The CoV patients without encephalitis displayed unaltered CSF levels of ACE2 and TMPRSS2 species.

Conclusions

Patients with encephalitis displayed an overall increase in CSF ACE2, probably as a consequence of brain inflammation. The increase of the shortest ACE2 fragment only in CoV-Enceph patients may reflect the enhanced cleavage of the receptor triggered by SARS-CoV-2, thus serving to monitor brain penetrance of the virus associated with the rare encephalitis complication. TMPRSS2 changes in the CSF appeared related to inflammation, but not with SARS-CoV-2 infection.

SARS-CoV-2, which originated in China in late 2019, quickly fueled the global COVID-19 pandemic, profoundly impacting health and the economy worldwide. A series of vaccines, mostly based on the full SARS-CoV-2 Spike protein, were rapidly developed, showing excellent humoral and cellular responses and high efficacy against both symptomatic infection and severe disease. However, viral evolution and the waning humoral neutralizing responses strongly challenged vaccine long term effectiveness, mainly against symptomatic infection, making necessary a strategy of repeated and updated booster shots. In this repeated vaccination context, antibody repertoire diversification was evidenced, although immune imprinting after booster doses or reinfection was also demonstrated and identified as a major determinant of immunological responses to repeated antigen exposures. Considering that a small domain of the SARS-CoV-2 Spike protein, the receptor binding domain (RBD), is the major target of neutralizing antibodies and concentrates most viral mutations, the following text aims to provide insights into the ongoing debate over the best strategies for vaccine boosters. We address the relevance of developing new booster vaccines that target the evolving RBD, thus focusing on the relevant antigenic sites of the SARS-CoV-2 new variants. A combination of this strategy with immunofusing and computerized approaches could minimize immune imprinting, therefore optimizing neutralizing immune responses and booster vaccine efficacy.

Animal models have been instrumental in elucidating the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and in testing coronavirus disease 2019 (COVID-19) vaccines and therapeutics. Wild-type (WT) mice are not susceptible to many SARS-CoV-2 variants, and therefore, transgenic K18-hACE2 mice have emerged as a standard model system. However, this model is characterized by a severe disease, particularly associated with neuroinfection, which leads to early humane endpoint euthanasia. Here, we established a novel knock-in (KI) mouse model by inserting the original K18-hACE2 transgene into the collagen type I alpha chain (COL1A1) locus using a recombinase-mediated cassette exchange (RMCE) system. Once the Col1a1-K18-hACE2 mouse colony was established, animals were challenged with a B.1 SARS-CoV-2 (D614G) isolate and were monitored for up to 14 days. Col1a1-K18-hACE2 mice exhibited an initial weight loss similar to the K18-hACE2 transgenic model but did not develop evident neurologic clinical signs. The majority of Col1a1-K18-hACE2 mice did not reach the pre-established humane endpoint, showing a progressive weight gain 9 days postinfection (dpi). Importantly, despite this apparent milder pathogenicity of the virus in this mouse model compared to the K18-hACE2 transgenic model, high levels of viral RNA were detected in the lungs, oropharyngeal swab, and nasal turbinates. Moreover, the remaining lesions and inflammation in the lungs were still observed 14 dpi. In contrast, although low-level viral RNA could be detected in a minority of Col1a1-K18-hACE2 animals, no brain lesions were observed at any timepoint. Overall, Col1a1-K18-hACE2 mice constitute a new model for investigating SARS-CoV-2 pathogenesis and treatments, with potential implications for studying long-term COVID-19 sequelae.IMPORTANCEK18-hACE2 mice express high levels of the human protein angiotensin-converting enzyme 2 (ACE2), the receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and are therefore susceptible to infection by this virus. These animals have been crucial to understanding viral pathogenesis and to testing coronavirus disease 2019 (COVID-19) vaccines and antiviral drugs. However, K18-hACE2 often dies after infection with initial SARS-CoV-2 variants, likely due to a massive brain infection that does not occur in humans. Here, we used a technology known as knock-in (KI) that allows for the targeted insertion of a gene into a mouse, and we have generated a new human ACE2 (hACE2) mouse. We have characterized this new animal model demonstrating that, upon challenge with SARS-CoV-2, the virus replicates in the respiratory tract, damaging lung tissue and causing inflammation. In contrast to K18-hACE2 mice, only limited or no brain infection could be detected in this new model. After 14 days, most animals recovered from the infection, although lung tissue lesions were still observed. This new model could be instrumental for the study of specific disease aspects such as post-COVID-19 condition, sequelae, and susceptibility to reinfection.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 19 (COVID-19) pandemic, significantly impacting global health, economies, and social stability. In February 2020, the first cases of SARS-CoV-2 infections in animals were documented, highlighting the potential risks posed by regular human-animal interactions in facilitating viral transmission. In consequence, it is essential to validate surveillance methods for SARS-CoV-2 in animals. In the present study, 101 sera from different animal species (36 cats, 41 dogs, 4 ferrets, 10 wild boar, 6 domestic goats, and 4 lions) were tested using three different ELISA kits to evaluate humoral responses against SARS-CoV-2. ELISA results were compared and correlated with a pseudovirus neutralization test (pVNT), considered as the reference assay. ELISA-1, targeting the receptor binding domain (RBD) neutralizing antibodies (nAbs) of SARS-CoV-2, exhibited the highest diagnostic performance, and proved to be a reliable tool for initial screenings in high-throughput animal studies. In contrast, ELISA-2 (also targeting RBD nAbs) and ELISA-3 (targeting nucleoprotein antibodies) demonstrated lower sensitivity for detecting seropositive animals.

Newly emerging SARS-CoV-2 variants of concern (VOCs) continue to drive COVID-19 waves and are typically associated with immune escape and increased resistance to current therapeutics including monoclonal antibodies. By contrast, VOCs still display strong binding to the host cell receptor ACE2. Consistent with these properties, we have now found that a soluble ACE2-Fc decoy produced in glycoengineered plants effectively neutralizes different SARS-CoV-2 isolates and exhibits even increased potency against VOCs as compared to an ancestral virus strain. In a golden Syrian hamster model, therapeutic intranasal delivery of ACE2-Fc effectively reduced weight loss and SARS-CoV-2 replication in the lungs when administered 24 h post-inoculation. This protective effect was not observed upon treatment of the infected animals with a non-binding ACE2-Fc mutant, demonstrating that the plant-derived ACE2-Fc decoy interferes specifically with the attachment of the virus to host cells. The results obtained provide support for further development of decoy-based antiviral approaches by plant molecular pharming.

The SARS-CoV-2 virus, responsible for the COVID-19 pandemic, has continuously evolved, generating numerous variants with varying degrees of infectivity and transmissibility. The EG.5 subvariant of SARS-CoV-2 emerged globally in mid-2023 as part of the ongoing evolution of the Omicron lineage. Derived from the recombinant XBB.1.9 sublineage, EG.5 has attracted attention due to its enhanced immune escape and sustained transmissibility. As a member of the FLip lineage, EG.5 harbors the convergent F456L mutation in the spike receptor-binding domain (RBD), a key residue for neutralizing antibody recognition. Understanding the molecular mechanisms underlying these variations is crucial for developing effective antiviral strategies. In this study, we employed accelerated molecular dynamics simulations, free-energy calculations, and interaction fingerprint analysis, to investigate the intricate molecular interactions between the spike RBD and the angiotensin-converting enzyme 2 (ACE2) receptor in wild-type SARS-CoV-2 and its variants, specifically Omicron, XBB.1.9.2, and the concerning EG.5 variant. Our findings reveal that electrostatic interactions are the predominant driving force behind the stabilization of the viral spike protein-ACE2 complex. The Omicron, XBB.1.9.2, and EG.5 variants exhibit distinct electrostatic profiles at the spike-ACE2 interface, with mutations at key residues reconfiguring local interactions. These changes enhance ACE2 binding specificity and stabilize the spike-ACE2 complex through intensified electrostatic interactions. The EG.5 variant, with its stronger binding affinity to ACE2, underscores the ongoing threat posed by SARS-CoV-2. The F456L mutation in EG.5 enhances protein stability, further supporting its increased affinity for ACE2. Our research provides valuable insights for designing targeted antiviral therapies, including peptide inhibitors and bioactive compounds. Continuous research is essential to effectively combat COVID-19 and its evolving variants.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects a variety of animal species. Susceptibility to SARS-CoV-2 is primarily determined by the utilization of the viral receptor, ACE2. SARS-CoV-2 can utilize a broad range of animal ACE2 isoforms in vitro, including the ACE2 from various camelid species. However, experimental infection of these animals does not lead to productive infection or seroconversion. In this study, we investigate the susceptibility of camelids to SARS-CoV-2 using novel well-differentiated camelid nasal organoids. We show that camelid nasal organoids are highly susceptible to Middle East respiratory syndrome coronavirus (MERS-CoV) infection, but not to infection with different SARS-CoV-2 variants (614G, BA.1 or EG.5.1.1). All viruses efficiently infected human airway organoids. Immunohistochemistry analysis revealed the absence of ACE2 on camelid nasal organoids and dromedary camel upper respiratory tract. In contrast, DPP4 was expressed in both camelid nasal organoids and the camel upper respiratory tract, which correlates with MERS-CoV infection. This study indicates that the camelid upper respiratory tract lacks expression of ACE2, which is associated with resistance to SARS-CoV-2 infection.

We used the data from a successful therapeutic assay that used icatibant in patients with hypoxemic COVID-19 pneumonia (the ICAT·COVID trial) to explore pathophysiological mechanisms. We performed concurrent-type, criterion-related validity analyses to assess the discriminative ability of a panel of nine potential serum markers (interleukin 6, ferritin, lactate dehydrogenase, C reactive protein, fibrin fragment D (D-dimer), complement 1 esterase inhibitor (antigenic and functional), complement 4 factor, and lymphocyte count) to predict the clinical milestones. Consistent with previous research, we evidenced a significant relationship between interleukin 6, lactate dehydrogenase and the lymphocyte count, and the clinical events. Furthermore, exposure to icatibant, a bradykinin B2 receptor antagonist (which improved pneumonia and mortality in the aforementioned randomised trial), attenuated this relationship, although this effect faded over time. The results reinforce the key role that the angiotensin-converting enzyme 2 has on COVID-19 pathophysiology as a point of convergence between the renin-angiotensin and kallikrein-kinin systems. This was shown clinically by the successful blocking of inflammatory pathways by icatibant at the bradykinin effector loop level early during the acute hyperinflammatory stage of the disease.

Although the COVID-19 pandemic was declared no longer a global emergency by the World Health Organization in May 2023, SARS-CoV-2 is still infecting people across the world. Many therapeutic oligonucleotides such as ASOs, siRNAs, or CRISPR-based systems emerged as promising antiviral strategies for the treatment of SARS-CoV-2. In this work, we explored the inhibitory potential on SARS-CoV-2 replication of Polypurine Reverse Hoogsteen Hairpins (PPRHs), CC1-PPRH, and CC3-PPRH, targeting specific polypyrimidine sequences within the replicase and Spike regions, respectively, and previously validated for COVID-19 diagnosis. Both PPRHs are bound to their target sequences in the viral genome with high affinity in the order of nM. In vitro, both PPRHs reduced viral replication by more than 92% when transfected into VERO-E6 cells 24 h prior to infection with SARS-CoV-2. In vivo intranasal administration of CC1-PPRH in K18-hACE2 mice expressing the human ACE receptor protected all the animals from SARS-CoV-2 infection. The properties of PPRHs position them as promising candidates for the development of novel therapeutics against SARS-CoV-2 and other viral infections.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a public health concern due to infections with new SARS-CoV-2 variants. Therefore, finding effective preventive and therapeutic treatments against all SARS-CoV-2 variants is of great interest. In this study, we examined the capacity of eucalyptus essential oil (EEO) and eucalyptol (EOL) to prevent SARS-CoV-2 infection, using as a model SARS-CoV-2 Spike pseudotyped lentivirus (SARS-CoV-2 pseudovirus) and 293T cells transfected with human angiotensin-converting enzyme 2 (hACE2-293T cells). First, we determined the cytotoxicity of EEO and EOL using the MTT colorimetric assay, selecting non-cytotoxic concentrations ≤ 0.1% (v/v) for further analysis. Subsequently, we evaluated the capacity of EEO and EOL in cell cultures to preclude infection of hACE2-293T cells by SARS-CoV-2 pseudovirus, using a luciferase-based assay. We found that EEO and EOL significantly reduced SARS-CoV-2 pseudovirus infection, obtaining IC₅₀ values of 0.00895% and 0.0042% (v/v), respectively. Likewise, EEO and EOL also reduced infection by vesicular stomatitis virus (VSV) pseudovirus, although higher concentrations were required. Hence, EEO and EOL may be able to inhibit SARS-CoV-2 infection, at least partially, through a Spike-independent pathway, supporting the implementation of aromatherapy with these agents as a cost-effective antiviral measure.

SARS-CoV- 2 continues to evolve, producing novel Omicron subvariants through recombinant lineages that acquire new mutations, undermining existing antiviral strategies. The viral fitness and adaptive potential of SARS-CoV- 2 present significant challenges to emergency treatments, particularly monoclonal antibodies, which demonstrate reduced efficacy with the emergence of each new variant. Consequently, immunocompromised individuals, who are more susceptible to severe manifestations of COVID- 19 and face heightened risks of critical complications and mortality, remain vulnerable in the absence of effective emergency treatments. To develop translational approaches that can benefit this at-risk population and establish broader therapeutic strategies applicable across variants, we previously designed and engineered in silico miniACE2 decoys (designated BP2, BP9, and BP11). These decoys demonstrated promising efficacy in neutralizing Omicron subvariants. In this study, we leveraged the therapeutic potential of mesenchymal stromal cells (MSCs) for tissue repair and immunomodulation in lung injuries and used these cells as a platform for the secretion of BP2. Our innovative assays, which were conducted with the BP2 protein secreted into the culture supernatant of BP2-MSCs, demonstrated the potential for neutralizing SARS-CoV- 2, including Omicron subvariants. The development of these advanced therapeutic platforms holds significant promise for scalability to effectively mitigate the impact of severe COVID- 19, contributing to broader and more resilient treatment strategies against the evolving landscape of SARS-CoV- 2 variants.

Background

The origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unknown. However, it is likely that the virus spillover occurred from an animal reservoir to humans. Identifying animal species susceptible to SARS-CoV-2 is crucial for understanding cross-species transmission to humans. This study distinguishes itself by focusing on the susceptibility of the European bison (Bison bonasus), an endangered species, to SARS-CoV-2. The objective of this study was to investigate the occurrence of SARS-CoV-2 antibodies in a substantial number (n = 238) of both free-living and captive Polish European bison using an in-house ELISA method and virus neutralization test (VNT).

Results

The seroprevalence of SARS-CoV-2 infection was found to be 1.29% (3/232). None of the seropositive European bison tested positive in the virus neutralization test. All seropositive animals were part of captive herds.

Conclusions

This study represents the first report of SARS-CoV-2 seroprevalence in both free-ranging and captive European bison in Poland. Based on these findings, the European bison appears to be a less susceptible species to SARS-CoV-2. The most probable route of transmission was from humans to European bison, as all seropositive animals belonged to captive herds with contact with indirect human sources, such as tourists and keepers.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the zoonotic virus responsible for the COVID-19 pandemic, has caused global health and economic disruption. American mink (Neovison vison) are highly susceptible to SARS-CoV-2 and capable of transmitting it to both mink and humans. We previously reported the first detection of SARS-CoV-2 in feral mink, with two positive cases among 13 animals in the upper courses of two rivers in the Valencian Community, eastern Spain. Here, we expand that study with 60 additional feral mink sampled from November 2020 to May 2022. Four new positives were identified by two-step RT-PCR assay on necropsy samples, including nasal and rectal swabs, lung tissue, lymph nodes, and fetuses from three pregnant females. In total, six of 73 mink tested positive, all with low viral loads. Sanger sequencing confirmed infection and revealed clustering with the B.1.177 and Alpha variants. Body weight and reproductive status analyses indicated seasonal breeding and high population turnover, consistent with other wild mink populations. Our findings reveal that SARS-CoV-2 circulation is limited in feral mink, at least in this region. They underscore the key importance of wildlife surveillance as an element of the One Health strategy, which encompasses humans, animals, and the environment.

Self/non-self-discrimination is a fundamental aspect of adaptive immunity, which helps prevent harmful autoimmune responses. However, infectious agents can also act as environmental catalysts for autoimmune diseases. In this study, we investigated the role of molecular mimicry to self-antigens in epitope recognition in relation to infectious and autoimmune diseases. To this end, we performed BLAST searches against the human proteome, utilizing known virus-specific B and T cell peptide epitopes identified in association with autoimmune or infectious diseases in humans as our queries. Additionally, similar control analyses were carried out using non-B and non-T cell epitopes, consisting of random viral peptide sequences. Overall, our results endorsed a major role of molecular mimicry in instigating or sustaining autoimmunity associated with viral infections and challenged the prevailing view on self/non-self-discrimination for T cells. Additionally, we uncovered many virus-specific epitopes among those identified in association with infectious diseases with high similarity to self-antigens, which are primarily derived from human coronaviruses and various flaviviruses. Recognition of these epitopes could lead to autoimmunity against human proteins that are in cellular components concerning cell motility, cell membrane projections, and cellular synapses.

To generate antibodies (Abs) against SARS-CoV-2 emerging variants, we integrated multiple tools and engineered molecules with excellent neutralizing breadth and potency. Initially, the screening of an immune library identified a nanobody (Nb), termed Nb4, specific to the receptor-binding domain (RBD) of the Omicron BA.1 variant. A Nb4-derived heavy chain antibody (hcAb4) recognized the spike (S) of the Wuhan, Beta, Delta, Omicron BA.1, and BA.5 SARS-CoV-2 variants. A high-resolution crystal structure of the Nb4 variable (VHH) domain in complex with the SARS-CoV-2 RBD (Wuhan) defined the Nb4 binding mode and interface. The Nb4 VHH domain grasped the RBD and covered most of its outer face, including the core and the receptor-binding motif (RBM), which was consistent with hcAb4 blocking RBD binding to the SARS-CoV-2 receptor. In mouse models, a humanized hcAb4 showed therapeutic potential and prevented the replication of SARS-CoV-2 BA.1 virus in the lungs of the animals. In vitro, hcAb4 neutralized Wuhan, Beta, Delta, Omicron BA.1, and BA.5 viral variants, as well as the BQ.1.1 subvariant, but showed poor neutralization against the Omicron XBB.1.5. Structure-based computation of the RBD-Nb4 interface identified three Nb4 residues with a reduced contribution to the interaction with the XBB.1.5 RBD. Site-saturation mutagenesis of these residues resulted in two hcAb4 mutants with enhanced XBB.1.5 S binding and virus neutralization, further improved by mutant Nb4 trimers. This research highlights an approach that combines library screening, Nb engineering, and structure-based computational predictions for the generation of SARS-CoV-2 Omicron-specific Abs and their adaptation to emerging variants.

BackgroundEvolution of SARS-CoV-2 is continuous.AimBetween 01/2020 and 02/2022, we studied SARS-CoV-2 variant epidemiology, evolution and association with COVID-19 severity.MethodsIn nasopharyngeal swabs of COVID-19 patients (n = 1,762) from France, Italy, Spain, and the Netherlands, SARS-CoV-2 was investigated by reverse transcription-quantitative PCR and whole-genome sequencing, and the virus variant/lineage (NextStrain/Pangolin) was determined. Patients' demographic and clinical details were recorded. Associations between mild/moderate or severe COVID-19 and SARS-CoV-2 variants and patient characteristics were assessed by logistic regression. Rates and genomic locations of mutations, as well as quasi-species distribution (≥ 2 heterogeneous positions, ≥ 50× coverage) were estimated based on 1,332 high-quality sequences.ResultsOverall, 11 SARS-CoV-2 clades infected 1,762 study patients of median age 59 years (interquartile range (IQR): 45-73), with 52.5% (n = 925) being male. In total, 101 non-synonymous substitutions/insertions correlated with disease prognosis (severe, n = 27; mild-to-moderate, n = 74). Several hotspots (mutation rates ≥ 85%) occurred in Alpha, Delta, and Omicron variants of concern (VOCs) but none in pre-Alpha strains. Four hotspots were retained across all study variants, including spike:D614G. Average number of mutations per open-reading-frame (ORF) increased in the spike gene (average < 5 per genome in January 2020 to > 15 in 2022), but remained stable in ORF1ab, membrane, and nucleocapsid genes. Quasi-species were most prevalent in 20A/EU2 (48.9%), 20E/EU1 (48.6%), 20A (38.8%), and 21K/Omicron (36.1%) infections. Immunocompromised status and age (≥ 60 years), while associated with severe COVID-19 or death irrespective of variant (odds ratio (OR): 1.60-2.25; p ≤ 0.014), did not affect quasi-species' prevalence (p > 0.05).ConclusionSpecific mutations correlate with COVID-19 severity. Quasi-species potentially shaping VOCs' emergence are relevant to consider.

mRNA vaccines have shown great efficacy against SARS-CoV-2, yet challenges remain in optimizing vaccine components to achieve enhanced immune response and vaccine stability. In this study, we developed CPVax-CoV, a new lyophilized mRNA vaccine that features novel thiolactone-based ionizable lipids and newly designed untranslated regions (UTRs) for enhanced expression. Incorporation of these optimized components into our vaccine candidate CPVax-CoV significantly improved immune responses in mice compared to commercially available mRNA vaccines. Moreover, lyophilized CPVax-CoV has proven to be thermostable, maintaining its biological activity for up to one year at 4 °C and 25 °C after lyophilization, overcoming the cold-chain limitations of current mRNA vaccines. This vaccine demonstrates protective efficacy against ancestral SARS-CoV-2 and the Omicron XBB variant, offering a scalable solution for global distribution and pandemic preparedness. These findings underscore the potential of this platform for future next-generation mRNA vaccine development.

In December 2019, the so-called "coronavirus disease 2019" (COVID-19) began. This disease is characterized by heterogeneous clinical manifestations, ranging from an asymptomatic process to life-threatening conditions associated with a "cytokine storm". This article (narrative review) summarizes the epidemiologic characteristics and clinical manifestations of COVID-19 and multi-system inflammatory syndrome in children (MIS-C). The effect of the pandemic confinement on vitamin D status and the hypotheses proposed to explain the age-related difference in the severity of COVID-19 are discussed. The role of vitamin D as a critical regulator of both innate and adaptive immune responses and the COVID-19 cytokine storm is analyzed. Vitamin D and its links to both COVID-19 (low levels of vitamin D appear to worsen COVID-19 outcomes) and the cytokine storm (anti-inflammatory activity) are detailed. Finally, the efficacy of vitamin D supplementation in COVID-19 is evaluated, but the evidence supporting vitamin D supplementation as an adjuvant treatment for COVID-19 remains uncertain.

Despite significant progress in drug discovery, there remains an urgent need to identify new structures capable of targeting drug-resistant diseases, as well as novel pathogens, to address the growing challenges in global health. This work highlights the underexplored potential of twistane-like structures as promising candidates for drug development, particularly as antiviral agents. We provide the first comprehensive study of their antiviral activity, in particular against SARS-CoV-2. We report the synthesis of a family of chiral indolyl-twistenediones, with the separation and characterization of both enantiomers via chiral semipreparative HPLC. The absolute configurations were determined using experimental and theoretical ECD techniques, supported by DFT calculations. A detailed biological study of their antiviral activity against various pathogenic RNA viruses demonstrates selective efficacy against members of the Coronaviridae family, specifically targeting a post-entry step in the viral replication cycle. Further investigation revealed a remarkable chiral distinction in the antiviral activity between the two enantiomers, opening new avenues for research in the 3D space of chiral cage compounds.

An anti-HIV screen of natural product extracts resulted in the discovery of a new antiviral protein through bioassay-guided fractionation of an aqueous extract of the ascidian Didemnum molle. The protein was sequenced through a combination of tandem mass spectroscopy and N-terminal Edman degradation of peptide fragments after a series of endoproteinase digestions. The primary amino acid sequence and disulfide bonding pattern of the 102-amino acid protein were closely related to the antiviral protein cyanovirin-N (CV-N). This new CV-N homolog was named Dm-CVNH. Alphafold2 prediction resulted in a tertiary structure, highly similar to CV-N, comprised of two symmetrically related domains that contained five β-strands and two α-helical turns each. Dm-CVNH showed specificity for high mannose and oligomannose structures, bound to HIV-1 gp-120 and potently inactivated HIV in neutralization assays (EC₅₀ of 0.95 nM). Dm-CVNH inhibited infection in a SARS-CoV-2 live virus assays and was shown to bind to the S1 domain of SARS-CoV-2 Spike glycoprotein. Dm-CVNH behaved in a manner similar to CV-N, binding with a 2:1 stoichiometry to Spike (both to WH-1 and Omicron variants) and preferring the Omicron variant (Kd 42 nM) to original WH-1 (Kd = 89 nM) Spike. This sensitivity to emergent strains was mirrored in viral neutralization assays where Dm-CVNH potently inhibited the infection of Omicron strains XBB.1.16 and JN.1 (IC₅₀ = 11-18 nM).

Background: SARS-CoV-2 was the causing agent of the COVID-19 pandemic, which resulted in millions of deaths worldwide and massive economic losses. Although there are already several vaccines licensed, as novel variants develop, understanding the immune response induced by vaccination and natural infection is key for the development of future vaccines. Methods: In this study, we have used flow cytometry and next-generation sequencing to assess the longitudinal CD8⁺ T-cell response against natural infection and vaccination in convalescent and vaccinated individuals, from early activation to immune memory establishment. Moreover, we have characterized the T-cell receptor clonality and diversity at different stages post-infection and post-vaccination. Results: We have found no significant differences in CD8⁺ T-cell activation during the first three weeks post-infection compared to the first three weeks after first vaccination. Conversely, natural infection resulted in sustained high levels of T-cell activation at four weeks post-infection, a point in which we observed a decline in T-cell activation post-vaccination despite boosting with a second vaccination shot. Moreover, additional vaccination did not result in enhanced T-cell activation. Of note, we have observed variations in the memory subset structure at every stage of disease and vaccination. Overall, both infection and immunization induced a highly diverse T-cell receptor repertoire, which was observed both between study groups and between patients inside a given group. Conclusions: These data contribute to expand our knowledge about the immune response to SARS-CoV-2 infection and vaccination and call for additional strategies to enhance T-cell responses by booster immunization.

Antigen recognition by human leukocyte antigen (HLA) restriction is critical for an adequate antiviral response in both natural infection and vaccination. However, the overwhelming polymorphism of HLA, with nearly 40,000 alleles identified, is an important limitation for the global analysis of cellular immune responses and vaccine efficacy. In this narrative review, we included several immunoinformatics studies performed in our laboratory to circumvent this limitation. These analyses focused on studying the cellular immune responses restricted by the most common HLA alleles, and their role in vaccine efficacy. Computational studies validated experimentally, such as our laboratory has carried out, represent a useful, rapid, and cost-effective strategy to combat future pandemics.

The receptor-binding domain (RBD) of SARS-CoV-2 spike protein is responsible for the recognition of the Angiotensin-Converting Enzyme 2 (ACE2) receptor in human cells and, thus, plays a critical role in viral infection. The therapeutic value of targeting this interaction has been proven by a sizable body of research investigating antibodies, small proteins, aptamers, and peptides. This study presents a novel peptide that impinges the interaction between RBD and ACE2. Starting from a very large pool of structurally designed peptides extracted from our database, PepI-Covid19, a diverse set of peptides were studied using molecular dynamics simulations. Ten of the most promising were chemically synthesized and validated both in vitro and in a cell-based assay. Our results indicate that one of the peptides (PEP10) exhibited the highest disruption of the RBD/ACE2 complex, effectively blocking the binding of two molecules and consequently inhibiting the SARS-CoV-2 spike-mediated cell entry of viruses pseudotyped with the spike of the D614G, Delta, and Omicron variants. PEP10 can potentially serve as a scaffold that can be further optimized for improved affinity and efficacy.

The membrane (M) protein of betacoronaviruses is well conserved and has a key role in viral assembly^1,2. Here we describe the identification of JNJ-9676, a small-molecule inhibitor targeting the coronavirus M protein. JNJ-9676 demonstrates in vitro nanomolar antiviral activity against SARS-CoV-2, SARS-CoV and sarbecovirus strains from bat and pangolin zoonotic origin. Using cryogenic electron microscopy (cryo-EM), we determined a binding pocket of JNJ-9676 formed by the transmembrane domains of the M protein dimer. Compound binding stabilized the M protein dimer in an altered conformational state between its long and short forms, preventing the release of infectious virus. In a pre-exposure Syrian golden hamster model, JNJ-9676 (25 mg per kg twice per day) showed excellent efficacy, illustrated by a significant reduction in viral load and infectious virus in the lung by 3.5 and 4 log₁₀-transformed RNA copies and 50% tissue culture infective dose (TCID₅₀) per mg lung, respectively. Histopathology scores at this dose were reduced to the baseline. In a post-exposure hamster model, JNJ-9676 was efficacious at 75 mg per kg twice per day even when added at 48 h after infection, when peak viral loads were observed. The M protein is an attractive antiviral target to block coronavirus replication, and JNJ-9676 represents an interesting chemical series towards identifying clinical candidates addressing the current and future coronavirus pandemics.

Background: Immunomodulatory treatments targeting excessive host immune responses favorably shifting the course of COVID-19. High doses of calcifediol may reduce the mortality of this infection. Objective: To evaluate how a high dose of calcifediol modifies the risk of death in patients hospitalized with COVID-19 during the first outbreaks. Design: A retrospective, observational study to evaluate the relationship between treatment with calcifediol and the risk of death in patients hospitalized with COVID-19 at the "Complejo Hospitalario Universitario de Albacete" (CHUA), Spain, during the months of January to March 2021. Patients were treated with corticosteroids, and some patients also received baricitinib and/or high doses of calcifediol, according to CHUA's therapeutic protocol 2021 for COVID-19. The primary outcome measure was mortality according to calcifediol treatment. Results: A total of 230 patients were included. 25(OH)D levels were measured on admission in 148 patients, showing a high prevalence of vitamin D deficiency [median 25(OH)D: 17.5 ng/mL]. Thirty-four (23%) had severe deficiency (25(OH)D ≤ 10 ng/mL). In the 119 patients (51.7%) who received in-hospital treatment with a high dose of calcifediol, the mortality rate was 12.6% (15 cases, 95% confidence interval [CI], 7.8-19.8%), while in 111 patients who did not receive treatment with calcifediol, the death rate was 23.4% (26 cases, 95% CI: 16.5-32.1%; p = 0.039). The odds ratio (OR) in treated vs. untreated patients was 0.47 (95% CI: 0.23-0.95). Among the patients admitted with severe deficiency, 16 received treatment with calcifediol, with a mortality rate of 0.0% (0 cases, 95% CI: 0.0-19.4%), while in the 18 not treated with calcifediol, a death rate of 38.9% was observed (7 cases, 95% CI: 20.3-61.4%; p = 0.008). The mortality rate was lower in patients treated with the combination of calcifediol and corticosteroids vs. those treated with corticosteroids alone (p = 0.038) and vs. those treated with corticosteroids and baricitinib (p = 0.033). Conclusions: In the ALBACOVIDIOL study, calcifediol treatment was associated with a lower observed mortality rate in hospitalized patients with COVID-19 treated with corticosteroids (with or without baricitinib), especially in those with severe vitamin D deficiency. Causality cannot be inferred due to the retrospective study design. (Public database: ClinicalTrials.gov, NCT05819918).

Background

Human activities including deforestation, urbanization, and wildlife exploitation increase the risk of transmission of zoonotic diseases. Urban and peri-urban wildlife species often flourish in human-altered environments, with their survival and behavior heavily influenced by human-generated food and waste. In Catalonia, Spain, and other Mediterranean regions, species of rodents, including the house mouse (Mus musculus), black rat (Rattus rattus), Norway rat (Rattus norvegicus), as well as wild boar (Sus scrofa) are common in urban and peri-urban areas. These species host numerous infectious agents, including coronaviruses (CoVs), posing potential human health risks. During the coronavirus disease 2019 (COVID-19) pandemic, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolved to infect previously non-susceptible species, with variants capable of infecting rodents, emphasizing their importance in surveillance studies.

Methods

The present study assessed SARS-CoV-2 presence and/or exposure in 232 rodents, 313 wild boar, and 37 Vietnamese Pot-bellied pigs in Catalonia during the pandemic period (2020-2023).

Results

All the animals tested for acute SARS-CoV-2 infection (232 rodents and 29 wild boar) were negative. For SARS-CoV-2 exposure, 3 out of 313 (0.96%) wild boar tested positive by ELISA, while the remaining 32 rodents, 310 wild boar, and 37 Vietnamese Pot-bellied pigs were all negative. Cross-reactivity with other CoVs was predicted for ELISA-positive samples, as the 3 wild boar tested negative by the virus neutralization assay, considered as the gold standard technique.

Conclusions

The absence of SARS-CoV-2 exposure or acute infection in wild boar and rodent species supports their negligible role in viral spread or transmission during the COVID-19 pandemic in Catalonia. However, their proximity to humans and the ongoing genetic evolution of SARS-CoV-2 underline the need for continued monitoring. Surveillance of SARS-CoV-2 infection in animal species can contribute to design measures to control the emergence of new animal reservoirs or intermediate hosts that could facilitate viral spillover events.

Introduction

Currently, there are no effective medications for treating all the clinical conditions of patients with COVID-19. We aimed to evaluate the antiviral activity of compounds derived from L-tyrosine against the B.1 lineage of SARS-CoV-2 in vitro and in silico.

Methodology

The cytotoxicities of 15 halogenated compounds derived from L-tyrosine were evaluated in Vero-E6 cells by the MTT assay. The antiviral activity of the compounds was evaluated using four strategies, and viral quantification was performed by a plaque assay and qRT-PCR. The toxicity of the compounds was evaluated by ADMET predictor software. The affinity of these compounds for viral or cellular proteins and the stability of their conformations were determined by docking and molecular dynamics, respectively.

Results

TODC-3M, TODI-2M, and YODC-3M reduced the viral titer >40% and inhibited the replication of viral RNA without significant cytotoxicity. In silico analyses revealed that these compounds presented low toxicity and binding energies between -4.3 and -5.2 Kcal/mol for three viral proteins (spike, Mpro, and RdRp). TODC-3M and YODC-3M presented the most stable conformations with the evaluated proteins.

Conclusions

The most promising compounds were TODC-3M, TODI-2M, and YODC-3M, which presented low in vitro and in silico toxicity, antiviral potential through different strategies, and favorable affinities for viral targets. Therefore, they are candidates for in vivo studies.

In this Review, we analysed the prevalence of viraemia during infection with SARS-CoV-2 and other relevant respiratory viruses, including other human coronaviruses such as MERS-CoV and SARS-CoV, adenovirus, human metapneumovirus, human rhinovirus/enterovirus, influenza A and B virus, parainfluenza virus, and respiratory syncytial virus. First, a preliminary systematic search was conducted to identify articles published before May 23, 2024 that reported on viraemia during infection with respiratory viruses. The articles were then analysed for relevant terms to identify the prevalence of viraemia, its association with the disease severity and long-term consequences, and host responses. A total of 202 articles were included in the final study. The pooled prevalence of viraemia was 34% for SARS-CoV-2 and between 6% and 65% for other viruses. Association of viraemia with disease severity was extensively reported for SARS-CoV-2 and also for SARS-CoV, MERS-CoV, adenoviruses, rhinoviruses, respiratory syncytial virus, and influenza A(H1N1)pdm09 (albeit with low evidence). SARS-CoV-2 viraemia was linked to memory problems and worsened quality of life. Viraemia was associated with signatures denoting dysregulated host responses. In conclusion, the high prevalence of viraemia and its association with disease severity suggests that viraemia could be a relevant pathophysiological event with important translational implications in respiratory viral infections.

Background/ Objectives: Long COVID or post-acute sequelae of SARS-CoV-2 infection (PASC) are symptoms that manifest despite passing the acute infection phase. These manifestations encompass a wide range of symptoms, the most common being fatigue, shortness of breath, and cognitive dysfunction. Genetic predisposition is clearly involved in the susceptibility of individuals to developing these persistent symptoms and the variation in the severity and forms. This review summarizes the role of genetic factors and gene polymorphisms in the development of major pulmonary vascular disorders associated with long COVID. Methods: A comprehensive review of current literature was conducted to examine the genetic contributions to pulmonary complications following SARS-CoV-2 infection. Studies investigating genetic polymorphisms linked to pulmonary hypertension, pulmonary thromboembolism, and pulmonary vascular endothelialitis were reviewed and summarized. Results: Findings show that specific genetic variants contribute to increased susceptibility to pulmonary vascular complications in long COVID patients. Variants associated with endothelial dysfunction, coagulation pathways, and inflammatory responses have been implicated in the development of pulmonary hypertension and thromboembolic events. Genetic predispositions influencing vascular integrity and immune responses appear to influence disease severity and progression. Conclusions: Understanding these mechanisms and genetic predispositions could pave the way for targeted therapeutic interventions to alleviate the burden on patients experiencing long COVID.

Mutations within the N-terminal domain (NTD) of the spike (S) protein are critical for the emergence of successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral lineages. The NTD has been repeatedly impacted by deletions, often exhibiting complex and dynamic patterns, such as the recurrent emergence and disappearance of deletions in dominant variants. This study investigates the influence of repair of NTD lineage-defining deletions found in the BA.1 lineage (Omicron variant) on viral success. We performed comparative genomic analyses of >10 million SARS-CoV-2 genomes from the Global Initiative on Sharing All Influenza Data (GISAID) EpiCov database to evaluate the detection of viruses lacking S:ΔH69/V70, S:ΔV143/Y145, or both. These findings were contrasted against a screening of publicly available raw sequencing data, revealing substantial discrepancies between data repositories, suggesting that spurious deletion repair observations in GISAID may result from systematic artifacts. Specifically, deletion repair events were approximately an order of magnitude less frequent in the read-run survey. Our results suggest that deletion repair events are rare, isolated events with limited direct influence on SARS-CoV-2 evolution or transmission. Nevertheless, such events could facilitate the emergence of fitness-enhancing mutations. To explore potential drivers of NTD deletion repair patterns, we characterized the viral phenotype of such markers in a surrogate in vitro system. Repair of the S:ΔH69/V70 deletion reduced viral infectivity, while simultaneous repair with S:ΔV143/Y145 led to lower fusogenicity. In contrast, individual S:ΔV143/Y145 repair enhanced both fusogenicity and susceptibility to neutralization by sera from vaccinated individuals. This work underscores the complex genotype-phenotype landscape of the spike NTD in SARS-CoV-2, which impacts viral biology, transmission efficiency, and immune escape potential, offering insights with direct relevance to public health, viral surveillance, and the adaptive mechanisms driving emerging variants.

Pulmonary fibrosis after severe SARS-CoV-2 pneumonia is a major sequela in surviving patients which requires evaluation. Fractional exhaled nitric oxide (FeNO) is a marker of airway inflammation, easy to obtain and available in most functional testing laboratories of pulmonology services. Our objective was to evaluate the capacity of FeNO as a biomarker of interstitial and fibrotic pulmonary sequelae in patients admitted for severe SARS-CoV-2 pneumonia. We recruited 335 patients admitted for severe pneumonia secondary to SARS-CoV-2 who were being followed up at the Diffuse Interstitial Lung Disease unit at Hospital Universitario Marqués de Valdecilla. FeNO levels were higher in patients with fibrotic interstitial sequelae: mean 24.3 vs. 19.8 ppbs, p = 0.002, with an area under the curve (AUC) of 0.63; 95% confidence interval (CI) 0.57-0.69 and an optimal cut-off point of 11 ppb maximizing the weighted combination of Sensitivity and specificity. FeNO ranked 6th among the 18 variables studied using various methods (forward selection, backward elimination, and stepwise regression) in evaluating the predictive ability for fibrotic interstitial sequelae, and it was the 5 th most predictive variable after using the cut-off point of 11 ppb. The joint predictive ability of the overall model with the 6 more predictive variables was higher than 0.8: AUC (Use of systemic corticosteroids + peak C-reactive Protein at admission + Age + Endotracheal intubation + Diffusing Capacity for CO (DLCO) + FeNO as quantitative continuous) = 0.81; 95%CI (0.77-0.86). AUC of the same model with FeNO as dichotomous (11 ppb cut-off point) = 0.82; 95%CI (0.78-0.87). Our study shows an increase in FeNO in patients who, after admission for severe SARS-CoV-2 pneumonia, present fibrotic interstitial sequelae at the three-month follow-up, as one of the different predictive variables related to the presence of these sequelae.

SARS-CoV-2, the causative virus for the COVID-19 disease, uses its spike glycoprotein to bind to human ACE2 as a first step for viral entry into the cell. For this reason, great efforts have been made to find mechanisms that disrupt this interaction, avoiding the infection. Nitric oxide (NO) is a soluble endogenous gas with known antiviral and immunomodulatory properties. In this study, we aimed to test whether NO could inhibit the binding of the viral spike to ACE2 in human cells and its effects on ACE2 enzymatic activity. Our results show that ACE2 activity was decreased by the NO donors DETA-NONOate and GSNO and by the NO byproduct peroxynitrite. Furthermore, we found that DETA-NONOate could break the spike-ACE2 interaction using the spike from two different variants (Alpha and Gamma) and in two different human cell types. Moreover, the same result was obtained when using NO-producing murine macrophages, while no significant changes were observed in ACE2 expression or distribution within the cell. These results support that it is worth considering NO as a therapeutic agent for COVID-19, as previous reports have suggested.

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to challenge global health despite widespread vaccination efforts, underscoring the need for innovative strategies to combat emerging infectious diseases effectively. Herein, LCB1-NPs and LCB3-NPs are engineered as a novel class of protein-only nanoparticles formed through coiled coil-driven self-assembly and tailored to interact specifically with the SARS-CoV-2 spike protein. The multivalency of LCB1-NPs and LCB3-NPs offers a strategy for efficiently targeting and neutralizing SARS-CoV-2 both in solution and when immobilized on surfaces. It is demonstrated that LCB1-NPs and LCB3-NPs bind to the SARS-CoV-2 spike protein's receptor-binding domain (RBD) with high affinity, effectively blocking the entry of SARS-CoV-2 virus-like particles into angiotensin-converting enzyme 2 (ACE2)-coated human cells. The cost-effectiveness, scalability, and straightforward production process of these protein nanoparticles make them suitable for developing novel anti-viral materials. Accordingly, it is shown how these nanostructures can be packed into columns to build up economic and highly potent trapping devices for SARS-CoV-2 adsorption.

The recent coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spurred intense research efforts to develop new materials with antiviral activity. In this study, we genetically engineered amyloid-based nanofibrils for capturing and neutralizing SARS-CoV-2. Building upon the amyloid properties of a short Sup35 yeast prion sequence, we fused it to SARS-CoV-2 receptor-binding domain (RBD) capturing proteins, LCB1 and LCB3. By tuning the reaction conditions, we achieved the spontaneous self-assembly of the Sup35-LCB1 fusion protein into a highly homogeneous and well-dispersed amyloid-like fibrillar material. These nanofibrils exhibited high affinity for the SARS-CoV-2 RBD, effectively inhibiting its interaction with the angiotensin-converting enzyme 2 (ACE2) receptor, the primary entry point for the virus into host cells. We further demonstrate that this functional nanomaterial entraps and neutralizes SARS-CoV-2 virus-like particles (VLPs), with a potency comparable to that of therapeutic antibodies. As a proof of concept, we successfully fabricated patterned surfaces that selectively capture SARS-CoV-2 RBD protein on wet environments. Collectively, these findings suggest that these protein-only nanofibrils hold promise as disinfecting coatings endowed with selective SARS-CoV-2 neutralizing properties to combat viral spread or in the development of sensitive viral sampling and diagnostic tools.

Background

Schizophrenia is a chronic and complex mental disorder resulting from interactions between cumulative and synergistic genetic and environmental factors. Viral infection during the prenatal stage constitutes one of the most relevant risk factors for the development of schizophrenia later in adulthood.

Methods

A narrative review was conducted to explore the link between viral infections and schizophrenia, as well as the neuropsychiatric effects of antiviral drugs, particularly in the context of this specific mental condition. Literature searches were performed using the PubMed, Scopus, and Web of Science databases.

Results

Several viral infections, such as herpesviruses, influenza virus, Borna disease virus, and coronaviruses, can directly or indirectly disrupt normal fetal brain development by modifying gene expression in the maternal immune system, thereby contributing to the pathophysiological symptoms of schizophrenia. In addition, neuropsychiatric effects caused by antiviral drugs are frequent and represent significant adverse outcomes for viral treatment.

Conclusions

Epidemiological evidence suggests a potential relationship between viruses and schizophrenia. Increases in inflammatory cytokine levels and changes in the expression of key genes observed in several viral infections may constitute potential links between these viral infections and schizophrenia. Furthermore, antivirals may affect the central nervous system, although for most drugs, their mechanisms of action are still unclear, and a strong relationship between antivirals and schizophrenia has not yet been established.

SARS-CoV-2 has evolved from early variants dominating the first (B.1.5, B.1.1) and second (B.1.177) pandemic waves, which exhibited a higher frequency of minority mutants with deletions leading to Defective Viral Genomes (DVGs) in the spike region near the S1/S2 cleavage site than the Alpha, Beta, and Delta variants. The emergence of Omicron has significantly altered the dominant variant profile, with Omicron subvariants now representing 100% of circulating viruses. To monitor the evolution and adaptation of Omicron in the human population, a deep-sequencing study was performed in RNA samples of BA.1, BA.1.1, BA.2, BA.5, BQ.1.1, XBB.1.5 and BA.2.86 Omicron subvariants. The findings reveal two occurrences of similar evolutionary patterns within SARS-CoV-2 characterized by a shift from a significant to a very low production of DVGs. This event suggests that DVGs might play a role in the virus's spread and adaptation for persistence in infected humans.

Background

Handwashing is essential for reducing the risk of cross-infection in the dental setting, as evidenced by the heightened significance of this practice during the COVID-19 pandemic.

Objectives

The extent of adherence to handwashing in the dental setting in the post-COVID-19 phase remains unclear, particularly regarding the pandemic's impact on this practice among dental students. This inquiry constitutes the primary objective of the present study.

Materials and methods

A cross-sectional study was designed involving 100 randomly selected undergraduated dental students at the Santiago de Compostela University (Spain). In 2023, the handwashing procedures performed by students at the end of practical classes were recorded through direct observation. The variables analyzed were: duration of the procedure, cleaning agent used, and the location of handwashing. Results were compared with those obtained from a similar study conducted in 2015, prior to the COVID-19 outbreak.

Results

In 2023, 29% of students washed their hands after practical classes, compared to 42% in 2015 (p = 0.046). No students adhered the WHO handwashing recommendations. Among senior students, the percentage practicing handwashing increased (p = 0.019), as did the duration of the procedure (p = 0.013), compared to mid-senior students. A higher percentage of students engaged in handwashing (p = 0.01) and for a longer duration (p = 0.038) at the conclusion of clinical training session compared to preclinical simulation session.

Conclusions

Despite the impact of the COVID-19 pandemic, handwashing is not a standard practice among dental students. Therefore, it is imperative to implement educational measures that promote genuine adherence to this hygiene practice.

BACKGROUNDSurveillance of severe acute respiratory infections (SARI) using ICD-10 codes from electronic health records (EHR) lacks consensus on optimal case-defining codes.AIMWe determined codes that maximise sensitivity (Se) and positive predictive value (PPV) for SARI associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus and respiratory syncytial virus (RSV) in Denmark, Iceland, Malta, Norway and Spain.METHODSWe included hospitalisations from week 21/2021 to 39/2023, with ICD-10 diagnostic codes for respiratory disease (three-character codes J00-J99) or COVID-19 (U07.1, U07.2, country-specific codes for Denmark). We assessed Se and PPV of individual codes against laboratory results. Based on Se and PPV rank-sum, we selected the top 10 codes and combined them into 10 sets per pathogen. We identified sets that maximised the clinical utility index (CUI = Se × PPV), categorised as excellent (≥ 0.81), good (0.64-0.80), satisfactory (0.49-0.63) and poor (< 0.49).RESULTSWe assessed 395,163 hospitalisations for SARI-SARS-CoV-2, 313,418 for SARI-influenza and 192,936 for SARI-RSV, all tested. For SARI-SARS-CoV-2, code U07.1 (B34.2A, B97.2A for Denmark) had excellent utility in Denmark, Malta, Norway, Spain (≥ 0.82), and good utility in Iceland (0.79). For SARI-influenza, J09, J10 and J11 performed excellently in Denmark, Norway, Spain (≥ 0.83), satisfactorily in Malta (0.52), and poorly in Iceland (0.43). For SARI-RSV, J12, J20 and J21 achieved highest CUI but had poor utility (0.17-0.34).CONCLUSIONSCOVID-19- and influenza-specific three-character ICD-10 codes accurately identified SARI associated with SARS-CoV-2 and influenza virus. For SARI-RSV, four-character codes should be explored. We recommend context-specific assessments in countries adopting EHR-based surveillance.

This study explores the relationship between specific SARS-CoV-2 mutations and obesity, focusing on how these mutations may influence COVID-19 severity and outcomes in high-BMI individuals. We analyzed 205 viral mutations from a cohort of 675 patients, examining the association of mutations with BMI, hospitalization, and mortality rates. Logistic regression models and statistical analyses were applied to assess the impact of significant mutations on clinical outcomes, including inflammatory markers and antibody levels. Our findings revealed three key mutations-C14599T, A20268G, and C313T-that were associated with elevated BMI. Notably, C14599T appeared to be protective against hospitalization, suggesting context-dependent effects, while A20268G was linked to a 50% increase in hospitalization risk and elevated antibody levels, potentially indicating an adaptive immune response. C313T showed a 428% increase in mortality risk, marking it as a possible poor-prognosis marker. Interestingly, all three mutations were synonymous, suggesting adaptive roles in obesity-driven environments despite not altering viral protein structures. These results emphasize the importance of studying mutations within the broader context of comorbidities, other mutations, and regional factors to enhance our understanding of SARS-CoV-2 adaptation in high-risk groups. Further validation in larger cohorts is necessary to confirm these associations and to assess their clinical significance.

Background: Patients with multiple sclerosis (pwMS) receiving disease-modifying therapies (DMTs) may exhibit altered immune responses to infections such as SARS-CoV-2. This study aimed to characterize the cytokine profiles associated with prior SARS-CoV-2 infection and to identify immune markers related to the persistence of the humoral response in pwMS. Methods: A total of 90 pwMS were recruited before the introduction of COVID-19 vaccination in Spain; 46 were seropositive-defined by the presence of IgG, IgM, or IgA antibodies against SARS-CoV-2-and 44 were seronegative. We compared baseline cytokine levels between groups and followed seropositive individuals for six months to assess IgG antibody persistence. Results: Seropositive patients showed significantly lower baseline levels of IL-10, IL-23, and IFN-α compared to seronegative individuals. Notably, elevated IL-18 at baseline was associated with persistent IgG seropositivity at six months. Conclusions: These findings suggest a distinct cytokine profile in SARS-CoV-2-exposed pwMS and highlight IL-18 as a potential marker of sustained humoral response. This study provides insight into host-virus immune dynamics in MS patients and may help guide future strategies for infection monitoring and immune evaluation in this population.

Background/objectives

COVID-19 is characterised by a wide variety of clinical manifestations, and clinical tests and genetic analysis might help to predict patient outcomes.

Methods

In the current study, the expression of genes related to immune response (CCL5, IFI6, OAS1, IRF9, IL1B, and TGFB1) was analysed in the upper airway and paired-blood samples from 25 subjects infected with SARS-CoV-2. Relative gene expression was determined by RT-qPCR.

Results

CCL5 expression was higher in the blood than in the upper airway (p < 0.001). In addition, a negative correlation was found between IFI6 and viral load (p = 0.033) in the upper airway, suggesting that the IFI6 expression inhibits the viral infection. Concerning sex, women expressed IL1B and IRF9 in a higher proportion than men at a systemic level (p = 0.008 and p = 0.049, respectively). However, an increased expression of IRF9 was found in men compared to women in the upper airway (p = 0.046), which could be due to the protective effect of IRF9, especially in men.

Conclusions

The higher expression of CCL5 in blood might be due to the key role of this gene in the migration and recruitment of immune cells from the systemic circulation to the lungs. Our findings confirm the existence of sex differences in the immune response to early stages of the infection. Further studies in a larger cohort are necessary to corroborate the current findings.

Individuals with Down Syndrome (DS) represent one of the most susceptible populations for developing severe COVID-19, and a unique human genetic condition for investigating molecular mechanisms underlying susceptibility of neurologically vulnerable individuals to SARS-CoV-2 infection. Human Chromosome-21 (HSA21) triplication in DS causes global transcriptional deregulation, affecting multiple genes that may directly (e.g., TMPRSS2) or indirectly influence the SARS-CoV-2 entry into central nervous system (CNS) cells. The anti-viral immune response may also be altered in cells with trisomy-21 (T21) due to triplication of genes encoding for several interferon receptor subunits and interferon-stimulated genes (ISGs). Here, we demonstrate that human cells derived from fetal cortical specimens and maintained in primary cultures are susceptible to infection with a molecular clone of vesicular stomatitis virus engineered to express the Spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and to authentic SARS-CoV-2. The level of SARS-CoV-2 infectivity in cultures originated from different cortical specimens varied, seemingly depending on ploidy and chromosomal sex of the cells. We confirmed the presence of ACE2 and TMPRSS2 in cultures and found that XY T21 group had the highest TMPRSS2 mRNA levels, which was associated with increased infectivity in XY-compared to XX T21 cultures. The XX T21 cultures exhibited elevated expression of several ISGs (MX1, STAT1, and STAT2) which was associated with lower infectivity. The comparisons of postmortem aged brain specimens revealed reduced ACE2, TMPRSS2, but elevated STAT2 protein levels in individuals with DS and Alzheimer's disease (DS-AD) compared to control and Alzheimer's disease (AD) group. Collectively, these results suggest multifactorial regulation of SARS-CoV-2 infectivity in cortical cells that involves ploidy, chromosomal sex, and the expression of genes implicated in regulation of virus entry and anti-viral response as contributing factors.

Genetics and epigenetics are mechanisms proposed for explaining post-COVID-19 condition. This secondary analysis aimed to investigate if DNA methylation levels of the ACE2 promoter are different depending on the genotype of five COVID-19-related polymorphisms in individuals who had been previously hospitalized due to SARS-CoV-2 infection. We collected non-stimulated saliva samples from 279 (48.7% female, age: 56.0 ± 12.5 years) previously hospitalized COVID-19 survivors. The participants self-reported for the presence of post-COVID symptomatology that started after the infection and persisted at the time of the appointment. Three potential genotypes of ACE2 rs2285666 and rs2074192, TMPRSS2 rs12329760 and rs2070788, and ACE1 rs1799752 polymorphisms were identified from saliva samples. Further, methylation levels at five different locations (CpG) of dinucleotides in the ACE2 promoter were quantified using bisulfited pyrosequencing. Differences in the methylation percentage (%) of each CpG according to the genotype of the five polymorphisms were analyzed. Participants were evaluated up to 17.8 (SD: 5.2) months after hospital discharge. Eighty-eight percent (88.1%) of patients reported at least one post-COVID symptom (mean number of post-COVID symptoms: 3.0; SD: 1.9). Overall, we did not observe significant differences in the methylation levels of the ACE2 promoter according to the genotype of ACE2 rs2285666 and rs2074192, TMPRSS2 rs12329760 and rs2070788, or ACE1 rs1799752 single nucleoid polymorphisms. This study did not find an association between genetics (genotypes of five COVID-19-associated polymorphisms) and epigenetics (methylation levels of the ACE2 promoter) in a cohort of COVID-19 survivors with post-COVID-19 condition who were hospitalized during the first wave of the pandemic.

Background

The coronavirus disease 2019 (COVID-19) pandemic was a global health emergency that significantly affected both the wellbeing of individuals and the global economy.

Objective

The aim of this study was to evaluate the degree of SARS-CoV-2 involvement, viral load, and immunological response in adults aged 18-65 who performed essential tasks in the municipality of Andratx (Balearic Islands, Spain) compared to those who did not. Additionally, the study examined these factors in children aged 2-18 years from both groups, if there were any.

Materials

Both groups were monitored between July 2020 and February 2021, in which the degree of involvement, the viral load, and the immunological response to the SARS-CoV-2 were analyzed using questionnaires, polymerase chain reaction (PCR) tests, and ELISA serology tests.

Results

A positive case of RT-PCR test was found in screening the general population. The highest 2019-nCoV(N)-Ig antibody levels in plasma were measured from 1 to 17 February 2021, with the following percentage of positives: 6.8% of essential workers, 9.5% of essential workers' sons, 7.3% of non-essential workers, and 2.2% of non-essential workers' sons. However, an increase in levels of anti-SARS-CoV-2 (N) immunoglobulin G (IgG) and anti-SARS-CoV-2 (N) immunoglobulin M (IgM) were produced in session 3, from 9 to 25 November 2020, in both cases in non-essential workers, with a mean of 218.1 ng/mL of anti-SARS-CoV-2 (N) IgG and 31.3 ng/mL of anti-SARS-CoV-2 (N) IgM.

Conclusion

The control measures taken to manage the COVID-19 pandemic in the municipality of Andratx, Mallorca, Spain, were effective.

Natural killer (NK) cells play a key role in the innate immune response against viral infections. Their activity is regulated by a balance of activating and inhibitory signals, which are modulated by interactions with HLA class I molecules, including HLA-E. The HLA-B 21M/T dimorphism influences the availability of HLA-B leader peptides that stabilize HLA-E expression and modulate NK cell function via the NKG2A/CD94 receptor. To investigate the association between the HLA-B -21M/T dimorphism and the clinical severity of COVID-19, we analyzed a cohort of hospitalized patients with primary SARS-CoV-2 infection, who were genotyped for the HLA-B -21M/T dimorphism. Clinical data, lymphocyte counts, the neutrophil-to-lymphocyte ratio (NLR), and inflammatory markers were compared across genotypes. Contrary to previous studies suggesting a protective effect of the M/M genotype, we found no significant association between the HLA-B -21M/T dimorphism and COVID-19 severity, lymphocyte parameters, or inflammatory biomarkers. Our findings do not support a role for the HLA-B -21M/T dimorphism in modulating COVID-19 outcomes. These results underscore the complexity of NK cell regulation and highlight the need for integrative studies combining genetic, immunological, and functional data to better understand host factors influencing disease progression.

The COVID-19 pandemic has overwhelmed healthcare systems and triggered global economic downturns. While vaccines have reduced the lethality rate of SARS-CoV-2 to 0.9% as of October 2024, the continuous evolution of variants remains a significant public health challenge. Next-generation medical therapies offer hope in addressing this threat, especially for immunocompromised individuals who experience prolonged infections and severe illnesses, contributing to viral evolution. These cases increase the risk of new variants emerging. This study explores miniACE2 decoys as a novel strategy to counteract SARS-CoV-2 variants. Using in silico design and molecular dynamics, blocking proteins (BPs) were developed with stronger binding affinity for the receptor-binding domain of multiple variants than naturally soluble human ACE2. The BPs were expressed in E. coli and tested in vitro, showing promising neutralizing effects. Notably, miniACE2 BP9 exhibited an average IC₅₀ of 4.9 µg/mL across several variants, including the Wuhan strain, Mu, Omicron BA.1, and BA.2 This low IC50 demonstrates the potent neutralizing ability of BP9, indicating its efficacy at low concentrations.Based on these findings, BP9 has emerged as a promising therapeutic candidate for combating SARS-CoV-2 and its evolving variants, thereby positioning it as a potential emergency biopharmaceutical.

Plitidepsin is an antitumoral compound safe for treating COVID-19 that targets the translation elongation factor eEF1A. Here we detect that plitidepsin decreases de novo cap-dependent translation of SARS-CoV-2 and non-viral RNAs but affects less than 13% of the host proteome, thus preserving cellular viability. In response to plitidepsin, cells upregulate EIF2AK3 and proteins that reduce translation, but also proteins that support proteostasis via ribosome synthesis and cap-independent translation by eIF4G2 and IGF2BP2. While plitidepsin inhibits cap- or internal ribosome entry sites (IRES)-mediated translation, its impact on N6-methyladenosine (m⁶A) translation is limited. In agreement, plitidepsin blocks members of Coronaviridae, Flaviviridae, Pneumoviridae and Herpesviridae families. Yet, it fails to inhibit retroviruses that exploit m⁶A synthesis routes and are blocked by drugs targeting IGF2BP2 m⁶A reader. By deciphering the molecular fingerprint of cells treated with therapies targeting translation we identify a rational approach to select broad-spectrum antivirals with potential to counteract future pandemic viruses.

Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play a key role in the infection, progression, and outcome of the disease. SARS-CoV-2 infection has been associated with nasopharyngeal and gut dysbiosis and higher abundance of opportunistic pathogens. To identify new prognostic markers for the disease, a multicentre prospective observational cohort study was carried out in COVID-19 patients divided into three cohorts based on symptomatology: mild (n = 24), moderate (n = 51), and severe/critical (n = 31). Faecal and nasopharyngeal samples were taken, and the microbiota was analysed. Linear discriminant analysis identified Mycoplasma salivarium, Prevotella dentalis, and Haemophilus parainfluenzae as biomarkers of severe COVID-19 in nasopharyngeal microbiota, while Prevotella bivia and Prevotella timonensis were defined in faecal microbiota. Additionally, a connection between faecal and nasopharyngeal microbiota was identified, with a significant ratio between P. timonensis (faeces) and P. dentalis and M. salivarium (nasopharyngeal) abundances found in critically ill patients. This ratio could serve as a novel prognostic tool for identifying severe COVID-19 cases.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can infect various human tissues and cell types, principally via interaction with its cognate receptor angiotensin-converting enzyme-2 (ACE2). However, how the virus evolves in different cellular environments is poorly understood. Here, we used experimental evolution to study the adaptation of the SARS-CoV-2 spike to four human cell lines expressing different levels of key entry factors. After twenty passages of a spike-expressing recombinant vesicular stomatitis virus (VSV), cell-type-specific phenotypic changes were observed and sequencing allowed the identification of sixteen adaptive spike mutations. We used VSV pseudotyping to measure the entry efficiency, ACE2 affinity, spike processing, TMPRSS2 usage, and entry pathway usage of all the mutants, alone or in combination. The fusogenicity of the mutant spikes was assessed with a cell-cell fusion assay. Finally, mutant recombinant VSVs were used to measure the fitness advantage associated with selected mutations. We found that the effects of these mutations varied across cell types, both in terms of viral entry and replicative fitness. Interestingly, two spike mutations (L48S and A372T) that emerged in cells expressing low ACE2 levels increased receptor affinity, syncytia induction, and entry efficiency under low-ACE2 conditions. Our results demonstrate specific adaptation of the SARS-CoV-2 spike to different cell types and have implications for understanding SARS-CoV-2 tissue tropism and evolution.

We evaluated homologous neutralizing antibody (NtAb) and T-cell responses after receipt of a JN.1-adapted mRNA vaccine in a mixed population comprising healthy controls (HC) (n = 15), end-stage chronic kidney disease (CKD) patients (n = 17), and allogeneic hematopoietic stem cell transplant recipients (allo-HCT) (n = 13). Most participants (42/45) were SARS-CoV-2-experienced at the time of immunological testing. JN.1-spike-binding NtAbs were measured with a vesicular stomatitis virus pseudotype-based neutralization assay, whereas interferon (IFN)-γ-producing spike-directed CD4⁺ or CD8⁺ T-cell frequencies were enumerated using flow cytometry for intracellular staining. All participants had detectable JN.1 NtAbs at baseline; overall, JN.1-NtAb levels increased in HC (median, ∼1 log₁₀; p < 0.001) and CKD patients (median, 0.8 log₁₀; p = 0.06) but not in allo-HCT (p = 0.10). JN.1-NtAb titers measured after vaccination were significantly higher in HC than in CKD and allo-HCT (p = 0.01). The number of participants exhibiting detectable JN.1 T-cell responses did not significantly increase following booster vaccination in any of the study groups. Likewise, receipt of the Omicron JN.1 vaccine failed to significantly boost SARS-CoV-2 JN.1 CD8⁺ and CD4⁺ T-cell frequencies in any study groups. Nevertheless, trends in JN.1 T-cell frequencies following the JN-1 booster varied widely on an individual basis. JN.1 T-cell frequencies following JN.1 vaccination were comparable across study groups. Our results could have implications for the development of vaccines for future SARS-CoV-2 variants and the optimization of booster vaccination policies in allogeneic hematopoietic transplant recipients and patients with end-stage chronic kidney diseases.

Proteases are produced and released in the mucosal cells of the respiratory tract and have important physiological functions, for example, maintaining airway humidification to allow proper gas exchange. The infectious mechanism of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), takes advantage of host proteases in two ways: to change the spatial conformation of the spike (S) protein via endoproteolysis (e.g., transmembrane serine protease type 2 (TMPRSS2)) and as a target to anchor to epithelial cells (e.g., angiotensin-converting enzyme 2 (ACE2)). This infectious process leads to an imbalance in the mucosa between the release and action of proteases versus regulation by anti-proteases, which contributes to the exacerbation of the inflammatory and prothrombotic response in COVID-19. In this article, we describe the most important proteases that are affected in COVID-19, and how their overactivation affects the three main physiological systems in which they participate: the complement system and the kinin-kallikrein system (KKS), which both form part of the contact system of innate immunity, and the renin-angiotensin-aldosterone system (RAAS). We aim to elucidate the pathophysiological bases of COVID-19 in the context of the imbalance between the action of proteases and anti-proteases to understand the mechanism of aprotinin action (a panprotease inhibitor). In a second-part review, titled "Aprotinin (II): Inhalational Administration for the Treatment of COVID-19 and Other Viral Conditions", we explain in depth the pharmacodynamics, pharmacokinetics, toxicity, and use of aprotinin as an antiviral drug.

Hypertension is one of the most common risk factors for COVID-19 clinical progression. The identification of plasma biomarkers for anticipating worse clinical outcomes and to better understand the shared mechanisms between hypertension and COVID-19 are needed. A hypothesis-generating study was designed to compare plasma proteomics and metabolomics between 22 hypertensives (HT) and 41 non-hypertensives (nHT) patients with the most unfavorable COVID-19 progression. A total of 43 molecules were significantly differed between HT (n = 22) and nHT (n = 41). Random Forest (RF) analysis identified myo-inositol, gelsolin and phosphatidylcholine (PC) 32:1 as the top molecules for distinguishing between HT and nHT. Plasma myo-inositol and gelsolin were higher (P = 0.03 and P = 0.02, respectively) and plasma PC 32:1 was lower (P = 0.03) in HT compared to nHT. Biological processes like stress response and blood coagulation, along with KEGG pathways including ascorbate and aldarate metabolism (P = 0.021) and linoleic acid metabolism (P = 0.028), were altered in hypertensive patients with the most unfavorable COVID-19 progression. There is a clear link between hypertension and severe COVID-19. Key biological pathways to consider for improving the prognosis and quality of life of hypertensive patients who become infected with SARS-CoV-2 include oxidative stress, ascorbate and aldarate metabolism, lipid metabolism, immune system and inflammation.

The coronavirus disease 2019 (COVID-19) pandemic remains an international health problem caused by the recent emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of May 2024, SARS-CoV-2 has caused more than 775 million cases and over 7 million deaths globally. Despite current vaccination programs, infections are still rapidly increasing, mainly due to the appearance and spread of new variants, variations in immunization rates, and limitations of current vaccines in preventing transmission. This underscores the need for pan-variant antivirals and treatments. The interferon (IFN) system is a critical element of the innate immune response and serves as a frontline defense against viruses. It induces a generalized antiviral state by transiently upregulating hundreds of IFN-stimulated genes (ISGs). To gain a deeper comprehension of the innate immune response to SARS-CoV-2, its connection to COVID-19 pathogenesis, and the potential therapeutic implications, this review provides a detailed overview of fundamental aspects of the diverse ISGs identified for their antiviral properties against SARS-CoV-2. It emphasizes the importance of these proteins in controlling viral replication and spread. Furthermore, we explore methodological approaches for the identification of ISGs and conduct a comparative analysis with other viruses. Deciphering the roles of ISGs and their interactions with viral pathogens can help identify novel targets for antiviral therapies and enhance our preparedness to confront current and future viral threats.

The emergence of SARS-CoV-2 in 2019 and its rapid spread throughout the world has caused the largest pandemic of our modern era. The zoonotic origin of this pathogen highlights the importance of the One Health concept and the need for a coordinated response to this kind of threats. Since its emergence, the virus has caused >7 million deaths worldwide. However, the animal source for human outbreaks remains unknown. The ability of the virus to jump between hosts is facilitated by the presence of the virus receptor, the highly conserved angiotensin-converting enzyme 2 (ACE2), found in various mammals. Positivity for SARS-CoV-2 has been reported in various species, including domestic animals and livestock, but their potential role in bridging viral transmission to humans is still unknown. Additionally, the virus has evolved over the pandemic, resulting in variants with different impacts on human health. Therefore, suitable animal models are crucial to evaluate the susceptibility of different mammalian species to this pathogen and the adaptability of different variants. In this work, we established a transgenic mouse model that expresses the feline ACE2 protein receptor (cACE2) under the human cytokeratin 18 (K18) gene promoter's control, enabling high expression in epithelial cells, which the virus targets. Using this model, we assessed the susceptibility, pathogenicity, and transmission of SARS-CoV-2 variants. Our results show that the sole expression of the cACE2 receptor in these mice makes them susceptible to SARS-CoV-2 variants from the initial pandemic wave but does not enhance susceptibility to omicron variants. Furthermore, we demonstrated efficient contact transmission of SARS-CoV-2 between transgenic mice that express either the feline or the human ACE2 receptor.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), considered a zoonotic agent of wildlife origin, can infect various animal species, including wildlife in free-range and captive environments. Detecting susceptible species and potential reservoirs is crucial for preventing the transmission, spread, genetic evolution, and further emergence of viral variants that are major threats to global health. This study aimed to detect exposure or acute infection by SARS-CoV-2 in 420 animals from 40 different wildlife species, including terrestrial and aquatic mammals, from different regions of Spain during the 2020-2023 coronavirus disease 19 (COVID-19) pandemic. In total, 8/137 animals were positive for SARS-CoV-2 antibodies against the receptor binding domain and/or viral nucleoprotein according to independent ELISAs. However, only one ELISA-positive sample of a captive bottlenose dolphin (Tursiops truncatus) tested positive for SARS-CoV-2 neutralizing antibodies with a low titre (SNT₅₀ 38.15) according to a virus neutralization test. Cetaceans are expected to have a high risk of infection with SARS-CoV-2 according to early predictive studies due to the similarity of their angiotensin converting enzyme 2 cell receptor to that of humans. Moreover, of 283 animals analysed for SARS-CoV-2 RNA using RT-qPCR, none tested positive. Our results reinforce the importance of considering cetaceans at risk for SARS-CoV-2 infection and support taking preventive biosecurity measures when interacting with them, especially in the presence of individuals with suspected or confirmed COVID-19. Although most animals in this study tested negative for acute infection or viral exposure, ongoing surveillance of wildlife species and potentially susceptible animals is important to prevent future spillover events and detect potential novel reservoirs.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was originally described as a respiratory illness; however, it is now known that the infection can spread to the gastrointestinal tract, leading to shedding in feces potentially being a source of infection through wastewater. We aimed to assess the prevalence and persistence of SARS-CoV-2 in fecal and saliva samples for up to 7 weeks post-detection in a cohort of 98 participants from Norfolk, United Kingdom using RT-qPCR. Secondary goals included sequencing the viral isolates present in fecal samples and comparing the genetic sequence with isolates in the saliva of the same participant. Furthermore, we sought to identify factors associated with the presence of detectable virus in feces or saliva after a positive SARS-CoV-2 test. Saliva remained SARS-CoV-2-positive for longer periods compared to fecal samples, with all positive fecal samples occurring within 4 weeks of the initial positive test. Detectable virus in fecal samples was positively associated with the number of symptoms experienced by the individuals. Based on the genome sequencing and taxonomic classification of the virus, one donor had a distinct strain in feces compared to saliva on the same collection date, which suggests that different isolates could dominate different tissues. Our results underscore the importance of considering multiple biological samples, such as feces, in the detection and characterization of SARS-CoV-2, particularly in clinical procedures involving patient fecal material transplant. Such insights could contribute to enhancing the safety protocols surrounding the handling of patient samples and aid in devising effective strategies for mitigating the spread of coronavirus disease.

Importance

This study provides critical insights into the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding in fecal and saliva samples, demonstrating that while viral RNA is detectable shortly after diagnosis, its prevalence declines rapidly over the course of infection. Detection was more common among individuals with more concurrent symptoms, emphasizing the potential influence of symptom burden on viral persistence. By analyzing a United Kingdom-based cohort, this study fills a significant gap in the literature, which has largely focused on Asian and North American populations, offering a geographically unique perspective on viral shedding dynamics. Our findings contribute to a globally relevant understanding of SARS-CoV-2 shedding by revealing differences in shedding durations compared to studies from other regions. These differences highlight the need for geographically diverse research to account for variations in genetic background, immune response, and healthcare practices.

COVID-19 manifests a broad spectrum of clinical outcomes, from asymptomatic cases to severe disease. While several biomarkers have been proposed, comprehensive immunological analyses integrating mass cytometry (CyTOF) and T-cell receptor sequencing (TCRseq) data remain limited. In this study, we applied the Latent Class Model based on the Bayesian Information Criterion (LCM-BIC) algorithm to integrate immunophenotyping, including monocyte-macrophage counts from CyTOF, T-cell receptor repertorie data via TCRseq, SNPs data from ACE2 (rs2285666), MX1 (rs469390), and TMPRSS2 (rs2070788), and symptomatology data from 61 Spanish COVID-19 patients (33 mild, 28 severe). We identified three novel and distinct patient clusters with significant differences in TCR diversity, monocyte subpopulations, and V allele usage and disease outcome. Cluster 1 was predominantly enriched in severe cases, characterized by unique immunological features. Deep learning analysis of TCR amino acid sequences further distinguished Cluster 1 from the others, identifying SARS-CoV-2-specific TCR sequences associated with disease severity. In addition, analysis of residue sensitivity of cluster 1 SARS-CoV-2-specific TCR sequences further identified conserved aminoacids located in key central positions of the complementarity-determining region 3. This study highlights the value of integrating immunophenotyping and genetic profiling to identify novel immunological markers and patterns, aiding in the stratification and management of COVID-19 patients based on their immune profiles and genetic background.

Background

We observed a COVID-19 survivor with a ventriculoperitoneal shunt who developed increased intracranial pressure during hemodialysis. We hypothesized that post-SARS-CoV-2 infection, patients may have altered cerebral perfusion pressure regulation in response to intracranial pressure changes.

Methods

From April to July 2021, we recruited dialysis patients with prior COVID-19 from two Madrid nephrology departments. We also recruited age- and sex-matched dialysis patients without prior SARS-CoV-2 infection. Transcranial Doppler ultrasound was used to measure the middle cerebral artery velocity before dialysis and 30, 60, and 90 min after the initiation of dialysis.

Results

The final sample included 37 patients (16 post-COVID-19 and 21 without). The COVID-19 survivors showed a significant pulsatility index increase between 30 and 60 min compared to those without COVID-19. They also had lower heart rates.

Conclusions

We propose two mechanisms: an increase in intracranial pressure or a decreased arterial elasticity. A lower heart rate was also observed in the COVID-19 survivors. This study highlights SARS-CoV-2's multifaceted effects, including potential long-term vascular and cerebral repercussions.

COVID-19 vaccination strategies are already available almost worldwide. However, it is also crucial to develop new therapeutic approaches, especially for vulnerable populations that may not fully respond to vaccination, such as the immunocompromised. In this project, we predicted 25 B-cell epitopes in silico in the SARS-CoV-2 Spike (S) protein and screened these against serum and plasma samples from 509 COVID-19 convalescent patients. The aim was to identify those epitopes with the highest IgG reactivity to produce monoclonal antibodies against them for COVID-19 treatment. We implemented Brewpitopes, a computational pipeline based on B-cell epitope prediction tools, such as BepiPred v2.0 and Discotope v2.0, and a series of antibody-epitope accessibility filters. We mapped the SARS-CoV-2 S protein epitopes most likely to be recognised by human neutralizing antibodies. Linear and structural epitope predictions were included and were further refined considering accessibility factors influencing their binding to antibodies like glycosylation status, localization in the viral membrane and accessibility on the 3D-surface of S. Blood samples were collected from 509 COVID-19 patients prospectively recruited 35 days after symptoms initiation, positive RT-qPCR or hospital/ICU discharge. Presence of IgG against SARS-CoV-2 was confirmed by lateral flow immunoassays. Epitopes immunogenicity was tested through the analysis of IgG levels and seropositivity in the convalescent serum and plasma samples and 126 pre-pandemic negative controls by Luminex to identify those with the highest reactivity. The seropositivity cut-offs for each epitope were calculated using a set of 126 pre-pandemic samples as negative controls (NC). Twenty-five SARS-CoV-2 S epitopes were predicted in silico as potentially the most immunogenic. These were synthesized and tested in a multiplex immunoassay against sera/plasmas from convalescent COVID-19 patients (5.7% asymptomatic, 35.6% mild, 13.8% moderate, 23% severe and 22% unknown because of anonymous donation). Among the 25 epitopes tested, 3 exhibited significantly higher IgG reactivity compared to the rest. The proportion of seropositive patients towards these 3 epitopes, based on median fluorescence intensity (MFI or Log₁₀ MFI) above that from NC, ranged between 11 and 48%. Two out of the three most immunogenic epitopes were scaled up, resulting in the generation of two monoclonal antibodies (mAbs). These two mAbs exhibited comparable levels of S protein affinity to commercialized mAbs. Our data shows that the candidate S epitopes predicted in silico are recognised by IgG present in convalescent serum and plasma. This evidence suggests that our computational and experimental pipeline is able to yield immunogenic epitopes against SARS-CoV-2 S. These epitopes are suitable for the development of novel antibodies for preventive or therapeutic approaches against COVID-19.

The nucleocapsid N is one of four structural proteins of the coronaviruses. Its essential role in genome encapsidation makes it a critical therapeutic target for COVID-19 and related diseases. However, the inherent disorder of full-length N hampers its structural analysis. Here, we describe a stepwise method using viral-derived RNAs to stabilize SARS-CoV-2 N for EM analysis. We identify pieces of RNA from the SARS-CoV-2 genome that promote the formation of structurally homogeneous N dimers, intermediates of assembly, and filamentous capsid-like structures. Building on these results, we engineer a symmetric RNA to stabilize N protein dimers, the building block of high-order assemblies, for EM studies. We combine domain-specific monoclonal antibodies against N with chemical cross-linking mass spectrometry to validate the spatial arrangement of the N domains within the dimer. Additionally, our cryo-EM analysis reveals novel antigenic sites on the N protein. Our findings provide insights into N protein´s architectural and antigenic principles, which can guide design of pan-coronavirus therapeutics.

A previously unknown coronavirus, named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), emerged in the city of Wuhan, China, in December 2019 [...].

Context

Experimental and observational studies suggest that circulating micronutrients, including vitamin D (VD), may increase COVID-19 risk and its associated outcomes. Mendelian randomization (MR) studies provide valuable insight into the causal relationship between an exposure and disease outcomes.

Objectives

The aim was to conduct a systematic review and meta-analysis of causal inference studies that apply MR approaches to assess the role of these micronutrients, particularly VD, in COVID-19 risk, infection severity, and related inflammatory markers.

Data sources

Searches (up to July 2023) were conducted in 4 databases.

Data extraction and analysis

The quality of the studies was evaluated based on the MR-STROBE guidelines. Random-effects meta-analyses were conducted where possible.

Results

There were 28 studies (2 overlapped) including 12 on micronutrients (8 on VD) and COVID-19, 4 on micronutrients (all on VD) and inflammation, and 12 on inflammatory markers and COVID-19. Some of these studies reported significant causal associations between VD or other micronutrients (vitamin C, vitamin B6, iron, zinc, copper, selenium, and magnesium) and COVID-19 outcomes. Associations in terms of causality were also nonsignificant with regard to inflammation-related markers, except for VD levels below 25 nmol/L and C-reactive protein (CRP). Some studies reported causal associations between cytokines, angiotensin-converting enzyme 2 (ACE2), and other inflammatory markers and COVID-19. Pooled MR estimates showed that VD was not significantly associated with COVID-19 outcomes, whereas ACE2 increased COVID-19 risk (MR odds ratio = 1.10; 95% CI: 1.01-1.19) but did not affect hospitalization or severity of the disease. The methodological quality of the studies was high in 13 studies, despite the majority (n = 24) utilizing 2-sample MR and evaluated pleiotropy.

Conclusion

MR studies exhibited diversity in their approaches but do not support a causal link between VD/micronutrients and COVID-19 outcomes. Whether inflammation mediates the VD-COVID-19 relationship remains uncertain, and highlights the need to address this aspect in future MR studies exploring micronutrient associations with COVID-19 outcomes.

Systematic review registration

PROSPERO registration no. CRD42022328224.

Background

SARS-CoV-2, the causative virus of the COVID-19 global pandemic, leads to a wide variety of responses among patients. Some of them present a very severe phenotype, while others only experience mild symptoms or are even asymptomatic. This differential prognosis is tightly related to the inflammatory status of the patient. Although WHO declared the end of the emergency, the pandemic caused a great socio-sanitary impact in all countries. Thus, the possible outbreak of new biological diseases in the future makes it necessary to deepen the knowledge of this uncontrolled immune response and look for reliable biomarkers to help us predict its potential health impact. Specialized pro-resolving lipid mediators (SPMs) as lipoxins are endogenous mediators synthesized from arachidonic acid in the resolution stage of any inflammatory process. These lipids have pro-resolving actions in several pathological models, including reducing NF-κB-mediated inflammation, and inducing the antioxidant response through the Nrf-2 pathway. Thus, although a potential relationship has already been suggested between low levels of SPMs and COVID-19 severity, their true role as a predictive biomarker is still unknown.

Methods and results

In this study, we have analyzed by ELISA the serum levels of lipoxin A₄ (LXA₄) in a representative Spanish cohort. We found reduced levels in deceased patients when compared to mild or severe patients, concomitant with a decrease in the LXA₄ biosynthetic pathway and an increase in its degradation pathway. Furthermore, we have studied the correlation between the levels of this SPM and several pathology indicators, finding a significant correlation between increased LXA₄ levels and a better prognosis of the patients.

Conclusion

We propose to measure systemic LXA₄ as a new promising biomarker to predict the survival in patients affected by SARS-CoV-2 and presumably to other viruses that can affect humanity in the future.

COVID-19 has been a challenge at the healthcare level not only in the early stages of the pandemic, but also in the subsequent appearance of long-term COVID-19. Several investigations have attempted to identify proteomic biomarkers in an attempt to improve clinical care, guide treatment and predict possible patient outcomes. Proteins such as C-reactive protein (CRP) or interleukin 6 (IL-6) are clear markers of severe disease, but many others have been proposed that could help in risk stratification and in the prediction of specific complications. This review aims to bring together the most relevant studies in this regard, providing information to identify the most notable biomarkers in relation to COVID-19 found to date.

Background

The ongoing evolution of SARS-CoV-2, particularly through the emergence of new variants, continues to challenge our understanding of immune protection. While antibody levels correlate with protection against earlier variants such as Alpha and Delta, their relationship with Omicron sub-variants remains unclear.

Methods

To investigate the role of antibody levels and neutralizing activity in preventing breakthrough infections, we analyzed longitudinal SARS-CoV-2 humoral responses and neutralizing activity against the ancestral virus and major emerging variants in a well-characterized cohort of healthcare workers in Spain (N = 405).

Results

We find that antibody levels and neutralization titers are key indicators of protection against SARS-CoV-2, including the more evasive BQ.1 and XBB Omicron variants. Higher IgG and IgA levels are associated with protection over three 6-month follow-up periods sequentially dominated by BA.1, BA.2, BA.5, BQ.1, and XBB Omicron sub-variants, although the strength of the association between antibody levels and protection declines over time.

Conclusions

Our findings demonstrate that binding antibody levels and neutralizing responses are valid correlates of protection against more evasive BQ.1 and XBB Omicron variants, although the strength of this association diminishes over time. Additionally, our results underscore the importance of continuous monitoring and updating vaccination strategies to maintain effective protection against emerging SARS-CoV-2 variants.

The SARS-CoV-2 virus and its rapid spread have made it a global health concern. The aim of this was to investigate the microbial and metabolic faecal profiles of paediatric patients hospitalised for COVID-19 to try to identify biomarkers of predisposition to severity. The study included 16 patients (aged 4-14 years old) from six different Spanish hospitals and 20 age-matched healthy controls. The gut microbiota was characterised by sequencing of 16S rDNA amplicons and internal transcribed space amplicons, while the metabolic profile was analysed by liquid chromatography high resolution mass spectrometry. A different microbial profile was observed between patients and controls, with a significantly higher abundance of sequences belonging to the phyla Bacteroidota and Pseudomonadota in patients. A different metabolic profile was observed between the two groups. Non-infected children had higher faecal levels of vitamins such as niacin, thiamine, and vitamin D3 derivatives, which were negatively correlated with the abundance of pathogenic bacteria, such as members of Enterobacteriaceae. Hospitalisation due to SARS-CoV-2 infection in children was associated with changes in the gut microbiota and an altered metabolomic profile. For the first time, several relevant biological compounds were found to be reduced in the faeces of children hospitalised with COVID-19 compared to healthy controls.

Polyphenol-rich extracts derived from agricultural by-products exhibit promising antiviral properties. This study evaluated the antiviral potential of extracts from red onion peels, vineyard prunings, olive prunings and chicory leaves against human coronavirus HuCoV-229E. Subcritical water extraction and resin adsorption techniques were applied to produce the extracts. The extracts were further characterised for their bioactive content, and three out of four extracts showed a high polyphenol content (>200 mg/g). The antiviral activity was assessed through viral infectivity and replication inhibition assays in human MRC-5 host cells. The results indicate that chicory leaf and red onion peel extracts demonstrated significant antiviral effects, with effective concentrations (EC₅₀) of 61.43 µg/mL and 10.1 µg/mL, respectively. Olive pruning extract exhibited moderate activity, while vineyard pruning extract showed limited efficacy. These findings suggest that polyphenol-rich agricultural by-products could serve as sustainable sources for antiviral agents, warranting further investigation into their mechanisms of action and potential applications against other coronaviruses, including SARS-CoV-2.

Objectives

Coronavirus disease 2019 (COVID-19) and SSc share multiple similarities in their clinical manifestations, alterations in immune response and therapeutic options. These resemblances have also been identified in other immune-mediated inflammatory diseases where a common genetic component has been found. Thus, we decided to evaluate for the first time this shared genetic architecture with SSc.

Methods

For this study, we retrieved genomic data from two European-ancestry cohorts: 2 597 856 individuals from The COVID-19 Host Genetics Initiative consortium, and 26 679 individuals from the largest genomic scan in SSc. We performed a cross-trait meta-analyses including >9.3 million single nucleotide polymorphisms. Finally, we conducted functional annotation to prioritize potential causal genes and performed drug repurposing analysis.

Results

Our results revealed a total of 19 non-HLA pleiotropic loci, including 2 novel associations for both conditions (BMP1 and PPARG) and 12 emerging as new shared loci. Functional annotation of these regions underscored their potential regulatory role and identified potential causal genes, many of which are implicated in fibrotic and inflammatory pathways. Remarkably, we observed an antagonistic pleiotropy model of the IFN signalling between COVID-19 and SSc, including the well-known TYK2 P1104A missense variant, showing a protective effect for SSc while being a risk factor for COVID-19, along with two additional novel pleiotropic associations (IRF8 and SENP7). Finally, our findings provide new therapeutic options that could potentially benefit both conditions.

Conclusion

Our study confirms the genetic resemblance between susceptibility to and severity of COVID-19 and SSc, revealing a novel common genetic contribution affecting fibrotic and immune pathways.

Consequences of the disease produced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have led to an urgent search for preventive and therapeutic strategies. Besides drug treatments, proposals have been made for supplementation with biomolecules possessing immunomodulatory and antioxidant properties. The objective of this study was to review published evidence on the clinical usefulness of supplementation with vitamin D, antioxidant vitamins (vitamin A, vitamin E, and vitamin C), melatonin, lactoferrin and natural products found in food (curcumin, luteolin, ginger, allicin, magnesium and zinc) as supplements in SARS-CoV-2 infection. In general, supplementation of conventional treatments with these biomolecules has been found to improve the clinical symptoms and severity of the coronavirus disease (COVID-19), with some indications of a preventive effect. In conclusion, these compounds may assist in preventing and/or improving the symptoms of COVID-19. Nevertheless, only limited evidence is available, and findings have been inconsistent. Further investigations are needed to verify the therapeutic potential of these supplements.

SARS-CoV-2 vaccination campaigns on current endemic situation would benefit from vaccine alternatives with easy logistics and accessibility, sustained response and cross-reactivity against emerging variants. Herein, safety and immunogenicity of PHH-1V, adjuvanted recombinant RBD-based vaccine, as fourth dose for the most prevalent SARS-CoV-2 variants in Spain in subjects ≥18 years was investigated for 6 months in HIPRA-HH-2 open-label extension study. Subjects received a fourth dose of PHH-1V after either two BNT162b2 doses plus one PHH-1V dose (cohort 1) or three BNT162b2 doses (cohort 2). As regulatory endpoint, neutralization titers were investigated for PHH-1 V as fourth dose vs BNT162b2 as third dose in subjects receiving previous BNT162b2-based regimens. PHH-1 V immunogenicity (GMT) was investigated against Beta, Delta, and Omicron BA.1, BA.4/5 and XBB.1.5 on Days 14, 98 and 182 post-immunization. Two hundred and eighty-eight subjects received PHH-1V. Neutralizing antibodies against Omicron BA.1 at Day 14 significantly increased after the PHH-1V as fourth booster vs the third BNT162b2 booster (GMT ratio 0.43 (95% CI: 0.28; 0.65; p-value < .0001)). PHH-1V fourth booster induced a significant increase in neutralizing titers vs baseline (GMFR on Day 14 [95% CI]: Beta 6.96 [5.23, 9.25]; Delta 6.27 [4.79, 8.22]; Omicron BA.1 9.21 [5.57, 15.21]; Omicron BA.4/5 11.80 [8.29, 16.80]; Omicron XBB.1.5 5.22 [3.97, 6.87]), remaining significantly higher up to 6 months. The most frequent adverse events were injection site pain and fatigue. As conclusion, PHH-1V booster induced sustained humoral and cellular immune response against Beta, Delta variants and cross reactivity against distant Omicron subvariants and could be an appropriate strategy for implementing heterologous vaccination campaigns.

Oxidative stress and inflammation influence immune response and epigenetic mechanisms in infectious diseases. In mild COVID-19, host-encoded miRNA profiles remain underexplored, although they reveal mechanistic insights into disease pathogenesis. This study evaluated ageing and oxidative stress biomarkers (telomere length (TL), TBARS, 8-OHdG, and circulating related-miRNA expression) in 75 mild cases and 30 non-COVID-19 controls. TL correlated with age (R = -0.384, p = 0.005) and was shorter in cases compared to controls (rTL 1.46 ± 0.51 vs. 0.99 ± 0.37; p < 0.001), being similar between saliva and blood samples (p = 0.917). miR-138-5p was upregulated in COVID-19 cases (p = 0.026) and correlated with 8-OHdG (R = 0.403, p = 0.05), which was increased in cases (p = 0.040); miR-210-3p was downregulated in infected individuals (p = 0.008), while miR-182-5p expression correlated with TBARS (R = 0.582, p = 0.018). miR-34a-5p and miR155-5p expression was not altered in mild COVID-19. These findings suggest early systemic cellular damage in mild COVID-19 and highlight miR-138-5p and miR-182-5p as potential early biomarkers of oxidative stress.

The approval of COVID-19 vaccines and antiviral drugs has been crucial to end the global health crisis caused by SARS-CoV-2. However, to prepare for future outbreaks from drug-resistant variants and novel zoonotic coronaviruses (CoVs), additional therapeutics with a distinct antiviral mechanism are needed. Here, we report a novel guanidine-substituted diphenylurea compound that suppresses CoV replication by interfering with the uridine-specific endoribonuclease (EndoU) activity of the viral non-structural protein-15 (nsp15). This compound, designated EPB-113, exhibits strong and selective cell culture activity against human coronavirus 229E (HCoV-229E) and also suppresses the replication of SARS-CoV-2. Viruses, selected under EPB-113 pressure, carried resistance sites at or near the catalytic His250 residue of the nsp15-EndoU domain. Although the best-known function of EndoU is to avoid induction of type I interferon (IFN-I) by lowering the levels of viral dsRNA, EPB-113 was found to mainly act via an IFN-independent mechanism, situated during viral RNA synthesis. Using a combination of biophysical and enzymatic assays with the recombinant nsp15 proteins from HCoV-229E and SARS-CoV-2, we discovered that EPB-113 enhances the EndoU cleavage activity of hexameric nsp15, while reducing its thermal stability. This mechanism explains why the virus escapes EPB-113 by acquiring catalytic site mutations which impair compound binding to nsp15 and abolish the EndoU activity. Since the EPB-113-resistant mutant viruses induce high levels of IFN-I and its effectors, they proved unable to replicate in human macrophages and were readily outcompeted by the wild-type virus upon co-infection of human fibroblast cells. Our findings suggest that antiviral targeting of nsp15 can be achieved with a molecule that induces a conformational change in this protein, resulting in higher EndoU activity and impairment of viral RNA synthesis. Based on the appealing mechanism and resistance profile of EPB-113, we conclude that nsp15 is a challenging but highly relevant drug target.

This study represents the first Bayesian network meta-analysis (NMA), which aimed to determine the virucidal efficacy of oral and nasal antiseptics against SARS-CoV-2 in saliva. Eligible studies evaluated the antiseptics' effect on viral load in SARS-CoV-2-infected subjects. The search was performed in September 2024 through PubMed, World Health Organisation, Embase, Scopus, bioRxiv, and medRxiv. The methodological quality was evaluated using the Cochrane RoB-2 checklist. Twenty-six articles and 16 antiseptics were assessed. Bayesian NMA was possible for seven antiseptics, ranked by probability of best option for viral load reduction (SUCRA values): PVP-I (0.85); CPC and CHX (0.72); H₂O₂ (0.70); CHX (0.64); CPC (0.50); H₂O₂ and CHX (0.38); and HClO (0.34). Virucidal efficacy at baseline was significant for (viral load reduction): PVP-I (42 %), H₂O₂ (34 %), and CHX (31 %). Compared to the control group, PVP-I remained significant (34 %), whereas H₂O₂ and CHX approached significance (26 % and 22 %, respectively). In conclusion, a single application of PVP-I, H₂O₂ or CHX are the best options for reducing the SARS-CoV-2 viral load in saliva, which can be particularly relevant in high-risk settings. However, methodologically well-designed studies using more appropriate quantification techniques are needed to clarify better the clinical efficacy of antiseptics against SARS-CoV-2 and other respiratory viruses.

Background

While there is wide evidence on concentrations of cytokines in patients attending health care facilities, evidence is scant on physiological, basal concentrations of cytokines in the general population and across sociodemographic groups, as well as on their potential stability over time. Furthermore, from a public health perspective it is remarkable that no studies have analyzed intraindividual changes in such concentrations from before the COVID-19 pandemic until its outbreak.

Objectives

To investigate: (a) prepandemic concentrations of cytokines and immunoglobulins to viral exposures in a general, non-institutionalized population, and their associated sociodemographic variables; (b) the intraindividual change in such concentrations between a prepandemic period (2016-17) and the initial pandemic period (2020-21); and (c) whether such change was similar in participants who in 2020-21 were SARS-CoV-2 seronegative and seropositive, and between participants who did and did not develop COVID-19.

Methods

We conducted a prospective cohort study in 240 individuals from the general population of Barcelona, Spain. Thirty cytokines and 31 immunoglobulins were measured in paired serum samples collected in 2016-17 and 2020-21 in the same individuals.

Results

The median value of the relative intraindividual change in cytokine concentrations between 2016 and 2020 was <15% for 29 of the 30 cytokines. A substantial number of participants had an intraindividual increase or decrease ≥15% in some cytokines. No major differences in intraindividual changes of cytokine and immunoglobulin levels between 2016 and 2020 were observed between participants who did and did not develop COVID-19.

Conclusion

We provide novel information on physiological, basal ex-vivo concentrations of cytokines and immunoglobulins in a general population, which should be relevant for clinical practice and public health. Intraindividual changes in cytokines and immunoglobulins during the 4 years from 2016-17 to 2020-21 were moderate, and they did not differ between participants who in 2020-21 were SARS-CoV-2 seropositive and seronegative, nor between participants who did and did not develop COVID-19 disease. These findings are also novel and relevant for medicine and public health. In particular, the stability in the biomarkers is relevant to assess the role of the immunological and inflammatory state (measured through baseline levels of cytokines and immunoglobulins) in the development of SARS-CoV-2 seropositivity and COVID-19 disease, as well as in the susceptibility to other infections and pathologies.

SARS-CoV-2 caused the devastating COVID-19 pandemic, which, to date, has resulted in more than 800 million confirmed cases and 7 million deaths worldwide. The rapid development and distribution (at least in high-income countries) of various vaccines prevented these overwhelming numbers of infections and deaths from being much higher. But would it have been possible to develop a prophylaxis against this pandemic more quickly? Since SARS-CoV-2 belongs to the subgenus sarbecovirus, with its highly homologous SARS-CoV-1, we propose here that while SARS-CoV-2-specific vaccines are being developed, phase II clinical trials of specific SARS-CoV-1 vaccines, which have been in the pipeline since the early 20th century, could have been conducted to test a highly probable cross-protection between SARS-CoV-1 and SARS-CoV-2.

A previously unknown coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was isolated in Wuhan, China in December 2019, from a patient with a respiratory disease linked to potential contact with wild animals [...].

The Coronavirus Disease 2019, commonly referred to as COVID-19, is responsible for one of the deadliest pandemics in human history. The direct, indirect and lasting repercussions of the COVID-19 pandemic on individuals and public health, as well as health systems can still be observed, even today. In the midst of the initial chaos, the role of tobacco as a prognostic factor for unfavourable COVID-19 outcomes was largely neglected. As of 2023, numerous studies have confirmed that use of tobacco, a leading risk factor for cardiovascular and other diseases, is strongly associated with increased risks of severe COVID-19 complications (e.g., hospitalisation, ICU admission, need for mechanical ventilation, long COVID, etc.) and deaths from COVID-19. In addition, evidence suggests that COVID-19 directly affects multiple organs beyond the respiratory system, disproportionately impacting individuals with comorbidities. Notably, people living with cardiovascular disease are more prone to experiencing worse outcomes, as COVID-19 often inherently manifests as thrombotic cardiovascular complications. As such, the triad of tobacco, COVID-19 and cardiovascular disease constitutes a dangerous cocktail. The lockdowns and social distancing measures imposed by governments have also had adverse effects on our lifestyles (e.g., shifts in diets, physical activity, tobacco consumption patterns, etc.) and mental well-being, all of which affect cardiovascular health. In particular, vulnerable populations are especially susceptible to tobacco use, cardiovascular disease and the psychological fallout from the pandemic. Therefore, national pandemic responses need to consider health equity as well as the social determinants of health. The pandemic has also had catastrophic impacts on many health systems, bringing some to the brink of collapse. As a result, many health services, such as services for cardiovascular disease or tobacco cessation, were severely disrupted due to fears of transmission and redirection of resources for COVID-19 care. Unfortunately, the return to pre-pandemic levels of cardiovascular disease care activity has stagnated. Nevertheless, digital solutions, such as telemedicine and apps, have flourished, and may help reduce the gaps. Advancing tobacco control was especially challenging due to interference from the tobacco industry. The industry exploited lingering uncertainties to propagate misleading information on tobacco and COVID-19 in order to promote its products. Regrettably, the links between tobacco use and risk of SARS-CoV-2 infection remain inconclusive. However, a robust body of evidence has, since then, demonstrated that tobacco use is associated with more severe COVID-19 illness and complications. Additionally, the tobacco industry also repeatedly attempted to forge partnerships with governments under the guise of corporate social responsibility. The implementation of the WHO Framework Convention on Tobacco Control could address many of the aforementioned challenges and alleviate the burden of tobacco, COVID-19, and cardiovascular disease. In particular, the implementation of Article 5.3 could protect public health policies from the vested interests of the industry. The world can learn from the COVID-19 pandemic to better prepare for future health emergencies of international concern. In light of the impact of tobacco on the COVID-19 pandemic, it is imperative that tobacco control remains a central component in pandemic preparedness and response plans.

Background

Although COVID-19 initially caused great concern about respiratory symptoms, mounting evidence shows that also the pancreas is productively infected by SARS-CoV-2. However, the severity of pancreatic SARS-CoV-2 infection and its pathophysiology is still under debate. Here, we investigate the consequences of SARS-CoV-2 pancreatic infection and the role of the host factor Placenta-associated protein (PLAC8).

Methods

We analyze plasma levels of pancreatic enzymes and inflammatory markers in a retrospective cohort study of 120 COVID-19 patients distributed in 3 severity-stratified groups. We study the expression of SARS-CoV-2 and PLAC8 in the pancreas of deceased COVID-19 patients as well as in non-infected donors. We perform pseudovirus infection experiments in PLAC8 knock-out PDAC and human beta cell-derived cell lines and validate results with SARS-CoV-2 virus.

Results

We find that analysis of circulating pancreatic enzymes aid the stratification of patients according to COVID-19 severity and predicts outcomes. Interestingly, we find an association between PLAC8 expression and SARS-CoV-2 infection in postmortem analysis of COVID-19 patients both in the pancreas and in other bonafide SARS-CoV-2 target tissues. Functional experiments demonstrate the requirement of PLAC8 in SARS-CoV-2 pancreatic productive infection by pseudovirus and full SARS-CoV-2 infectious virus inoculum from Wuhan-1 and BA.1 strains. Finally, we observe an overlap between PLAC8 and SARS-CoV-2 immunoreactivities in the pancreas of deceased patients.

Conclusions

Our data indicate the human pancreas as a SARS-CoV-2 target with plausible signs of injury and demonstrate that the host factor PLAC8 is required for SARS-CoV-2 pancreatic infection, thus defining new target opportunities for COVID-19-associated pancreatic pathogenesis.

Sepsis is a life-threatening condition caused by the body's overwhelming response to an infection, such as pneumonia or urinary tract infection. It occurs when the immune system releases cytokines into the bloodstream, triggering widespread inflammation. If not treated, it can lead to organ failure and death. Unfortunately, sepsis has a high mortality rate, with studies reporting rates ranging from 20% to over 50%, depending on the severity and promptness of treatment. According to the World Health Organization (WHO), the annual death toll in the world is about 11 million. One of the main toxins responsible for inflammation induction are lipopolysaccharides (LPS, endotoxin) from Gram-negative bacteria, which rank among the most potent immunostimulants found in nature. Antibiotics are consistently prescribed as a part of anti-sepsis-therapy. However, antibiotic therapy (i) is increasingly ineffective due to resistance development and (ii) most antibiotics are unable to bind and neutralize LPS, a prerequisite to inhibit the interaction of endotoxin with its cellular receptor complex, namely Toll-like receptor 4 (TLR4)/MD-2, responsible for the intracellular cascade leading to pro-inflammatory cytokine secretion. The pandemic virus SARS-CoV-2 has infected hundreds of millions of humans worldwide since its emergence in 2019. The COVID-19 (Coronavirus disease-19) caused by this virus is associated with high lethality, particularly for elderly and immunocompromised people. As of August 2023, nearly 7 million deaths were reported worldwide due to this disease. According to some reported studies, upregulation of TLR4 and the subsequent inflammatory signaling detected in COVID-19 patients "mimics bacterial sepsis". Furthermore, the immune response to SARS-CoV-2 was described by others as "mirror image of sepsis". Similarly, the cytokine profile in sera from severe COVID-19 patients was very similar to those suffering from the acute respiratory distress syndrome (ARDS) and sepsis. Finally, the severe COVID-19 infection is frequently accompanied by bacterial co-infections, as well as by the presence of significant LPS concentrations. In the present review, we will analyze similarities and differences between COVID-19 and sepsis at the pathophysiological, epidemiological, and molecular levels.

Several viruses hijack various forms of endocytosis in order to infect host cells. Here, we report the discovery of a molecule with antiviral properties that we named virapinib, which limits viral entry by macropinocytosis. The identification of virapinib derives from a chemical screen using high-throughput microscopy, where we identified chemical entities capable of preventing infection with a pseudotype virus expressing the spike (S) protein from SARS-CoV-2. Subsequent experiments confirmed the capacity of virapinib to inhibit infection by SARS-CoV-2, as well as by additional viruses, such as mpox virus and TBEV. Mechanistic analyses revealed that the compound inhibited macropinocytosis, limiting this entry route for the viruses. Importantly, virapinib has no significant toxicity to host cells. In summary, we present the discovery of a molecule that inhibits macropinocytosis, thereby limiting the infectivity of viruses that use this entry route such as SARS-CoV2.

In the frame of the I-MOVE-COVID-19 project, a cohort of 2050 patients admitted in two Spanish reference hospitals between March 2020 and December 2021 was selected and a range of clinical factor data were collected at admission to assess their impact on the risk COVID-19 severity outcomes through a multivariate adjusted analysis and nomograms. The need for ventilation and intensive care unit (ICU) admission were found to be directly associated with a higher death risk (OR 6.9 and 3.2, respectively). The clinical predictors of death were the need for ventilation and ICU, advanced age, neuromuscular disorders, thrombocytopenia, hypoalbuminemia, dementia, cancer, elevated creatin phosphokinase (CPK), and neutrophilia (OR between 1.8 and 3.5), whilst the presence of vomiting, sore throat, and cough diminished the risk of death (OR 0.5, 0.2, and 0.1, respectively). Admission to ICU was predicted by the need for ventilation, abdominal pain, and elevated lactate dehydrogenase (LDH) (OR 371.0, 3.6, and 2.2, respectively) as risk factors; otherwise, it was prevented by advanced age (OR 0.5). In turn, the need for ventilation was predicted by low oxygen saturation, elevated LDH and CPK, diabetes, neutrophilia, obesity, and elevated GGT (OR between 1.7 and 5.2), whilst it was prevented by hypertension (OR 0.5). These findings could enhance patient management and strategic interventions to combat COVID-19.

Background/Objectives: The COVID-19 pandemic resulted in 675 million cases and 6.9 million deaths by 2022. Despite substantial declines in case fatalities following widespread vaccination campaigns, the threat of future coronavirus outbreaks remains a concern. Current treatments for COVID-19 have been repurposed from existing therapies for other infectious and non-infectious diseases. Emerging evidence suggests a role for genetic factors in both susceptibility to SARS-CoV-2 infection and response to treatment. However, comprehensive studies correlating clinical outcomes with genetic variants are lacking. The main aim of our study is the identification of host genetic biomarkers that predict the clinical outcome of COVID-19 pharmacological treatments. Methods: In this study, we present findings from GWAS and candidate gene and pathway enrichment analyses leveraging diverse patient samples from the Spanish Coalition to Unlock Research of Host Genetics on COVID-19 (SCOURGE), representing patients treated with immunomodulators (n = 849), corticoids (n = 2202), and the combined cohort of both treatments (n = 2487) who developed different outcomes. We assessed various phenotypes as indicators of treatment response, including survival at 90 days, admission to the intensive care unit (ICU), radiological affectation, and type of ventilation. Results: We identified significant polymorphisms in 16 genes from the GWAS and candidate gene studies (TLR1, TLR6, TLR10, CYP2C19, ACE2, UGT1A1, IL-1α, ZMAT3, TLR4, MIR924HG, IFNG-AS1, ABCG1, RBFOX1, ABCB11, TLR5, and ANK3) that may modulate the response to corticoid and immunomodulator therapies in COVID-19 patients. Enrichment analyses revealed overrepresentation of genes involved in the innate immune system, drug ADME, viral infection, and the programmed cell death pathways associated with the response phenotypes. Conclusions: Our study provides an initial framework for understanding the genetic determinants of treatment response in COVID-19 patients, offering insights that could inform precision medicine approaches for future epidemics.

Wastewater-based epidemiology (WBE) has traditionally served as a tool for monitor pathogens, biomarkers, and consumption of pharmaceuticals or illicit drugs. In particular, enteric viruses have been extensively studied in wastewater due to their high titer of excretion. In this study, we investigated the presence of six clinically significant enteric viruses in twelve different areas of a Spanish middle-size city (Burgos), over a 3-year period from November 2021 to November 2024 (n = 600). Viral concentration was performed using an aluminum-based adsorption-precipitation method, followed by nucleic acid extraction and quantification via RT-qPCR. Process controls were included in each experiment to ensure assay accuracy and to calculate viral recovery rates, providing reliable estimates of enteric virus concentrations. The findings revealed that norovirus genogroup II was the most prevalent virus detected in 97.50% of the samples, followed by human astroviruses (90.00%), norovirus genogroup I (85.33%), rotavirus (83.83%), hepatitis E Virus (12.17%), and hepatitis A Virus (0.33%). Spatial heterogeneity in viral distribution was observed among sampling sites, along with temporal and seasonal variations between the COVID-19 pandemic and the post-pandemic periods. A positive correlation was found between enteric viruses and SARS-CoV-2, with both groups of viruses generally displaying stable co-existence. In our hands, this study represents the first long-term WBE analysis of enteric viruses conducted in a middle-sized city, providing valuable insights into the distribution, dynamics, and behavior of major enteric viruses across an extended temporal frame and different areas of the city, spanning both pandemic and post-pandemic contexts.

Effective control of zoonotic infectious diseases requires identifying the animal species involved in the infectious cycle as transmitters or reservoirs where the pathogen could persist and evolve, increasing the risk of reintroduction of new variants in humans and animals. Multiple surveillance studies have detected the presence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) or specific antibodies in free-ranging white-tailed deer (Odocoileus virginianus) in North America, being the wild mammal species with the most reported cases of SARS-CoV-2 infection. However, so far, all attempts to detect the infection in European cervids have been unsuccessful. In this study, we demonstrated the presence of specific antibodies against SARS-CoV-2 in European fallow deer (Dama dama) and red deer (Cervus elaphus) in Spain. However, all samples of European roe deer (Capreolus capreolus), taxonomically related to the American white-tailed deer, were seronegative for the virus. We tested 215 serum samples from roe deer (n = 116), red deer (n = 63), and fallow deer (n = 36) collected in eight provinces of central-southern Spain between 2017 and 2022. We first screened sera by a surrogate virus neutralization test (sVNT) ELISA based on the binding of the receptor-binding domain of SARS-CoV-2 to the angiotensin-converting enzyme 2 (ACE2) receptor and then confirmed positive samples by a conventional virus neutralization test (cVNT) against the Alpha, Delta, and Omicron variants. Four fallow deer and two red deer samples were seropositive in both neutralization assays. Four samples of fallow deer and one of red deer, collected in a suburban park near Madrid in February 2022, had antibodies against the Alpha, Delta, and Omicron variants, while a seropositive sample of red deer, collected in a rural area in February 2021, was specific for the Delta variant. All samples collected before the start of the pandemic in Spain were seronegative for sVNT, which also indicates that there are not cross-reactive antibodies potentially elicited by other viruses antigenically related to SARS-CoV-2. The results indicate probable human-to-deer transmission of SARS-CoV-2, but do not clarify whether there was subsequent spread within herds.

The outbreak of COVID-19, led to an ongoing pandemic with devastating consequences for the global economy and human health. With the global spread of SARS-CoV-2, multidisciplinary initiatives were launched to explore new diagnostic, therapeutic, and vaccination strategies. From this perspective, proteomics could help to understand the mechanisms associated with SARS-CoV-2 infection and to identify new therapeutic options. A TMT-based quantitative proteomics and phosphoproteomics analysis was performed to study the proteome remodeling of human lung alveolar cells expressing human ACE2 (A549-ACE2) after infection with SARS-CoV-2. Detectability and the prognostic value of selected proteins was analyzed by targeted PRM. A total of 6802 proteins and 6428 phospho-sites were identified in A549-ACE2 cells after infection with SARS-CoV-2. The differential proteins here identified revealed that A549-ACE2 cells undergo a time-dependent regulation of essential processes, delineating the precise intervention of the cellular machinery by the viral proteins. From this mechanistic background and by applying machine learning modeling, 29 differential proteins were selected and detected in the serum of COVID-19 patients, 14 of which showed promising prognostic capacity. Targeting these proteins and the protein kinases responsible for the reported phosphorylation changes may provide efficient alternative strategies for the clinical management of COVID-19.

Introduction

The COVID-19 pandemic underscored the need to understand the zoonotic transmission of pathogens. SARS-CoV-2 has been reported to be transmitted from humans to pets, including cats and dogs, particularly after close contact with infected individuals. Studies have shown that cats are more susceptible to natural infection and can transmit the virus to other cats and humans. The zoonotic transmission route represents a risk for animal health workers. Despite global reports, data from Romania remain sparse. This study aimed to evaluate the presence of SARS-CoV-2 specific antibodies in household dogs and cats in Romania during the COVID-19 pandemic.

Methods

The study was conducted at a veterinary clinic in Iasi City, Romania, from March 2020 to December 2022. Blood samples were collected from 84 cats and 82 dogs that had been in contact with COVID-19-positive owners. Plasma samples were tested for anti-SARS-CoV-2 antibodies using an ELISA test, followed by confirmation with a seroneutralisation (SN) assay. The SN assay used the SARS-CoV-2 MAD6 strain and Omicron strain to determine neutralising antibody titers.

Results

ELISA testing showed a seroprevalence of 9.5% in cats and 11% in dogs. Further SN assay testing confirmed SARS-CoV-2 specific antibodies in 9.4% of cats and 2.4% of dogs. One cat maintained antibodies for over a year, though with reduced titers. Most cats' antibodies did not cross-react with the Omicron strain, indicating limited cross-reactivity. The study highlighted higher seroprevalence and antibody titers in cats compared to dogs, likely due to more efficient viral replication in cats.

Conclusions

This study provides the first serological evidence of SARS-CoV-2 exposure in household pets during the pandemic in Romania, with findings suggesting cats are more susceptible to infection from their owners than dogs. The cats that were living in households in one area of the city were prone to be infected with SARS-CoV-2 from their owners and high levels of seroconversion were detected. These results align with global reports, demonstrating that cats are particularly susceptible to SARS-CoV-2 when living with infected owners.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects various mammalian species, with farmed minks experiencing the highest number of outbreaks. In Spain, we analyzed 67 whole genome sequences and eight spike sequences from 18 outbreaks, identifying four distinct lineages: B.1, B.1.177, B.1.1.7, and AY.98.1. The potential risk of transmission to humans raises crucial questions about mutation accumulation and its impact on viral fitness. Sequencing revealed numerous not-lineage-defining mutations, suggesting a cumulative mutation process during the outbreaks. We observed that the outbreaks were predominantly associated with different groups of mutations rather than specific lineages. This clustering pattern by the outbreaks could be attributed to the rapid accumulation of mutations, particularly in the ORF1a polyprotein and in the spike protein. Notably, the mutations G37E in NSP9, a potential host marker, and S486L in NSP13 were detected. Spike protein mutations may enhance SARS-CoV-2 adaptability by influencing trimer stability and binding to mink receptors. These findings provide valuable insights into mink coronavirus genetics, highlighting both host markers and viral transmission dynamics within communities.

The vasa vasorum of the large pulmonary vessels is involved in the pathology of COVID-19. This specialized microvasculature plays a major role in the biology and pathology of the pulmonary vessel walls. We have evidence that thrombosis of the vasa vasorum of the large and medium-sized pulmonary vessels during severe COVID-19 causes ischemia and subsequent death of the pulmonary vasculature endothelium. Subsequent release of thrombi from the vasa interna into the pulmonary circulation and pulmonary embolism generated at the ischemic pulmonary vascular endothelium site, are the central pathophysiological mechanisms in COVID-19 responsible for pulmonary thromboembolism. The thrombosis of the vasa vasorum of the large and medium-sized pulmonary vessels is an internal event leading to pulmonary thromboembolism in COVID-19.

Background

Hyperinflammation, hypercoagulation and endothelial injury are major findings in acute and post-COVID-19. The SARS-CoV-2 S protein has been detected as an isolated element in human tissues reservoirs and is the main product of mRNA COVID-19 vaccines. We investigated whether the S protein alone triggers pro-inflammatory and pro-coagulant responses in primary cultures of two cell types deeply affected by SARS-CoV-2, such are monocytes and endothelial cells.

Methods

In human umbilical vein endothelial cells (HUVEC) and monocytes, the components of NF-κB and the NLRP3 inflammasome system, as well as coagulation regulators, were assessed by qRT-PCR, Western blot, flow cytometry, or indirect immunofluorescence.

Results

S protein activated NF-κB, promoted pro-inflammatory cytokines release, and triggered the priming and activation of the NLRP3 inflammasome system resulting in mature IL-1β formation in both cell types. This was paralleled by enhanced production of coagulation factors such as von Willebrand factor (vWF), factor VIII or tissue factor, that was mediated, at least in part, by IL-1β. Additionally, S protein failed to enhance ADAMTS-13 levels to counteract the pro-coagulant activity of vWF multimers. Monocytes and HUVEC barely expressed angiotensin-converting enzyme-2. Pharmacological approaches and gene silencing showed that TLR4 receptors mediated the effects of S protein in monocytes, but not in HUVEC.

Conclusion

S protein behaves both as a pro-inflammatory and pro-coagulant stimulus in human monocytes and endothelial cells. Interfering with the receptors or signaling pathways evoked by the S protein may help preventing immune and vascular complications driven by such an isolated viral element. Video Abstract.

Aims

During the early stages of the COVID-19 pandemic, significant differences in mortality patterns emerged based on sex and geographical regions. While we were studying on the heredity of variants of the Y chromosome, we observed that regional variations in mortality rates appeared to correlate with the geographical distribution of certain variants of the Y chromosome. This observation led us to propose that some genes on the Y chromosome, with an influence on immune responses, may represent a confounding factor in the observed geographical mortality differences.

Methods

In this analysis, we investigate the potential associations between COVID-19 morbidity and disease-specific mortality and specific Y chromosome variants. The study is based on publicly available pandemic data validated by state authorities or presented in scientific literature documented in PubMed and Medline.

Results

We find that Y chromosome haplogroups in different populations exhibit wave-like patterns corresponding with persistent global disparities in COVID-19-related mortality.

Conclusions

These findings warrant further research to uncover possible new pathophysiological mechanisms.

Background

The coronavirus disease-19 (COVID-19) pandemic has affected global health, influencing the prevalence of different respiratory pathogens. The aim of this study is to evaluate the distribution of agents causing acute respiratory infections in children under 5 years old before and after the COVID-19 pandemic in Praia, Cabo Verde, and to describe associated clinical variables.

Methods

Conducted at the University Hospital Dr. Agostinho Neto, this study replicated methods from a previous work from 2019 (Correia et al. 2021). Nasopharyngeal samples were analysed using FilmArray® Respiratory Panel 2.1 (BioFire) to identify agents of acute respiratory infections. Molecular identification of human respiratory syncytial virus subtypes was performed using a real-time duplex reverse transcription polymerase chain reaction. Statistical analysis was performed using IBM SPSS version 29 and R 3.5.1 software.

Results

In 2022, 86.5% (83/96) of nasopharyngeal samples were positive for at least one pathogen. Human rhinovirus/human enterovirus was the most frequent agent, followed by human respiratory syncytial virus, adenovirus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Co-infections were observed in 43.3% of positive cases. Infection rates were significantly higher in children under 1 year of age, particularly for SARS-CoV-2 and human respiratory syncytial virus. Seasonal variations were observed, with human respiratory syncytial virus predominating in November, SARS-CoV-2 in January and human parainfluenza virus-4 in May. Molecular analysis of human respiratory syncytial virus revealed a shift in subtype prevalence, with both human respiratory syncytial virus-A and -B co-circulating in the pre-pandemic period, whereas only human respiratory syncytial virus-B was detected in the post-pandemic period.

Conclusion

Our data indicate changes in the distribution of respiratory viruses in the post-pandemic period compared to pre-pandemic period. The high prevalence of co-infections highlights the complexity of acute respiratory infection aetiology, emphasising the need for enhanced respiratory virus surveillance systems in Cabo Verde. Identifying seasonal trends and risk factors can contribute to targeted interventions and improved public health strategies to mitigate the burden of acute respiratory infections in young children.

Background

Patients with severe COVID-19 may develop lung fibrosis. Pirfenidone is an anti-fibrotic drug approved for idiopathic pulmonary fibrosis. The efficacy and safety of pirfenidone in patients with fibrotic interstitial lung changes after recovery from severe COVID-19 pneumonia were evaluated.

Methods

This was a phase 2, double-blind, placebo-controlled, Spanish multicentre clinical trial. Patients were randomised to receive pirfenidone or placebo (2:1) for 24 weeks. The primary end-point was the proportion of patients that improved, considered when percentage change in forced vital capacity (FVC) was ≥10% and/or any reduction in the fibrotic score on chest high-resolution computed tomography (HRCT). Secondary end-points included health-related quality of life (HRQoL), exercise capacity and drug safety profile.

Results

From 119 eligible patients, 113 were randomised and 103 were analysed (pirfenidone n=69 and placebo n=34). Most patients were male (73.5%) and were receiving low-dose prednisone; mean age was 63.7 years and mean body mass index was 29 kg·m^-2. The percentage of patients that improved was similar in the pirfenidone and placebo groups (79.7% versus 82.3%, respectively). The mean predicted FVC increased by 12.74±20.6% with pirfenidone and 4.35±22.3% with placebo (p=0.071), and the HRCT (%) fibrotic score decreased by 5.44±3.69% with pirfenidone and 2.57±2.59% with placebo (p=0.52). Clinically meaningful improvement in HRQoL was not statistically different (55.2% in the pirfenidone group and 39.4% in the placebo group). Exercise capacity, adverse events and hospitalisations were similar between groups. No deaths were reported.

Conclusions

The overall improvements in lung function and HRCT fibrotic score after 6 months with pirfenidone were not significantly different than with placebo.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19 and responsible for the global coronavirus pandemic which started in 2019. Despite exhaustive efforts to trace its origins, including potential links with pangolins and bats, the precise origins of the virus remain unclear. Bats have been recognized as natural hosts for various coronaviruses, including the Middle East respiratory coronavirus (MERS-CoV) and the SARS-CoV. This study presents a comparative analysis of the SARS-CoV-2 nucleocapsid protein (N) interactome in human and bat cell lines. We identified approximately 168 cellular proteins as interacting partners of SARS-CoV-2 N in human cells and 196 cellular proteins as interacting partners with this protein in bat cells. The results highlight pathways and events that are both common and unique to either bat or human cells. Understanding these interactions is crucial to comprehend the reasons behind the remarkable resilience of bats to viral infections. This study provides a foundation for a deeper understanding of host-virus interactions in different reservoirs.

Unlocking the potential of broadly reactive coronavirus monoclonal antibodies (mAbs) and their derivatives offers a transformative therapeutic avenue against severe COVID-19, especially crucial for safeguarding high-risk populations. Novel mAb-based immunotherapies may help address the reduced efficacy of current vaccines and neutralizing mAbs caused by the emergence of variants of concern (VOCs). Using phage display technology, we discovered a pan-SARS-CoV-2 mAb (C10) that targets a conserved region within the receptor-binding domain (RBD) of the virus. Noteworthy, C10 demonstrates exceptional efficacy in recognizing all assessed VOCs, including recent Omicron variants. While C10 lacks direct neutralization capacity, it efficiently binds to infected lung epithelial cells and induces their lysis via natural killer (NK) cell-mediated antibody-dependent cellular cytotoxicity (ADCC). Building upon this pan-SARS-CoV-2 mAb, we engineered C10-based, Chimeric Antigen Receptor (CAR)-T cells endowed with efficient killing capacity against SARS-CoV-2-infected lung epithelial cells. Notably, NK and CAR-T-cell mediated killing of lung infected cells effectively reduces viral titers. These findings highlight the potential of non-neutralizing mAbs in providing immune protection against emerging infectious diseases. Our work reveals a pan-SARS-CoV-2 mAb effective in targeting infected cells and demonstrates the proof-of-concept for the potential application of CAR-T cell therapy in combating SARS-CoV-2 infections. Furthermore, it holds promise for the development of innovative antibody-based and cell-based therapeutic strategies against severe COVID-19 by expanding the array of therapeutic options available for high-risk populations.Trial registration: ClinicalTrials.gov identifier: NCT04093596.

Background/aim

Understanding the mechanism of host transcriptomic response to infection by the SARS-CoV-2 virus is crucial, especially for patients suffering from long-term effects of COVID-19, such as long COVID or pericarditis inflammation, potentially linked to side effects of the SARS-CoV-2 spike proteins. We conducted comprehensive transcriptome and enrichment analyses on lung and peripheral blood mononuclear cells (PBMCs) infected with SARS-CoV-2, as well as on SARS-CoV and MERS-CoV, to uncover shared pathways and elucidate their common disease progression and viral replication mechanisms.

Materials and methods

We developed CompCorona, the first interactive online tool for visualizing gene response variance among the family Coronaviridae through 2D and 3D principal component analysis (PCA) and exploring systems biology variance using pathway plots. We also made preprocessed datasets of lungs and PBMCs infected by SARS-CoV-2, SARS-CoV, and MERS-CoV publicly available through CompCorona.

Results

One remarkable finding from the lung and PBMC datasets for infections by SARS-CoV-2, but not infections by other coronaviruses (CoVs), was the significant downregulation of the angiogenin (ANG) and vascular endothelial growth factor A (VEGFA) genes, both directly involved in epithelial and vascular endothelial cell dysfunction. Suppression of the TNF signaling pathway was also observed in cells infected by SARS-CoV-2, along with simultaneous activation of complement and coagulation cascades and pertussis pathways. The ribosome pathway was found to be universally suppressed across all three viruses. The CompCorona online tool enabled the comparative analysis of 9 preprocessed host transcriptome datasets of cells infected by CoVs, revealing the specific host response differences in cases of SARS-CoV-2 infection. This included identifying markers of epithelial dysfunction via interactive 2D and 3D PCA, Venn diagrams, and pathway plots.

Conclusion

Our findings suggest that infection by SARS-CoV-2 might induce pulmonary epithelial dysfunction, a phenomenon not observed in cells infected by other CoVs. The publicly available CompCorona tool, along with the preprocessed datasets of cells infected by various CoVs, constitutes a valuable resource for further research into CoV-associated syndromes.

Despite the decrease in mortality and morbidity due to SARS-CoV-2 infection, the incidence of infections due to Omicron subvariants of SARS-CoV-2 remains high. The mutations acquired by these subvariants, mainly concentrated in the receptor-binding domain (RBD), have caused a shift in infectivity and transmissibility, leading to a loss of effectiveness of the first authorized COVID-19 vaccines, among other reasons, by neutralizing antibody evasion. Hence, the generation of new vaccine candidates adapted to Omicron subvariants is of special interest in an effort to overcome this immune evasion. Here, an optimized COVID-19 vaccine candidate, termed MVA-S(3P_BA.1), was developed using a modified vaccinia virus Ankara (MVA) vector expressing a full-length prefusion-stabilized SARS-CoV-2 spike (S) protein from the Omicron BA.1 variant. The immunogenicity and efficacy induced by MVA-S(3P_BA.1) were evaluated in mice in a head-to-head comparison with the previously generated vaccine candidates MVA-S(3P) and MVA-S(3Pbeta), which express prefusion-stabilized S proteins from Wuhan strain and Beta variant, respectively, and with a bivalent vaccine candidate composed of a combination of MVA-S(3P) and MVA-S(3P_BA.1). The results showed that all four vaccine candidates elicited, after a single intramuscular dose, protection of transgenic K18-hACE2 mice challenged with SARS-CoV-2 Omicron BA.1, reducing viral loads, histopathological lesions, and levels of proinflammatory cytokines in the lungs. They also elicited anti-S IgG and neutralizing antibodies against various Omicron subvariants, with MVA-S(3P_BA.1) and the bivalent vaccine candidate inducing higher titers. Additionally, an intranasal immunization in C57BL/6 mice with all four vaccine candidates induced systemic and mucosal S-specific CD4⁺ and CD8⁺ T-cell and humoral immune responses, and the bivalent vaccine candidate induced broader immune responses, eliciting antibodies against the ancestral Wuhan strain and different Omicron subvariants. These results highlight the use of MVA as a potent and adaptable vaccine vector against new emerging SARS-CoV-2 variants, as well as the promising feature of combining multivalent MVA vaccine candidates.

MicroRNAs (miRNAs) are gene regulators essential for cell homeostasis, their alteration is related to a pathological state, including infectious diseases like COVID-19. Identifying an altered profile of circulating miRNAs in mild COVID-19 may enhance our knowledge of the pathogenesis of SARS-CoV-2 and the range of clinical phenotypes. In the present study, a miRNA screening was performed by Next Generation Sequencing (NGS), and the expression levels of 13 resulting miRNAs were validated through RT-qPCR in the serum of 40 mild cases compared to 29 non-infected individuals. An in-silico analysis was performed to detect target genes and their related pathways. From the validated miRNAs, miR-1246 (p < 0.001), miR-423-5p (p < 0.001), miR-21-5p (p = 0.005), miR-146a-5p (p < 0.001), miR-4508 (p = 0.001), miR-629-5p (p < 0.001), and miR-210-3p (p = 0.002) were found downregulated in infected individuals. Only miR-27a-5p was overexpressed in subjects with COVID-19 (p = 0.013) and associated with SARS-CoV-2 infection (p = 0.010). The KEGG pathways and GO analysis revealed that the differentially expressed miRNAs were related to viral processes or immunological pathways: miR-27a-5p acts on the TGF-beta pathway; miR-21-5p targets SMAD7, which is associated with the inflammatory response in the lung; miR-1246 acts on p53 pathway; and miR-4508 acts on ICAM2. In conclusion, the most relevant miRNAs, miR-27a-5p and miR-21-5p, were differently expressed in mild forms of COVID-19. The higher expression of miR-27a-5p observed in mild COVID-19 cases may suggest a protective effect against severe forms of the disease. Reduced expression of miR-21-5p may prevent pulmonary inflammation and the progression of fibrosis. The downregulation of miR-1246 and miR-4508 in mild COVID-19 cases may conduct the correct control of the infection. Moreover, miR-423-5p might be a suitable biomarker in the early stages of SARS-CoV-2 infection.

Background

Pregnant and recently pregnant women infected with SARS-CoV-2 are at increased risk of death and serious complications than those without the infection. The extent of variation in mortality rates in pregnant women with SARS-CoV-2 infection across regions, and the causes of death are not known. We systematically reviewed all available evidence on the variation in mortality rates in pregnant women with SARS-CoV-2 infection across geographical and country income groups, and the reported cause of death.

Methods

We searched major databases (December 2019-January 2023) including Medline, LILACS, BIREME and Embase. We included studies that reported deaths in at least 10 consecutive pregnant or recently pregnant women with confirmed SARS-CoV-2 infection and assessed the studies' risk of bias. We calculated the summary estimates of any cause of death as proportions with 95% CIs using a multilevel random-effects logistic regression model. Subgroup analyses were performed by geographical region and country income groups. We used International Statistical Classification of Diseases and Related Health Problems-Maternal Mortality to categorise the reported cause of death.

Findings

From 1 326 315 citations, we included 169 studies (319 172 women with confirmed SARS-CoV-2 infection; 4253 women died). The overall rate of unspecified maternal death was 0.87% (95% CI 0.64% to 1.16%). There were significant differences between geographical regions in rates of maternal mortality, with the highest rates in Sub-Saharan Africa (3.48%; 95% CI 0.66% to 16.42%) and Latin America and the Caribbean (3.16%, 95% CI 1.53% to 6.43%). Rates of maternal mortality varied by country income groups, with the highest rates in low-income countries (4.66%, 95% CI 0.75% to 24.07%). Among women with reported cause of death, 98.6% (2,390/2,423) of deaths were attributable to COVID-19.

Interpretation

Rates of deaths in pregnant and recently pregnant women with SARS-CoV-2 infection vary significantly across regions and by country income groups, with the highest burden in Sub-Saharan Africa and low-income countries. COVID-19 is the main reported cause of death.

Prospero registration number

CRD42020224120.

Introduction

COVID-19, caused by the SARS-CoV-2 virus, had a significant global impact since its emergence in December 2019. In Spain, the pandemic caused multiple waves of infections, with variations in clinical presentation and predominant viral strains. This study analyzed the evolution of COVID-19 in pediatric patients in a pediatric emergency department in Madrid (Spain), focusing on the changes in clinical manifestations over time.

Methods

This single-center, retrospective study was conducted from March 2020 to October 2024, including pediatric patients aged 0-18 years with confirmed SARS-CoV-2 infection. Data collected included demographic characteristics, clinical manifestations, and hospital admission rates. The sample was divided into groups based on the predominant circulating variant during specific periods.

Results

A total of 1,949 confirmed COVID-19 cases were analyzed. The median age of the patients was 1.2 years (IQR: 0.4-7.4). The highest number of recorded cases was in infants aged 1-12 months (43.4%). Fever (77.6%) and respiratory symptoms (68.8%) were the most common clinical manifestations. A statistically significant association was observed between the presence of fever and the XBB variant (p < 0.015), the presence of upper respiratory symptoms and the XBB variant (p = 0.015), the presence of gastrointestinal symptoms and the Omicron BA.2 variant (p = 0.009), and the presence of laryngitis and the XBB variant (p < 0.001). The highest number of admissions was recorded in patients aged 1-12 months (61/133; 45.9%), followed by school-aged children aged 6-11 years (22/133; 16.5%).

Conclusion

The clinical presentation and age distribution of COVID-19 infections have changed over time. Infants aged 1-12 months were the most affected, a consistent trend across the pandemic. Fever remained the most common clinical manifestation throughout the study period, followed by upper respiratory symptoms.

Background

SARS-CoV-2 neutralizing antibodies may protect against symptomatic infection in immunized individuals. However, vaccine-induced antibody levels wane over time, reducing vaccine efficacy. The definition of the waning kinetics of neutralizing SARS-CoV-2 responses and the potential impact of sequential antigen encounters are still poorly defined.

Methods

Plasma neutralizing activity was determined in longitudinally collected samples from SARS-CoV-2 infected, primo-vaccinated and boosted individuals. Neutralizing activity decay kinetics were modeled against time using Log-Log and biexponential models.

Results

Neutralizing antibody levels wane after an initial peak in all groups of vaccinated individuals with half-life ranging from 29 to 60 days. Exponential models showed a subsequent stabilization of neutralizing titers to a plateau. Both the peak response and the plateau values depended on vaccine type, infection status and severity of infection. Booster immunization by either vaccines or breakthrough infections did not modify peak, plateau or decay rate values.

Conclusions

Our results indicate that the waning of SARS-CoV-2 neutralizing antibody responses was recurrent even after several antigen encounters. Repeated immunizations would be required to maintain high levels of neutralizing antibodies and protect vulnerable individuals from symptomatic infection.

The COVID-19 pandemic has had a devastating impact, with more than 7 million deaths worldwide. Advanced age and comorbidities partially explain severe cases of the disease, but genetic factors also play a significant role. Genome-wide association studies (GWASs) have been instrumental in identifying loci associated with SARS-CoV-2 infection. Here, we report the results from a >820 K variant GWAS in a COVID-19 patient cohort from the hospitals associated with IIS Biobizkaia. We compared intensive care unit (ICU)-hospitalized patients with non-ICU-hospitalized patients. The GWAS was complemented with an integrated phenotype and genetic modeling analysis using HLA genotypes, a previously identified COVID-19 polygenic risk score (PRS) and clinical data. We identified four variants associated with COVID-19 severity with genome-wide significance (rs58027632 in KIF19; rs736962 in HTRA1; rs77927946 in DMBT1; and rs115020813 in LINC01283). In addition, we designed a multivariate predictive model including HLA, PRS and clinical data which displayed an area under the curve (AUC) value of 0.79. Our results combining human genetic information with clinical data may help to improve risk assessment for the development of a severe outcome of COVID-19.

Defective genomes are part of SARS-CoV-2 quasispecies. High-resolution, ultra-deep sequencing of bulk RNA from viral populations does not distinguish RNA mutations, insertions, and deletions in viable genomes from those in defective genomes. To quantify SARS-CoV-2 infectious variant progeny, virus from four individual plaques (biological clones) of a preparation of isolate USA-WA1/2020, formed on Vero E6 cell monolayers, was subjected to further biological cloning to yield 9 second-generation and 15 third-generation sub-clones. Consensus genomic sequences of the biological clones and sub-clones included an average of 2.8 variations per viable genome, relative to the consensus sequence of the parental USA-WA1/2020 virus. This value is 6.5-fold lower than the estimates for biological clones of other RNA viruses such as bacteriophage Qβ, foot-and-mouth disease virus, or hepatitis C virus in cell culture. The mutant spectrum complexity of the nsp12 (polymerase)- and spike (S)-coding region was unique in the progeny of each of 10 third-generation sub-clones; they shared 2.4% of the total of 164 different mutations and deletions scored in the 3,719 genomic residues that were screened. The presence of minority out-of-frame deletions revealed the ease of defective genome production from an individual infectious genome. Several low-frequency point mutations and deletions were clade-discordant in that they were not typical of USA-WA1/2020 but served to define the consensus sequences of future SARS-CoV-2 clades. Implications for SARS-CoV-2 adaptability and COVID-19 control of the viable genome heterogeneity and the generation of complex mutant spectra from individual genomes are discussed.IMPORTANCESequencing of biological clones is a means to identify mutations, insertions, and deletions located in viable genomes. This distinction is particularly important for viral populations, such as those of SARS-CoV-2, that contain large proportions of defective genomes. By sequencing biological clones and sub-clones, we quantified the heterogeneity of the viable complement of USA-WA1/2020 to be lower than exhibited by other RNA viruses. This difference may be due to a reduced mutation rate or to limited tolerance of the large coronavirus genome to incorporate mutations and deletions and remain functional or a combination of both influences. The presence of clade-discordant residues in the progeny of individual biological sub-clones suggests limitations in the occupation of sequence space by SARS-CoV-2. However, the complex and unique mutant spectra that are rapidly generated from individual genomes suggest an aptness to confront selective constraints.

Purpose

In this study, we present DeepVirusClassifier, a tool capable of accurately classifying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral sequences among other subtypes of the coronaviridae family. This classification is achieved through a deep neural network model that relies on convolutional neural networks (CNNs). Since viruses within the same family share similar genetic and structural characteristics, the classification process becomes more challenging, necessitating more robust models. With the rapid evolution of viral genomes and the increasing need for timely classification, we aimed to provide a robust and efficient tool that could increase the accuracy of viral identification and classification processes. Contribute to advancing research in viral genomics and assist in surveilling emerging viral strains.

Methods

Based on a one-dimensional deep CNN, the proposed tool is capable of training and testing on the Coronaviridae family, including SARS-CoV-2. Our model's performance was assessed using various metrics, including F1-score and AUROC. Additionally, artificial mutation tests were conducted to evaluate the model's generalization ability across sequence variations. We also used the BLAST algorithm and conducted comprehensive processing time analyses for comparison.

Results

DeepVirusClassifier demonstrated exceptional performance across several evaluation metrics in the training and testing phases. Indicating its robust learning capacity. Notably, during testing on more than 10,000 viral sequences, the model exhibited a more than 99% sensitivity for sequences with fewer than 2000 mutations. The tool achieves superior accuracy and significantly reduced processing times compared to the Basic Local Alignment Search Tool algorithm. Furthermore, the results appear more reliable than the work discussed in the text, indicating that the tool has great potential to revolutionize viral genomic research.

Conclusion

DeepVirusClassifier is a powerful tool for accurately classifying viral sequences, specifically focusing on SARS-CoV-2 and other subtypes within the Coronaviridae family. The superiority of our model becomes evident through rigorous evaluation and comparison with existing methods. Introducing artificial mutations into the sequences demonstrates the tool's ability to identify variations and significantly contributes to viral classification and genomic research. As viral surveillance becomes increasingly critical, our model holds promise in aiding rapid and accurate identification of emerging viral strains.

Safe and effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are crucial to fight against the coronavirus disease 2019 pandemic. Most vaccines are based on a mutated version of the Spike glycoprotein [K986P/V987P (S-2P)] with improved stability, yield and immunogenicity. However, S-2P is still produced at low levels. Here, we describe the V987H mutation that increases by two-fold the production of the recombinant Spike and the exposure of the receptor binding domain (RBD). S-V987H immunogenicity is similar to S-2P in mice and golden Syrian hamsters (GSH), and superior to a monomeric RBD. S-V987H immunization confer full protection against severe disease in K18-hACE2 mice and GSH upon SARS-CoV-2 challenge (D614G or B.1.351 variants). Furthermore, S-V987H immunized K18-hACE2 mice show a faster tissue viral clearance than RBD- or S-2P-vaccinated animals challenged with D614G, B.1.351 or Omicron BQ1.1 variants. Thus, S-V987H protein might be considered for future SARS-CoV-2 vaccines development.

Oncology patients are more susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection due to hospital contact and an immunological system that can be compromised by antineoplastic therapy and supportive treatments. Certain similarities have been described in the physiopathology of coronavirus disease 2019 (COVID-19) and lung cancer (LC) that may explain the higher probability of these patients of developing a more serious disease with more frequent hospitalizations and even death, especially with the addition of smoking, cardiovascular and respiratory comorbidities, old age and corticosteroids use. Pre-existing lesions and cancer therapies change the normal architecture of the lungs, so diagnostic scales such as COVID-19 Reporting and Data System (CO-RADS) are of vital importance for a correct diagnosis and patient homogenization, with a high inter-observer correlation. Moreover, anticancer treatments have required an adaptation to reduce the number of visits to the hospital [hypofractionated radiotherapy (RT), larger intervals between chemotherapy cycles, delay in follow-up tests, among others]. In a way, this has also caused a delay in the diagnosis of new cancers. On the other hand, vaccination has had a positive impact on the mortality of these patients, who maintain a similar seroprevalence to the rest of the population, with a similar impact in mortality.

Background

Patients with rheumatoid arthritis (RA) and spondyloarthritis (SpA) are at an increased risk for infection related to the use of immunomodulatory therapies (ITs). The objective of this study is to assess the impact of ITs on the adaptive immune responses to SARS-CoV-2.

Methods

The study population comprised 94 patients (48 SpA; 46 RA; mean age of 53±14 years) with a confirmed SARS-CoV-2 infection. 20 age-matched individuals (50±17 years), corresponding to the patients' household contacts infected at the same time, were included as the control population. Patients were stratified by treatment groups: methotrexate (MTX)/sulfasalazine (n=17/2), anti-TNF (n=24), anti-TNF+MTX (n=23), RTX (N=11), anti-IL17 (n=7) and others (n=11). The study compared the viral loads in plasma, stools and nasal swabs and the SARS-CoV-2-specific humoral and cellular immune responses (antibodies, B and T lymphocytes) following SARS-CoV-2 infection.

Results

Viral persistence was not observed in the blood, nasopharynx and stools of patients undergoing ITs. Overall, the SARS-CoV-2-specific humoral and T-cell responses were preserved. Patients receiving RTX showed significantly lower IgA and IgG responses to SARS-CoV-2 compared with other treatment groups. Most patients, including RTX recipients, exhibited significant CD4+T cell responses. However, RTX therapy was associated with reduced SARS-CoV-2-specific activated CD8+T cells. A correlation was observed between humoral immune parameters and CD8⁺ T cell activation.

Conclusions

While most patients demonstrated the capacity to mount an immune response to SARS-CoV-2, treatment with RTX impacted both humoral and CD8+cell responses. Developing vaccines that elicit robust CD8+T cell responses could offer benefits to individuals undergoing ITs for inflammatory rheumatic diseases.

(1) Background: Respiratory viral infections, including those caused by SARS-CoV-2, respiratory syncytial virus (RSV), influenza viruses, rhinovirus, and adenovirus, are major causes of acute respiratory infections (ARIs) in children. Symptom-based predictive models are valuable tools for expediting diagnoses, particularly in primary care settings. This study assessed the effectiveness of machine learning-based models in estimating infection probabilities for these common pediatric respiratory viruses, using symptom data. (2) Methods: Data were collected from 868 children with ARI symptoms evaluated across 14 primary care centers, members of COPEDICAT (Coronavirus Pediatria Catalunya), from October 2021 to October 2023. Random forest and boosting models with 10-fold cross-validation were used, applying SMOTE-NC to address class imbalance. Model performance was evaluated via area under the curve (AUC), sensitivity, specificity, and Shapley additive explanations (SHAP) values for feature importance. (3) Results: The model performed better for RSV (AUC: 0.81, sensitivity: 0.64, specificity: 0.77) and influenza viruses (AUC: 0.71, sensitivity: 0.70, specificity: 0.59) and effectively ruled out SARS-CoV-2 based on symptom absence, such as crackles and wheezing. Predictive performance was lower for non-enveloped viruses like rhinovirus and adenovirus, due to their nonspecific symptom profiles. SHAP analysis identified key symptoms patterns for each virus. (4) Conclusions: The study demonstrated that symptom-based predictive models effectively identify pediatric respiratory infections, with notable accuracy for those caused by RSV, SARS-CoV-2, and influenza viruses.

Background

Despite growing evidence of reduced invasive and non-invasive pneumococcal disease attributed to public health measures against the COVID-19 pandemic, the effect of these measures on pneumococcal carriage remains unclear. This study aimed to assess pneumococcal nasopharyngeal carriage among children and adults self-confined at home during the COVID-19 national lockdown in Spain while identifying predictors of pneumococcal carriage in children.

Methods

Household study conducted across the metropolitan area of Barcelona (Spain) between April-June 2020. Nasopharyngeal samples were collected from young children and adults for real-time PCR pneumococcal lytA and wgz gene detection, quantification, and serotyping, as well as for detection of respiratory viruses.

Results

Among 332 children (median age: 3.1 years [IQR: 1.9-4.0 years]; 59% male) and 278 adults (median age: 38.9 years [IQR: 36.1-41.3 years]; 64% female), pneumococcal carriage rates were 28.3% and 2.5%, respectively. Highly invasive serotypes 3, 7F/7A, and 19A were detected in 14.0% of samples from children carriers. Pneumococcal co-infections with respiratory syncytial virus (RSV), human metapneumovirus (hMPV), and influenza virus (IV) were not identified in children. Attendance to kindergarten before the lockdown (aOR: 2.65; IQR: 1.57-4.47; p<0.001) and household crowding (aOR: 1.85; IQR: 1.09-3.15; p = 0.02) were independent risk factors for children's pneumococcal carriage.

Conclusions

Pneumococcal carriage rate among quarantined children during a full COVID-19 lockdown was moderate and correlated with limited presence of highly invasive serotypes and absence of pneumococcal co-infections with RSV, hMPV, and IV. Pre-lockdown daycare and household crowding predisposed children to carriage.

Although SARS-CoV-2 reinfections remain a concern for healthcare systems worldwide, the factors driving them are still not fully understood. In this study, we examined data for 3303 individuals who experienced two SARS-CoV-2 infections between March 2020 and May 2022 from both clinical and viral genomics perspectives. Our findings indicate that viral evolution was the primary driver of reinfection. However, chronic conditions were common among reinfected individuals, including those under 26 years old, suggesting that the presence of underlying and/or chronic conditions increases susceptibility to reinfection. The median time elapsed between infections was one year, often coinciding with the emergence of new variants. While vaccination showed only a limited protective effect against reinfection, it drastically decreased the hospitalization rate, underscoring its role in mitigating disease severity. Our findings point to the need for more flexible vaccination strategies, especially for individuals with chronic conditions. Understanding the interactions between host factors and viral evolution is critical to strengthening prevention strategies and reducing the burden of reinfections and their possible long-term complications.

Aim: To analyse the degree of compliance of the care times of hospital emergency departments (EDs) in Spain with the recommended standards and their evolution during the SARS-CoV-2 pandemic. Design and Methods: An observational, correlational, cross-sectional and retrospective study was carried out. All adult patients attended in the EDs of 8 Spanish public hospitals from 2018 to 2021 were consecutively included. The main variables were time spent in the ED, time to triage, waiting time until the start of care, triage level, classified according to the Spanish Triage System and year of care. Other sociodemographic variables were collected, in addition to discharge destination. For each triage level, a negative binomial regression model was performed, adjusted for year, hospital and waiting times. The analysis was performed with R 4.2.2 software. Results: A total of 2,282,555 patients were included; ED lengths of stay varied according to triage levels: Level 1, 21.6 h; Level 2, 26.3 h; Level 3, 22.2 h; Level 4, 8.1 h and Level 5, 10.3 h. Statistically significant differences were detected only in 2021, in all hospitals and from priority Level 2-5. An increase in dwell times was observed in all hospitals, with longer dwell times in high complexity hospitals. Longer waiting times at triage Levels 3, 4 and 5 presented a higher risk of mortality. The percentage of patients leaving the ED was high (3.6%). Conclusions: The degree of compliance with ED care times according to recommended standards was low. The dropout rate, waiting times for initial triage and ED attendance were higher than desired. The SARS-CoV-2 pandemic changed the pattern of ED visits, decreasing the frequentation of patients, but did not decrease the length of stay in the ED. This pattern normalised the following year.

COVID-19 remains a significant global health problem with uncertain long-term consequences for convalescents. We investigated the relationships between anti-N protein antibody levels, severe acute respiratory syndrome (SARS)-CoV-2-associated TCR repertoire parameters, HLA type and epidemiological information from three cohorts of 524 SARS-CoV-2-infected subjects subgrouped in acute phase, seronegative and seropositive convalescents from the Emilia Romagna region. Epidemiological information and anti-N antibody index were associated with TCR repertoire data. HLA type was inferred from TCR repertoire using the HLA3 tool and its association with clonal breadth (CB) and clonal depth (CD) was assessed. Age above 58 years, male and COVID-19 hospitalisation were significantly and independently associated with seropositivity (p = 0.004; p = 0.004; p = 0.04), suggesting an association between high antibody titres and symptoms' severity. As for the TCR repertoire analysis, we found no difference in CB among the cohorts, while CD was higher in seronegative than acute (p = 0.04). However, clustering analysis supported that seronegative patients are endowed with broader CB and deeper CD indicating a compensatory mechanism without effective seroconversion. The CD calculated on the TCRs associated with the single SARS-CoV-2 ORFs in convalescents is higher when compared to the acute. Lastly, we identified and reported on novel HLAs significantly associated with increased risk of hospitalisation such as HLA-C*07:02 carriers (OR = 3.9, CI = 1.1-13.4, p = 0.03) and on HLAs that associate significantly with lower or higher TCR repertoire parameters in a population exposed for the first time to SARS-CoV-2.

Patients with chronic obstructive pulmonary disease (COPD) are more vulnerable to infections that may favor disease progression. Vaccination in COPD is an effective intervention that helps reduce infectious exacerbations, as well as associated morbidity and mortality. In recent years, the use of new vaccines has become widespread, not only targeting specific infections but also contributing to long-lasting immunity and slowing the process of immune aging (immunosenescence). Current clinical practice guidelines recommend the administration of six vaccines (against Streptococcus pneumoniae, influenza virus, SARS-CoV-2, respiratory syncytial virus, Bordetella pertussis, and varicella-zoster virus) for all COPD patients. However, vaccination rates in many countries still fall short of the established targets. Therefore, it is crucial to design a specific vaccination schedule tailored for COPD patients.

Mitochondria play a crucial role in cellular respiration and immune responses. Mitochondrial DNA (mtDNA) haplogroups and variants have been associated with various diseases, including COVID-19. This study analyzed complete mtDNA sequences from 467 Brazilian patients with COVID-19 to investigate associations between mtDNA ancestry and mortality risk. Using classical statistical methods and a machine learning model, we identified key contributors to outcomes, with age as the primary risk factor, followed by male sex. Several mtDNA variants-663G, 1736G, 2706G, 3010A, 4248C, 4824G, 8027A, 8794T, and 10873C-were significantly associated with increased mortality risk. Most are characteristic of haplogroup A2, prevalent in populations with Native American ancestry. Notably, the 8027A allele, a non-synonymous substitution (Alanine > Threonine at position 148 of Cytochrome C Oxidase II), was predicted to be potentially damaging and emerged as the most significant marker. Rather than being disease-causing, these variants may amplify risk through interactions with other genetic, environmental, and clinical factors. Our findings emphasize that mtDNA variants and haplogroups are not phenotypically neutral and could serve as biomarkers of COVID-19 severity. Genetic studies prioritizing Indigenous populations and their descendants, who may be particularly susceptible to certain viruses, are urgently needed, especially given the predominant focus on European populations.

Engineering of reverse genetics systems for newly emerged viruses allows viral genome manipulation, being an essential tool for the study of virus life cycle, virus-host interactions and pathogenesis, as well as for the development of effective antiviral strategies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emergent human coronavirus that has caused the coronavirus disease (COVID-19) pandemic. The engineering of a full-length infectious cDNA clone and a fluorescent replicon of SARS-CoV-2 Wuhan-Hu-1, using a bacterial artificial chromosome, is reported. Viral growth and genetic stability in eleven cell lines were analyzed, showing that both VeroE6 cells overexpressing transmembrane serin protease 2 (TMPRSS2) and human lung derived cells resulted in the optimization of a cell system to preserve SARS-CoV-2 genetic stability. The recombinant SARS-CoV-2 virus and a point mutant expressing the D614G spike protein variant were virulent in a mouse model. The RNA replicon was propagation-defective, allowing its use in BSL-2 conditions to analyze viral RNA synthesis. The SARS-CoV-2 reverse genetics systems developed constitute a useful tool for studying the molecular biology of the virus, the development of genetically defined vaccines and to establish systems for antiviral compounds screening.

COVID-19 is characterized by a wide range of symptoms where the genetic background plays a key role in SARS-CoV-2 infection. In this study, the relative expression of IRF9, CCL5, IFI6, TGFB1, IL1B, OAS1, and TFRC genes (related to immunity and antiviral activity) was analyzed in upper airway samples from 127 individuals (97 COVID-19 positive and 30 controls) by using a two-step RT-PCR. All genes excepting IL1B (p=0.878) showed a significantly higher expression (p<0.005) in COVID-19 cases than in the samples from the control group suggesting that in asymptomatic-mild cases antiviral and immune system cells recruitment gene expression is being promoted. Moreover, IFI6 (p=0.002) and OAS1 (p=0.044) were upregulated in cases with high viral loads, which could be related to protection against severe forms of this viral infection. In addition, a higher frequency (68.7%) of individuals infected with the Omicron variant presented higher viral load values of infection when compared to individuals infected with other variants (p<0.001). Furthermore, an increased expression of IRF9 (p<0.001), IFI6 (p<0.001), OAS1 (p=0.011), CCL5, (p=0.003) and TGFB1 (p<0.001) genes was observed in individuals infected with SARS-CoV-2 wildtype virus, which might be due to immune response evasion of the viral variants and/or vaccination. The obtained results indicate a protective role of IFI6, OAS1 and IRF9 in asymptomatic -mild cases of SARS-CoV-2 infection while the role of TGFB1 and CCL5 in the pathogenesis of the disease is still unclear. The importance of studying the dysregulation of immune genes in relation to the infective variant is stand out in this study.

Worldwide urbanization and subsequent migration have accelerated the emergence and spread of diverse novel human diseases. Among them, diseases caused by viruses could result in epidemics, typified by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which hit the globe towards the end of December 2019. The global battle against SARS-CoV-2 has reignited interest in finding alternative treatments for viral infections. The marine world offers a large repository of diverse and unique bioactive compounds. Over the years, many antiviral compounds from marine organisms have been isolated and tested in vitro and in vivo. However, given the increasing need for alternative treatment, in silico analysis appears to provide a time- and cost-effective approach to identifying the potential antiviral compounds from the vast pool of natural metabolites isolated from marine organisms. In this perspective review, we discuss marine-derived bioactive metabolites as potential therapeutics for all known disease-causing viruses including the SARS-CoV-2. We demonstrate the efficacy of marine-derived bioactive metabolites in the context of various antiviral activities and their in silico, in vitro, and in vivo capacities.

Molecular simulations play important roles in understanding the lifecycle of the SARS-CoV-2 virus and contribute to the design and development of antiviral agents and diagnostic tests for COVID. Here, we discuss the insights that such simulations have provided and the challenges involved, focusing on the SARS-CoV-2 main protease (M^pro) and the spike glycoprotein. M^pro is the leading target for antivirals, while the spike glycoprotein is the target for vaccine design. Finally, we reflect on lessons from this pandemic for the simulation community. Data sharing initiatives and collaborations across the international research community contributed to advancing knowledge and should be built on to help in future pandemics and other global challenges such as antimicrobial resistance.

Whenever a new COVID-19 vaccination season starts, we must face new challenges, including which vaccines to use, the update of the high-risk groups to be vaccinated, and especially the type and amount of information to be communicated to people in order to promote vaccination. COVID-19 vaccination recommendations should fit these specific conditions. The use of effective vaccines against the predominant SARS-CoV-2 virus variants and the extent of the immune response (waning immunity) are key aspects to try to protect better the high-risk populations. Updated vaccines are currently swiftly available. However, the number of people vaccinated with any additional booster dose is declining. Improved health information and training for health care professionals, together with the use of better tools to make simpler vaccination recommendations, can encourage higher vaccination rates. Addressing these challenges is essential to improve vaccination coverage and ensure adequate protection in the face of evolving COVID-19 threats. The SARS-CoV-2 virus has become a constant presence in our society. The virus changes but is neither endemic nor seasonal so far. The Omicron variant prevailed for nearly 2 years and now several of its subvariants like JN.1, KP.2, or XEC are or can be the dominant ones. In the face of this moving situation, the main message must be the same: COVID-19 vaccines are safe and effective. The role of current COVID-19 vaccination efforts is to mitigate the severity of the disease and reduce the risk of complications and death, instead of preventing most SARS-CoV-2 infections. New vaccines against COVID-19 are now at different stages of clinical research.

The COVID-19 pandemic has brought to the forefront the intricate relationship between SARS-CoV-2 and its impact on neurological complications, including potential links to neurodegenerative processes, characterized by a dysfunction of the protein quality control systems and ER stress. This review article explores the role of protein quality control systems, such as the Unfolded Protein Response (UPR), the Endoplasmic Reticulum-Associated Degradation (ERAD), the Ubiquitin-Proteasome System (UPS), autophagy and the molecular chaperones, in SARS-CoV-2 infection. Our hypothesis suggests that SARS-CoV-2 produces ER stress and exploits the protein quality control systems, leading to a disruption in proteostasis that cannot be solved by the host cell. This disruption culminates in cell death and may represent a link between SARS-CoV-2 and neurodegeneration.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a fast-spreading viral pathogen and poses a serious threat to human health. New SARS-CoV-2 variants have been arising worldwide; therefore, is necessary to explore more therapeutic options. The interaction of the viral spike (S) protein with the angiotensin-converting enzyme 2 (ACE2) host receptor is an attractive drug target to prevent the infection via the inhibition of virus cell entry. In this study, Ligand- and Structure-Based Virtual Screening (LBVS and SBVS) was performed to propose potential inhibitors capable of blocking the S receptor-binding domain (RBD) and ACE2 interaction. The best five lead compounds were confirmed as inhibitors through ELISA-based enzyme assays. The docking studies and molecular dynamic (MD) simulations of the selected compounds maintained the molecular interaction and stability (RMSD fluctuations less than 5 Å) with key residues of the S protein. The compounds DRI-1, DRI-2, DRI-3, DRI-4, and DRI-5 efficiently block the interaction between the SARS-CoV-2 spike protein and receptor ACE2 (from 69.90 to 99.65% of inhibition) at 50 µM. The most potent inhibitors were DRI-2 (IC₅₀ = 8.8 µM) and DRI-3 (IC₅₀ = 2.1 µM) and have an acceptable profile of cytotoxicity (CC₅₀ > 90 µM). Therefore, these compounds could be good candidates for further SARS-CoV-2 preclinical experiments.

The COVID-19 pandemic caused by the coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides. Host-derived sncRNAs, including microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), and small nucleolar RNA-derived small RNAs (sdRNAs) exhibited significant differential expression in infected patients compared to controls. Importantly, miRNA expression was predominantly down-regulated in response to SARS-CoV-2 infection, especially in patients with severe symptoms. Furthermore, we identified specific tsRNAs derived from Glu- and Gly-tRNAs as major altered elements upon infection, with 5' tRNA halves being the most abundant species and suggesting their potential as biomarkers for viral presence and disease severity prediction. Additionally, down-regulation of C/D-box sdRNAs and altered expression of tinyRNAs (tyRNAs) were observed in infected patients. These findings provide valuable insights into the host sncRNA response to SARS-CoV-2 infection and may contribute to the development of further diagnostic and therapeutic strategies in the clinic.

COVID-19 is an infectious disease caused by SARS-CoV-2 with devastating effects on health-care systems. The magnitude of the problem has moved physicians and investigators to identify strategies to detect patients at a high risk of severe disease. The aim of this study was to identify the most relevant biomarkers in the published literature and their correlation with clinical outcomes. To this end, we performed a revision of studies that investigated laboratory abnormalities in patients with COVID-19, comparing non-severe and severe patients. Blood biomarkers were classified into five main categories: hematological, coagulation related to the liver or kidney, and inflammatory. From our analysis, the most relevant biomarkers associated with severe infection for each category were increased levels of leukocytes, neutrophils, and neutrophil-to-lymphocyte ratio; decreased platelet count; and high levels of aspartate transaminase, alanine transaminase, creatine kinase, troponin, creatinine, and blood urea nitrogen, C-reactive protein, ferritin, and IL-6. Moreover, lactate dehydrogenase and D-dimer levels were independent risk factors for death.

As early as in the acute phase of the coronavirus disease 2019 (COVID-19) pandemic, the research community voiced concerns about the long-term implications of infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), like many other viruses, can trigger chronic disorders that last months or even years. Long COVID, the chronic and persistent disorder lasting more than 12 weeks after the primary infection with SARS-CoV-2, involves a variable number of neurological manifestations, ranging from mild to severe and even fatal. In vitro and in vivo modeling suggest that SARS-CoV-2 infection drives changes within neurons, glia and the brain vasculature. In this Review, we summarize the current understanding of the neuropathology of acute and long COVID, with particular emphasis on the knowledge derived from brain organoid models. We highlight the advantages and main limitations of brain organoids, leveraging their human-derived origin, their similarity in cellular and tissue architecture to human tissues, and their potential to decipher the pathophysiology of long COVID.

Previous studies suggest that butyrylcholinesterase (BChE), an enzyme involved in the cholinergic anti-inflammatory pathway, may be linked to inflammation, disease severity, and risk of death in COVID-19 patients. Extending earlier work on BChE and COVID-19 severity, this study investigates additional factors such as age, sex, vaccination status, and symptom profiles. We analyzed 462 patients with polymerase chain reaction (PCR)-confirmed COVID-19 from the first epidemic wave in Spain, examining the association between BChE activity, clinical outcomes, demographic factors, and symptoms. The cohort consisted of 78 asymptomatic patients, 200 patients with mild symptoms, 122 patients with severe symptoms, and 62 critically ill patients. Of the patients in the severe symptoms group and critically ill patients, 26 died within 30 days of diagnosis. Our results showed that BChE activity was not affected by sex but decreased significantly with age (P < 0.0001). Patients with severe COVID-19 symptoms and critically ill patients exhibited lower BChE activity than asymptomatic or mildly symptomatic individuals (P < 0.0001). Furthermore, lower BChE activity was observed in patients with respiratory symptoms, such as pneumonia (P = 0.0027) and dyspnea (P = 0.0120), while higher BChE activity was seen in patients with neurological symptoms, such as anosmia (P < 0.0001), ageusia (P = 0.0012), and headache (P = 0.0005). No significant association was found between BChE activity and gastrointestinal, algesic, musculoskeletal, or systemic inflammatory symptoms. Additionally, vaccinated patients, particularly those who received two doses, had lower BChE activity compared to unvaccinated individuals (P = 0.0465). In conclusion, serum BChE activity is significantly associated with the severity, mortality, and specific symptoms of COVID-19, and is influenced by age and vaccination status. These findings imply that BChE may be a potential biomarker to support prognosis and risk stratification in COVID-19 patients. However, further research is needed to understand the underlying mechanisms and to validate the role of BChE in clinical practice.

Background/Objectives: The spread of the COVID-19 pandemic has spurred the development of advanced healthcare tools to effectively manage patient outcomes. This study aims to identify key predictors of mortality in hospitalized patients with some level of natural immunity, but not yet vaccinated, using machine learning techniques. Methods: A total of 363 patients with COVID-19 admitted to Río Hortega University Hospital in Spain between the second and fourth waves of the pandemic were included in this study. Key characteristics related to both the patient's previous status and hospital stay were screened using the Random Forest (RF) machine learning technique. Results: Of the 19 variables identified as having the greatest influence on predicting mortality, the most powerful ones could be identified at the time of hospital admission. These included the assessment of severity in community-acquired pneumonia (CURB-65) scale, age, the Glasgow Coma Scale (GCS), and comorbidities, as well as laboratory results. Some variables associated with hospitalization and intensive care unit (ICU) admission (acute renal failure, shock, PRONO sessions and the Acute Physiology and Chronic Health Evaluation [APACHE-II] scale) showed a certain degree of significance. The Random Forest (RF) method showed high accuracy, with a precision of >95%. Conclusions: This study shows that natural immunity generates significant changes in the evolution of the disease. As has been shown, machine learning models are an effective tool to improve personalized patient care in different periods.

Providing viral load numbers of infection events aids in the identification of disease severity and in the effective overall patient management. Gold-standard polymerase chain reaction (PCR) techniques make this possible but cannot be applied at the point of need and in low-resource settings. Here, we report on the development of a compact analytical platform that can detect a conserved sequence of the RNA of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in 40 min in nasopharyngeal swab samples without the need for any previous purification or gene amplification steps. It combines electrochemical and paper fluidic approaches together with a sandwich hybridization assay performed on magnetic nanoparticles (MNPs) modified with a tailor-designed capture DNA hairpin. The device proves to quantitatively detect viral RNA in a retrospective study carried out with nasopharyngeal swab samples. A sensitivity of 100% and a specificity of 93% were estimated by the receiver operating characteristic (ROC) analysis. However, although molar concentration values of the target RNA sequence are provided, these estimates do not fully correlate with the viral load numbers estimated by RT-qPCR over the whole Ct sample range. Empirical studies have been carried out that have provided clear insights into this hurdle and simple solutions to overcome it, without depriving the device of the features required for potential use in a point-of-care (PoC) environment.

From the first reports of SARS-CoV-2, at the end of 2019 to the present, the global mortality associated with COVID-19 has reached 6,952,522 deaths as reported by the World Health Organization (WHO). Early intubation and mechanical ventilation can increase the survival rate of critically ill patients. This prospective study was carried out on 885 patients in the ICU of Mureș County Clinical Hospital, Romania. After applying inclusion and exclusion criteria, a total of 54 patients were included. Patients were monitored during hospitalization and at 6-month follow-up. We analyzed the relationship between invasive mechanical ventilation (IMV) and non-invasive mechanical ventilation (NIMV) and radiological changes on thoracic CT scans performed at 6-month follow-up and found no significant association. Regarding paraclinical analysis, there was a statistically significant association between patients grouped by IMV and ferritin level on day 1 of admission (p = 0.034), and between patients grouped by PaO₂/FiO₂ ratio with metabolic syndrome (p = 0.03) and the level of procalcitonin (p = 0.01). A significant proportion of patients with COVID-19 admitted to the ICU developed pulmonary fibrosis as observed at a 6-month evaluation. Patients with oxygen supplementation or mechanical ventilation require dynamic monitoring and radiological investigations, as there is a possibility of long-term pulmonary fibrosis that requires pharmacological interventions and finding new therapeutic alternatives.

Background

One of the main challenges with COVID-19 has been that although there are known factors associated with a worse prognosis, clinicians have been unable to predict which patients, with similar risk factors, will die or require intensive care unit (ICU) care.

Objective

This study aimed to develop a personalized artificial intelligence model to predict the patient risk of mortality and ICU admission related to SARS-CoV-2 infection during the initial medical evaluation before any kind of treatment.

Methods

It is a population-based, observational, retrospective study covering from February 1, 2020, to January 24, 2023, with different circulating SARS-CoV-2 viruses, vaccinated status, and reinfections. It includes patients attended by the reference hospital in Fuenlabrada (Madrid, Spain). The models used the random forest technique, Shapley Additive Explanations method, and processing with Python (version 3.10.0; Python Software Foundation) and scikit-learn (version 1.3.0). The models were applied to different epidemic SARS-CoV-2 infection waves. Data were collected from 11,975 patients (4998 hospitalized and 6737 discharged). Predictive models were built with records from 4758 patients and validated with 6977 patients after evaluation in the emergency department. Variables recorded were age, sex, place of birth, clinical data, laboratory results, vaccination status, and radiologic data at admission.

Results

The best mortality predictor achieved an area under the receiver operating characteristic curve (AUC) of 0.92, sensitivity of 0.89, specificity of 0.82, positive predictive value (PPV) of 0.35, and mean negative predictive value (NPV) of 0.98. The ICU admission predictor had an AUC of 0.89, sensitivity of 0.75, specificity of 0.88, PPV of 0.37, and NPV of 0.98. During validation, the mortality model exhibited good performance for the nonhospitalized group, achieving an AUC of 0.95, sensitivity of 0.88, specificity of 0.98, PPV of 0.21, and NPV of 0.99, predicting the death of 30 of 34 patients who were not hospitalized. For the hospitalized patients, the mortality model achieved an AUC of 0.85, sensitivity of 0.86, specificity of 0.74, PPV of 0.24, and NPV of 0.98. The model for predicting ICU admission had an AUC of 0.82, sensitivity of 1.00, specificity of 0.59, PPV of 0.05, and NPV of 1.00. The models' metrics presented stability along all pandemic waves. Key mortality predictors included age, Charlson value, and tachypnea. The worse prognosis was linked to high values in urea, erythrocyte distribution width, oxygen demand, creatinine, procalcitonin, lactate dehydrogenase, heart failure, D-dimer, oncological and hematological diseases, neutrophil, and heart rate. A better prognosis was linked to higher values of lymphocytes and systolic and diastolic blood pressures. Partial or no vaccination provided less protection than full vaccination.

Conclusions

The artificial intelligence models demonstrated stability across pandemic waves, indicating their potential to assist in personal health services during the 3-year pandemic, particularly in early preventive and predictive clinical situations.

Objective

To identify and synthesize evidence on Coronavirus-two infection (SARS-CoV-2) among adults diagnosed by polymerase chain reaction.

Methods

The protocol was registered on Open Science Forum (doi: 10.17605/OSF.IO/2837X). Three bibliographic databases (Medline, SCOPUS, and Web of Science) were searched from July 2024 to December 2024. Peer-reviewed, quantitative studies with participants aged 18 and over were eligible to enlist potential risk factors of SARS-CoV-2 infection confirmed by Polymerase Chain Reaction PCR). The evidence was summarized as illustrations and tabulations with risk factors grouped into various categories. EndNote 20 was used for deduplications and organization of the literature.

Results

Of 28,688 unique entries searched, 299 were shortlisted and 32 full-text manuscripts selected from 17 countries. There were two (6.2%) manuscripts based on real-time surveillance of at-risk populations. A total of 42 individual risk factors were examined in the evidence.

Conclusion

Low socioeconomic status and occupation were consistent risk factors of SARS-CoV-2 infection, with minimal representation from low- and middle-income countries in the evidence body. Future research should prioritize standardized methods and inclusion of underrepresented regions to enhance global applicability and inform targeted public health interventions.

SARS-CoV-2 amino acid variants that contribute to an increased transmissibility or to host immune system escape are likely to increase in frequency due to positive selection and may be identified using different methods, such as codeML, FEL, FUBAR, and MEME. Nevertheless, when using different methods, the results do not always agree. The sampling scheme used in different studies may partially explain the differences that are found, but there is also the possibility that some of the identified positively selected amino acid sites are false positives. This is especially important in the context of very large-scale projects where hundreds of analyses have been performed for the same protein-coding gene. To account for these issues, in this work, we have identified positively selected amino acid sites in SARS-CoV-2 and 15 other coronavirus species, using both codeML and FUBAR, and compared the location of such sites in the different species. Moreover, we also compared our results to those that are available in the COV2Var database and the frequency of the 10 most frequent variants and predicted protein location to identify those sites that are supported by multiple lines of evidence. Amino acid changes observed at these sites should always be of concern. The information reported for SARS-CoV-2 can also be used to identify variants of concern in other coronaviruses.

Background

With SARS-CoV-2 self-tests, persons with acute respiratory infections (ARI) can know their COVID-19 status. This may alter their decision to consult a general practitioner (GP), potentially biasing COVID-19 vaccine effectiveness (VE) studies. We explore bias mechanisms, simulate magnitude, and verify control methods.

Methods

We used directed acyclic graphs (DAGs) to illustrate the bias mechanisms. Based on the European primary care VEBIS multicentre test-negative design (TND) study, we simulated populations with varying true VE (20%-60%), proportions of persons with ARI self-testing (10%-30%), effect of COVID-19 vaccination on self-testing (1.5-2.5), and effect of self-test result on GP consultation (0.5-2). We performed 5000 runs per scenario, estimating VE among those consulting a GP. We calculated bias as true VE minus mean simulated VE, unadjusted and adjusted for self-testing, using logistic regression.

Results

DAGs suggested collider stratification bias if vaccination had an effect on self-testing and if self-test results affected GP consultation. Bias was -12% to 18% at 20% true VE, with the most extreme associations and 30% self-testing. With 60% true VE and 10%-20% self-testing, bias was lower. Bias was higher (-18% to 45%) if both positive and negative self-test results affected GP consultation. Adjusting for self-testing removed the bias.

Conclusions

Self-testing may bias COVID-19 VE TND studies in primary care if self-testing is high, particularly with low VE. We recommend primary care TND VE studies collect self-testing information to eliminate potential bias. Observational studies are needed to understand the relationship between vaccination, self-testing, and GP consultation, in these studies' source population.

The novel disease produced by SARS-CoV-2 mainly harms the respiratory tract, but it has shown the capacity to affect multiple organs. Epidemiologic evidence supports the relationship between Coronavirus Disease 2019 (COVID-19) and pancreatic and hepatic injury development, identified by alterations in these organ function markers. In this regard, it is important to ascertain how the current prevalence of non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) might affect COVID-19 evolution and complications. Although it is not clear how SARS-CoV-2 affects both the pancreas and the liver, a multiplicity of potential pathophysiological mechanisms seem to be implicated; among them, a direct viral-induced injury to the organ involving liver and pancreas ACE2 expression. Additionally, immune system dysregulation, coagulopathies, and drugs used to treat the disease could be key for developing complications associated with the patient's clinical decline. This review aims to provide an overview of the available epidemiologic evidence regarding developing liver and pancreatic alterations in patients with COVID-19, as well as the possible role that NAFLD/NASH might play in the pathophysiological mechanisms underlying some of the complications associated with COVID-19. This review employed a comprehensive search on PubMed using relevant keywords and filters. From the initial 126 articles, those aligning with the research target were selected and evaluated for their methodologies, findings, and conclusions. It sheds light on the potential pathophysiological mechanisms underlying this relationship. As a result, it emphasises the importance of monitoring pancreatic and hepatic function in individuals affected by COVID-19.

The SARS-CoV-2 (COVID-19) pandemic outbreak led to enormous social and economic repercussions worldwide, felt even to this date, making the design of new therapies to combat fast-spreading viruses an imperative task. In the face of this, diverse cutting-edge nanotechnologies have risen as promising tools to treat infectious diseases such as COVID-19, as well as challenging illnesses such as cancer and diabetes. Aside from these applications, nanoscale metal-organic frameworks (nanoMOFs) have attracted much attention as novel efficient drug delivery systems for diverse pathologies. However, their potential as anti-COVID-19 therapeutic agents has not been investigated. Herein, we propose a pioneering anti-COVID MOF approach by studying their potential as safe and intrinsically antiviral agents through screening various nanoMOF. The iron(III)-trimesate MIL-100 showed a noteworthy antiviral effect against SARS-CoV-2 at the micromolar range, ensuring a high biocompatibility profile (90% of viability) in a real infected human cellular scenario. This research effectively paves the way toward novel antiviral therapies based on nanoMOFs, not only against SARS-CoV-2 but also against other challenging infectious and/or pulmonary diseases.

The pulmonary route for drug administration has garnered a great deal of attention in therapeutics for treating respiratory disorders. It allows for the delivery of drugs directly to the lungs and, consequently, the maintenance of high concentrations at the action site and a reduction in systemic adverse effects compared to other routes, such as oral or intravenous. Nevertheless, the pulmonary administration of drugs is challenging, as the respiratory system tries to eliminate inhaled particles, being the main responsible mucociliary escalator. Nanomedicines represent a primary strategy to overcome the limitations of this route as they can be engineered to prolong pulmonary retention and avoid their clearance while reducing drug systemic distribution and, consequently, systemic adverse effects. This review analyses the use of pulmonary-administered nanomedicines to treat infectious diseases affecting the respiratory system and lung carcinoma, two pathologies that represent major health threats.

COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still a pandemic with high mortality and morbidity rates. Clinical manifestation is widely variable, including asymptomatic or mild respiratory tract illness to severe pneumonia and death. Myocardial injury is a significant pathogenic feature of COVID-19 and it is associated with worse in-hospital outcomes, mainly due to a higher number of hospital readmissions, with over 50% mortality. These findings suggest that myocardial injury would identify COVID-19 patients with higher risk during active infection and mid-term follow-up. Potential contributors responsible for myocardial damage are myocarditis, vasculitis, acute inflammation, type 1 and type 2 myocardial infarction. However, there are few data about cardiac sequelae and its long-term consequences. Thus, the optimal screening tool for residual cardiac sequelae, clinical follow-up, and the benefits of a specific cardiovascular therapy during the convalescent phase remains unknown. This mini-review explores the different mechanisms of myocardial injury related to COVID-19 and its short and long-term implications.

Background/Objectives: Although articles and reviews have been published on the effect of SARS-CoV-2 infection on pregnancy outcomes, they show mixed results with different hypotheses, and no work has focused specifically on the prevalence of thrombocytopenia. The objective of this systematic review and meta-analysis was to synthesize previous evidence and estimate the prevalence of thrombocytopenia in pregnant women with COVID-19. Methods: This systematic review was conducted according to the PRISMA-2020 and MOOSE guidelines. The Medline and Web of Science databases were searched in February 2024, and a meta-analysis of the overall prevalence of thrombocytopenia in pregnant women with COVID-19 was performed. The risk of bias was assessed using the Joanna Briggs Institute checklists. A leave-1-out sensitivity analysis was performed to test for disproportionate effect. Publication bias was assessed by visual inspection of funnel plots and Egger's test. Results: A total of 23 studies met the inclusion criteria, of which 8 were included in the meta-analysis. There was significant (Q = 101.04) and substantial heterogeneity among the studies (I² = 93.07%). There were no quality-based exclusions from the review of eligible studies. The combined effect of the studies showed a prevalence of thrombocytopenia of 22.9% (95%CI 4.8-41.0%). Subgroup analysis revealed no statistically significant difference in the pooled prevalence of thrombocytopenia ([16.5%; 30.3%]; p = 0.375. Egger's test for bias was not significant, indicating that smaller studies did not report larger estimates of prevalence (t = 1.01, p = 0.353). Moreover, no potential publication bias was found. Our results are consistent with those obtained in pregnant women without COVID-19 infection and extend those of previous reviews of the effect of COVID-19 infection on pregnancy outcomes. Conclusions: Infection during pregnancy does not seem to be an additional risk factor for platelet count, although monitoring platelet count in pregnant women with COVID-19 may be of great importance to determine possible therapeutic strategies, especially in emergency cases.

Introduction

Despite the high efficacy of the anti-coronavirus disease 2019 (COVID-19) BNT162b2 vaccine (Comirnaty^®, Pfizer-BioNTech), variability in the antibody titers following vaccination has been described. However, little is known about the risk factors that are associated with a poorer antibody response to the BNT162b2 vaccine.

Methodology

We studied the determinants of the humoral response to the anti-COVID-19 vaccine BNT162b2 in 200 healthcare workers followed up for 2 years. Serum samples were tested for the anti-spike immunoglobulin G (IgG) levels and neutralizing antibody titers against selected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants at different time points after primary and booster vaccinations. Anthropometric data and clinical and lifestyle information were also collected. Statistical analyses consisted of linear and logistical regressions for point estimations and the Mann-Whitney, Friedman, and generalized estimating equations for repeated measures.

Results

After the primary vaccination, the antibody titers and the percentage of seroconverted individuals peaked at 5 weeks but declined after 1 year; however, they remained high after the booster administration. After the first dose of the vaccine, negative associations of the anti-spike IgG levels with age (β = -0.01, 95%CI = -0.03 to -0.003), smoking habit (β = -1.08, 95%CI = -1.70 to -0.46), and alcohol consumption (β = -1.43, 95%CI = -2.20 to -0.65) were found. With regard to the booster vaccine, the following associations were retained in the stepwise multivariate model: anti-Delta neutralizing antibodies with hip circumference (OR = 1.07, 95%CI = 1.01-1.12, p = 0.008), anti-Delta-K antibodies with hip circumference (OR = 1.06, 95%CI = 1.01-1.11, p = 0.007), and anti-Omicron antibodies with the Mediterranean diet score (OR = 0.74, 95%CI = 0.58-0.96, p = 0.023).

Conclusion

Lifestyle habits and age had an association with the humoral response to the BNT162b2 vaccine.

Infiltration of the myocardium with various cell types, cytokines and chemokines plays a crucial role in the pathogenesis of cardiomyopathies including inflammatory cardiomyopathies and myocarditis. A more comprehensive understanding of the precise immune mechanisms involved in acute and chronic myocarditis is essential to develop novel therapeutic approaches. This review offers a comprehensive overview of the current knowledge of the immune landscape in cardiomyopathies based on etiology. It identifies gaps in our knowledge about cardiac inflammation and emphasizes the need for new translational approaches to improve our understanding thus enabling development of novel early detection methods and more effective treatments.

Background/Objective: Evidence suggests that the administration of antivirals at the acute phase of SARS-CoV-2 infection is associated with lower COVID-19 severity, accordingly, the administration of antivirals at the acute phase of the infection could prevent post-COVID-19 symptoms. The current study investigated the effects of the intravenous administration of Remdesivir at hospitalization (acute phase of SARS-CoV-2 infection) in COVID-19 survivors on the development of post-COVID-19 pain symptoms. Methods: A cohort of previously hospitalized COVID-19 survivors who received intravenous administration of Remdesivir at the acute COVID-19 phase (n = 216) were matched with a cohort of previously hospitalized COVID-19 survivors who did not receive any antiviral treatment at the acute phase of the infection (n = 216). In a face-to-face interview, they were asked for the development of pain symptoms attributed to SARS-CoV-2 infection and whether the symptom persisted at the time of the study (mean follow-up: 18.4, SD: 0.8 months). Clinical/hospitalization data were collected from medical records. Anxiety/depressive symptoms and sleep quality were also assessed with validated self-reported questionnaires. Results: No differences in hospitalization data and the presence of previous chronic conditions were seen between patients receiving or not receiving intravenous administration of Remdesivir during hospitalization. The multivariate analysis revealed that the intravenous administration of Remdesivir at the acute COVID-19 phase was a protective factor for the development of overall post-COVID-19 pain (OR 0.444, 95% CI 0.292-0.674, p < 0.001). A protective effect of administrating intravenous Remdesivir was specifically seen for thorax/chest (OR 0.277, 95% CI 0.100-0.766, p = 0.01) and lumbar spine (OR 0.347, 95% CI 0.143-0.844, p = 0.02) pain. Conclusions: Current results support a potential protective role of the intravenous administration of Remdesivir at the acute phase of SARS-CoV-2 infection for developing long-term post-COVID-19 pain in previously hospitalized COVID-19 survivors. Studies investigating the effects of the oral administration of antivirals in non-hospitalized populations are needed to generalize these findings.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the causal agent behind coronavirus disease 2019 (COVID-19), a disease declared pandemic in 2020. Because of the zoonotic origin of SARS-CoV-2 and the close contact kept by domestic dogs with their owners, it became imperative to understand the role of dogs in the epidemiology of the disease and in the virus transmission. In the present study, we determined the presence of virus and described the long-term immune effects of SARS-CoV-2 in 24 dogs exposed to SARS-CoV-2 in the domestic environment. Our findings highlight that only a subset of dogs, naturally exposed to SARS-CoV-2, exhibit a humoral response to the new virus (close to 17% had IgM antibodies and close to 33% has IgG antibodies). We identified for the first time SARS-CoV-2-specific IFN-γ-secreting cells in dogs (approximately in half of our dogs). While 56% of dogs maintained humoral response 8 months, only 22% of dogs maintained cellular response after 4 and 8 months. Although some alterations in blood parameters and proinflammatory cytokines were described, there was no evidence indicating an exacerbated cytokine release process. Considering that none of the animals enrolled in this study showed viral shedding and presented specific immune responses, it is reasonable to propose that the canine immune system in certain companion dogs is effective at blocking the negative effects of viral replication, thereby suggesting that dogs would not be potential transmitters of this pathogen to the other dogs or other species and could aid in promoting collective immunity.

Venous thromboembolism (VTE) is a recognized complication of SARS-CoV-2 infection, but its clinical features and both sort- and long-term outcomes remain incompletely characterized. We aimed to compare the clinical profile and outcomes of patients with VTE with and without recent COVID-19. We conducted a prospective cohort study including 2012 patients with objectively confirmed VTE. COVID-19-associated VTE was defined as VTE diagnosed within 30 days of a microbiologically confirmed SARS-CoV-2 infection. Clinical characteristics, treatment, and outcomes were compared between groups. Propensity score matching (1:1) and competing risk models were used to adjust for confounding. The primary outcomes-assessed at both 30 days and 365 days-included all-cause mortality, major bleeding, and VTE recurrence. A total of 272 patients (13.5%) had COVID-19-associated VTE. Compared with non-COVID cases, these patients more often had pulmonary embolism, higher D-dimer levels, and greater use of unfractionated heparin. At 30 days, COVID-19 was associated with increased mortality (HR 2.29; 95% CI 1.19-4.40) and major bleeding (HR 2.11; 95% CI 1.06-4.21). At one year, the bleeding risk remained higher (HR 1.54; 95% CI 1.02-2.33), while VTE recurrence was lower (HR 0.34; 95% CI 0.13-0.94). These results were consistent after propensity score matching. COVID-19-associated VTE is linked to worse short-term outcomes, including early mortality and bleeding, and to a persistently elevated bleeding risk at one year. Lower recurrence rates support the consideration of COVID-19 as a transient provoking factor.

Background

COVID-19 appears to have a progression of three stages. The latter stage is characterized by a high level of cytokine release, which in turn triggers an uncontrolled reaction known as cytokine storm where mast cells are involved. The presence of anti-IgE antibodies against SARS-CoV-2 in this phase has been previously reported, suggesting an association with the severity of the disease. Our study aims to assess the prognostic significance of IgE antibodies against SARS-CoV-2 across a spectrum of clinical presentations, including individual with mild symptoms, hospitalized patients, and those who presented a critical progression.

Methods

The study included 64 patients distributed into the following groups: 22 critically ill hospitalized individuals (Critical); 21 non-critical hospitalized patients (Severe); 21 mild symptomatic non-hospitalized cases (Mild); and 22 healthy blood donors with samples collected in October 2019. Anti-IgE antibodies against Spike (S) protein were detected using a homemade ELISA, where the plate was sensitized with the RBD of recombinant S protein.

Results

Among 64 SARS-CoV-2 infected patients, 28.1% tested positive for IgE isotype antibodies against S protein RBD, whose prevalence was similar across severity groups: Mild 23.8%, Severe 28.6%, and Critical 31.8% (p = 0.842). Patients with IgE response exhibited higher levels of LDH compared to non-IgE responders, with a 40% increase (p = 0.037), and a non-significantly higher tendency in other inflammatory markers.

Conclusion

In SARS-CoV-2 infection, roughly a fourth of patients presented an IgE isotype response, regardless of disease severity, which is associated with higher levels of LDH.

The global impact of the novel coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was significant, including in Spain. The initial outbreak in late January 2020 prompted a frantic effort to comprehend the virus and contain its spread, given the limited knowledge available at the time. The study by Amich et al. (2022) in Frontiers in Endocrinology aimed to investigate the influence of thyroid hormone levels and age on the severity of COVID-19 in euthyroid and levothyroxine-treated patients. Although a direct correlation between thyroid hormone levels and the severity of COVID-19 has not been established, it is known that thyroid dysfunction affects immune function and general health, which may impact the outcomes of COVID-19. The research included patients from the Clinic San Carlos Hospital in Madrid, and a comprehensive range of data was collected from each patient, including demographic information, symptoms, comorbidities, and laboratory test results. This approach was employed in order to accurately match patients and identify factors that may influence the severity of COVID-19 outcomes. Blood samples were analyzed using chemiluminescence on a DXI-800® instrument, with the following hormones quantified: thyroid-stimulating hormone (TSH), free thyroxine (FT4), and free triiodothyronine (FT3). These insights contribute to an understanding of the interplay between thyroid function and the severity of COVID-19, highlighting the need for careful patient management in those with thyroid disorders during the pandemic.

Background

Information on the microbiome's human pathways and active members that can affect SARS-CoV-2 susceptibility and pathogenesis in the salivary proteome is very scarce. Here, we studied a unique collection of samples harvested from April to June 2020 from unvaccinated patients.

Methods

We compared 10 infected and hospitalized patients with severe (n = 5) and moderate (n = 5) coronavirus disease (COVID-19) with 10 uninfected individuals, including non-COVID-19 but susceptible individuals (n = 5) and non-COVID-19 and nonsusceptible healthcare workers with repeated high-risk exposures (n = 5).

Results

By performing high-throughput proteomic profiling in saliva samples, we detected 226 unique differentially expressed (DE) human proteins between groups (q-value ≤ 0.05) out of 3376 unambiguously identified proteins (false discovery rate ≤ 1%). Major differences were observed between the non-COVID-19 and nonsusceptible groups. Bioinformatics analysis of DE proteins revealed human proteomic signatures related to inflammatory responses, central cellular processes, and antiviral activity associated with the saliva of SARS-CoV-2-infected patients (p-value ≤ 0.0004). Discriminatory biomarker signatures from human saliva include cystatins, protective molecules present in the oral cavity, calprotectins, involved in cell cycle progression, and histones, related to nucleosome functions. The expression levels of two human proteins related to protein transport in the cytoplasm, DYNC1 (p-value, 0.0021) and MAPRE1 (p-value, 0.047), correlated with angiotensin-converting enzyme 2 (ACE2) plasma activity. Finally, the proteomes of microorganisms present in the saliva samples showed 4 main microbial functional features related to ribosome functioning that were overrepresented in the infected group.

Conclusion

Our study explores potential candidates involved in pathways implicated in SARS-CoV-2 susceptibility, although further studies in larger cohorts will be necessary.

Although global vaccination campaigns alleviated the SARS-CoV-2 pandemic in terms of morbidity and mortality, the ability of the virus to originate mutants may reduce the efficacy of vaccines, posing a serious risk of a renewed pandemic. There is therefore a need to develop small molecules capable of targeting conserved viral targets, such as the main protease (M^pro). Here, a series of benzisoselenazolones and diselenides were tested for their ability to inhibit M^pro; then the most potent compounds were measured for antiviral activity in vitro, and the mechanism of action was investigated. Density functional theory calculations, molecular docking and molecular dynamics simulations were also used to elucidate the protein/drug interaction. Finally, a bio-organic model was established to study the reaction between selenorganic compounds and biologically relevant thiols to unveil possible metabolic pathways of such compounds. The overall results contribute to the identification of a series of novel Se-containing molecules active against SARS-CoV-2 and to the clarification of some important aspects in the mechanisms of action of such inhibitors targeting SARS-CoV-2 M^pro.

BackgroundBetween 2020 and 2023, ECDC has supported 21 of 30 EU/EEA and six Western Balkan countries by enhancing severe acute respiratory infection (SARI) surveillance to monitor trends, detect unexpected events, evaluate public health interventions, identify risk factors and support vaccine effectiveness studies. Using diverse strategies, countries have implemented SARI surveillance and reported data at national/European levels.AimWe evaluated European-level SARI surveillance and provided recommendations to achieve objectives and improve key attribute performance.MethodsWe analysed 2022/23 surveillance data for completeness. We administered a questionnaire, targeting country-level representatives, to evaluate surveillance attributes (meeting objectives, usefulness, acceptability, timeliness, representativeness) and identify strengths, weaknesses, opportunities and threats.ResultsThirteen countries (13/27) reported data at European level. Data showed good overall completeness but varied across countries and some variables need improvement (vaccination, sequencing). The questionnaire was completed by all 27 countries. Most countries (23/27) reported that the system effectively monitored trends and considered it useful and acceptable (25/27), but only 16 found it timely and 14 representative. Challenges included insufficient case-based data, data linkage issues and insufficient data completeness. Slow/inefficient manual data extraction affected timeliness, while insufficient geographical coverage affected representativeness. Multi-pathogen surveillance was identified as the main strength, heterogeneity of systems the main weakness, improvements of hospital information systems the main opportunity, and lack of sustainable funding the main threat.ConclusionsSARI surveillance was perceived as effective in monitoring trends, useful and acceptable. To achieve additional objectives and enhance timeliness and representativeness, we recommend improving data completeness, digitalisation/automation and geographical coverage.

The underlying mechanisms explaining the differential course of SARS-CoV-2 infection and the potential clinical consequences after COVID-19 resolution have not been fully elucidated. As a dysregulated mitochondrial activity could impair the immune response, we explored long-lasting changes in mitochondrial functionality, circulating cytokine levels, and metabolomic profiles of infected individuals after symptoms resolution, to evaluate whether a complete recovery could be achieved. Results of this pilot study evidenced that different parameters of aerobic respiration in lymphocytes of individuals recuperated from a severe course lagged behind those shown upon mild COVID-19 recovery, in basal conditions and after simulated reinfection, and they also showed altered glycolytic capacity. The severe groups showed trends to enhanced superoxide production in parallel to lower OPA1-S levels. Unbalance of pivotal mitochondrial fusion (MFN2, OPA1) and fission (DRP1, FIS1) proteins was detected, suggesting a disruption in mitochondrial dynamics, as well as a lack of structural integrity in the electron transport chain. In serum, altered cytokine levels of IL-1β, IFN-α2, and IL-27 persisted long after clinical recovery, and growing amounts of the latter after severe infection correlated with lower basal and maximal respiration, ATP production, and glycolytic capacity. Finally, a trend for higher circulating levels of 3-hydroxybutyrate was found in individuals recovered after severe compared to mild course. In summary, long after acute infection, mitochondrial and metabolic changes seem to differ in a situation of full recovery after mild infection versus the one evolving from severe infection.

In public health emergencies or in resource-constrained settings, laboratory-based diagnostic methods, such as RT-qPCR, need to be complemented with accurate, rapid, and accessible approaches to increase testing capacity, as this will translate into better outcomes in disease prevention and management. Here, we develop an original nucleic acid detection platform by leveraging CRISPR-Cas9 and lateral flow immunochromatography technologies. In combination with an isothermal amplification that runs with a biotinylated primer, the system exploits the interaction between the CRISPR-Cas9 R-loop formed upon targeting a specific nucleic acid and a fluorescein-labeled probe to generate a visual readout on a lateral flow device. Our method enables rapid, sensitive detection of nucleic acids, achieving a limit of 1-10 copies/μL in 1 h at a low temperature. We validated the efficacy of the method by using clinical samples of patients infected with SARS-CoV-2. Compared with other assays, it operates with more accessible molecular elements and showcases a robust signal-to-noise ratio. Moreover, multiplexed detection was demonstrated using primers labeled with biotin and digoxigenin, achieving the simultaneous identification of target genes on lateral flow devices with two test lines. We successfully detected SARS-CoV-2 and Influenza A (H1N1) in spiked samples, highlighting the potential of the method for multiplexed diagnostics of respiratory viruses. All in all, this represents a versatile and manageable platform for point-of-care testing, thereby supporting better patient outcomes and enhanced pandemic preparedness.

The Coronavirus Disease 2019 (COVID-19) pandemic disrupted maternity care, highlighting the need for rapid, high-quality clinical practice guidelines (CPGs) to ensure safe care for pregnant women. We assessed the quality and recommendations of CPGs related to COVID-19 in pregnancy. Following prospective registration (PROSPERO number: CRD42022346031) we searched Medline, Web of Science, and UpToDate from inception until July 2024. The methodological quality was appraised using the Appraisal of Guidelines for Research and Evaluation II (AGREE II). A total of 27 CPGs were included. High scores were achieved in scope and purpose (21/27, 78%) and clarity (17/27, 63%). The most poorly addressed domains were rigour of development and applicability to clinical practice (18/27, 67% and 19/27, 70% scored low quality, respectively). Overall, only four (15%) guidelines were recommended. Most CPGs (25/27, 93%) addressed COVID-19 screening and transmission prevention, but few covered psychological care (3/27, 11%) or maternal delivery preferences (4/21, 19%). Consensus was found on timing and mode of delivery (16/17, 94%), but there was disagreement on delayed cord clamping and virus transmission interventions. Evidence-based practice requires health care providers, patients and stakeholders to be aware of variations in both the quality and recommendations of CPGs, especially during times of uncertainty.

An unprecedented global social and economic impact as well as a significant number of fatalities have been brought on by the coronavirus disease 2019 (COVID-19), produced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Acute SARS-CoV-2 infection can, in certain situations, cause immunological abnormalities, leading to an anomalous innate and adaptive immune response. While most patients only experience mild symptoms and recover without the need for mechanical ventilation, a substantial percentage of those who are affected develop severe respiratory illness, which can be fatal. The absence of effective therapies when disease progresses to a very severe condition coupled with the incomplete understanding of COVID-19's pathogenesis triggers the need to develop innovative therapeutic approaches for patients at high risk of mortality. As a result, we investigate the potential contribution of promising combinatorial cell therapy to prevent death in critical patients.

Wastewater surveillance has become a valuable tool to monitor the emergence of SARS-CoV-2 variants of concern (VOCs) at the community level. In this study, we aimed to evaluate the presence of Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1617.2), and Omicron (B.1.1.529) VOCs in samples from the inlet of a wastewater treatment plant (WWTP) as well as from two different sewer interceptors (SI-1 and SI-2) from the urban sewage system in Santiago de Compostela (Galicia, NW of Spain) throughout 2021 and January 2022. For this purpose, detection and quantification of the four VOCs was performed using four duplex SARS-CoV-2 allelic discrimination RT-qPCR assays, targeting the S-gene. An N1 RT-qPCR gene assay was used as a reference for the presence of SARS-CoV-2 RNA in wastewater samples. All VOCs were detected in wastewater samples. Alpha, Beta, Delta, and Omicron VOCs were detected in 45.7%, 7.5%, 66.7%, and 72.7% of all samples, respectively. Alpha VOC was dominant during the first part of the study, whereas Delta and Omicron detection peaks were observed in May-June and December 2021, respectively. Some differences were observed among the results obtained for the two city sectors studied, which could be explained by the differences in the characteristics of the population between them. Wastewater-based epidemiology allowed us to track the early circulation and emergence of SARS-CoV-2 variants at a local level, and our results are temporally concordant with clinical data and epidemiological findings reported by the health authorities.

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has spurred an extraordinary scientific effort to better understand the disease's pathophysiology and develop diagnostic and prognostic tools to guide more precise and effective clinical management. Among the biological samples analyzed for biomarker identification, urine stands out due to its low risk of infection, non-invasive collection, and suitability for frequent, large-volume sampling. Integrating data from omics studies with standard biochemical analyses offers a deeper and more comprehensive understanding of COVID-19. This review aims to provide a detailed summary of studies published to date that have applied omics and clinical analyses on urine samples to identify potential biomarkers for COVID-19. In July 2024, an advanced search was conducted in Web of Science using the query: "covid* (Topic) AND urine (Topic) AND metabol* (Topic)". The search included results published up to 14 October 2024. The studies retrieved from this digital search were evaluated through a two-step screening process: first by reviewing titles and abstracts for eligibility, and then by retrieving and assessing the full texts of articles that met the specific criteria. The initial search retrieved 913 studies, of which 45 articles were ultimately included in this review. The most robust biomarkers identified include kynurenine, neopterin, total proteins, red blood cells, ACE2, citric acid, ketone bodies, hypoxanthine, amino acids, and glucose. The biological causes underlying these alterations reflect the multisystemic impact of COVID-19, highlighting key processes such as systemic inflammation, renal dysfunction, critical hypoxia, and metabolic stress.

The SARS-CoV-2 coronavirus infects cells through the cellular receptor angiotensin-converting enzyme 2 (ACE2), and the protease TMPRSS2 for the priming of viral spike protein. Thus, changes in these key proteins due to chronic conditions can increase risk for SARS-CoV2 infection; but significance of changes may differ is these changes correspond to full-length species or proteolytic fragments. Here, we determined that full-length ACE2 decreased in the plasma of uninfected Crohn's disease (CD) patients before treatment onset compared to controls. TMPRSS2 is mostly presented in plasma as full-length species and as an active peptidase fragment, but also as a prodomain fragment, which is the unique species remarkably decreased in plasma from CD patients. Patients treated with the anti-TNFα adalimumab showed recovery in ACE2 levels, while those treated with infliximab, or with the anti-IL-12/23 ustekinumab, still displayed a decrease in full-length species, as well as in cleaved fragments. Patients treated with azathioprine displayed similar ACE2 levels to that of controls, except a decrease in one of the ACE2 fragments. Uniquely, patients treated with azathioprine or with ustekinumab showed partial recovery in the reduction of the TMPRSS2-prodomain fragment characterized in treatment-naïve patients. Our data suggest that CD and common therapies are not related to increased susceptibility for SARS-CoV-2.

Introduction

Four years after the start of the pandemic, there is limited evidence on the impact of COVID-19 on the women's health regardless of their reproductive status.

Objective

The aim was to analyze the prevalence and associated factors of menstrual-related disturbances in formerly menstruating women following SARS-CoV-2 infection.

Study design

A retrospective observational study of adult women in Spain was conducted during the month of December 2021 using an online survey (N = 17,512). The present analysis includes a subpopulation of SARS-CoV-2-infected and formerly menstruating women (n = 72). The collected data included general characteristics, medical history, and specific information on COVID-19. Chi-square and Mann-Whitney U-tests were performed. Bivariate logistic regression analysis was then performed to investigate possible associations between the occurrence of menstrual-related disturbances after SARS-CoV-2 infection.

Results

38.8% of participants experienced menstrual-related disturbances following COVID-19. Among these, unexpected vaginal bleeding (20.8%) was the most common event, followed by spotting (11.1%) ( Table 1). Other reported changes were in the length (shorter = 12.5%) and flow (heavier = 30.3%) of menstrual bleeding in comparison to their previous experience. Regression analysis revealed that being a perimenopausal woman [adjusted odds ratio (AOR) 4.721, CI 95%, 1.022-21.796, p = 0.047] and having a previous diagnosis of menorrhagia (AOR 5.824 CI 95%, 1.521-22.310, p = 0.010) were factors associated with the event.

Conclusion

These findings could help health professionals provide their patients with up-to-date scientific information to empower them to actively manage their reproductive health, especially in societies where menstrual health is still taboo.

Background

The Coronavirus disease 2019 (COVID-19) pandemic has robustly affected the global healthcare and economic systems and it was caused by coronavirus-2 (SARS-CoV-2). The clinical presentation of the disease ranges from a flu-like illness to severe pneumonia and death. Till September 2022, the cumulative number of cases exceeded 600 million worldwide and deaths were more than 6 million. Colchicine is an alkaloid drug that is used in many autoinflammatory conditions e.g., gout, familial Mediterranean fever, and Behçet's syndrome. Colchicine inhibits the production of superoxide and the release of interleukins that stimulate the inflammatory cascade. Colchicine decreases the differentiation of myofibroblast and the release of fibrotic mediators including transforming growth factor (TGF-β1) that are related to the fibrosis. Moreover, colchicine has been used to traet viral myocarditis caused by CMV or EBV, interstitial pneumonia, and pericarditis resulting from influenza B infection. Additionally, colchicine is considered safe and affordable with wide availability.

Objective

The aim of the current study was to assess the evidence of colchicine effectiveness in COVID-19 treatment.

Methods

A comprehensive review of the literature was done till May 2022 and yielded 814 articles after ranking the articles according to authors and year of publication. Only 8 clinical trials and cohort studies fulfilling the inclusion criteria were included for further steps of data collection, analysis, and reporting.

Results

This meta-analysis involved 16,488 patients; 8146 patients in the treatment group and 8342 patients in the control group. The results showed that colchicine resulted in a significant reduction in the mortality rate among patients received colchicine in comparison with placebo or standard care (RR 0.35, 95%CI: 0.15-0.79). Colchicine resulted in a significant decrease in the need for O2 therapy in patients with COVID-19 (RR 0.07, 95%CI 0.02-0.27, P = 0.000024). However, colchicine had no significant effect on the following outcomes among COVID-19 patients: the need for hospitalization, ICU admission, artificial ventilation, and hospital discharge rate. Among the PCR confirmed COVID-19 patients, colchicine decreased the hospitalization rate (RR 0.75, 95%CI 0.57-0.99, P = 0.042). However, colchicine had no effect on mortality and the need for mechanical ventilation among this subgroup.

Conclusion

Colchicine caused a significant clinical improvement among COVID-19 patients as compared with the standard care or placebo, in terms of the need for O2, and mortality. This beneficial effect could play a role in the management of COVID-19 especially severe cases to decrease need for oxygen and to decrease mortality among these patients.

More than 40% of individuals infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have experienced persistent or relapsing multi-systemic symptoms months after the onset of coronavirus disease 2019 (COVID-19). This post-COVID-19 condition (PCC) has debilitating effects on the daily life of patients and encompasses a broad spectrum of neurological and neuropsychiatric symptoms including olfactory and gustative impairment, difficulty with concentration and short-term memory, sleep disorders and depression. Animal models have been instrumental to understand acute COVID-19 and validate prophylactic and therapeutic interventions. Similarly, studies post-viral clearance in hamsters, mice and nonhuman primates inoculated with SARS-CoV-2 have been useful to unveil some of the aspects of PCC. Transcriptomic alterations in the central nervous system, persistent activation of immune cells and impaired hippocampal neurogenesis seem to have a critical role in the neurological manifestations observed in animal models infected with SARS-CoV-2. Interestingly, the proinflammatory transcriptomic profile observed in the central nervous system of SARS-CoV-2-inoculated mice partially overlaps with the pathological changes that affect microglia in humans during Alzheimer's disease and aging, suggesting shared mechanisms between these conditions. None of the currently available animal models fully replicates PCC in humans; therefore, multiple models, together with the fine-tuning of experimental conditions, will probably be needed to understand the mechanisms of PCC neurological symptoms. Moreover, given that the intrinsic characteristics of the new variants of concern and the immunological status of individuals might influence PCC manifestations, more studies are needed to explore the role of these factors and their combinations in PCC, adding further complexity to the design of experimental models.

The therapeutic management and short-term consequences of the coronavirus disease 2019 (COVID-19) are well known. However, COVID-19 post-acute sequelae are less known and represent a public health problem worldwide. Patients with COVID-19 who present post-acute sequelae may display immune dysregulation, a procoagulant state, and persistent microvascular endotheliopathy that could trigger microvascular thrombosis. These elements have also been implicated in the physiopathology of postural orthostatic tachycardia syndrome, a frequent sequela in post-COVID-19 patients. These mechanisms, directly associated with post-acute sequelae, might determine the thrombotic consequences of COVID-19 and the need for early anticoagulation therapy. In this context, heparin has several potential benefits, including immunomodulatory, anticoagulant, antiviral, pro-endothelial, and vascular effects, that could be helpful in the treatment of COVID-19 post-acute sequelae. In this article, we review the evidence surrounding the post-acute sequelae of COVID-19 and the potential benefits of the use of heparin, with a special focus on the treatment of postural orthostatic tachycardia syndrome.

Enveloped viruses enter cells by binding to receptors present on host cell membranes, which trigger internalization and membrane fusion. For many viruses, this either directly or indirectly involves interaction with membrane-anchored carbohydrates, such as heparan sulfate, providing a potential target for a broad-spectrum antiviral approach. Based on this hypothesis, we screened a library of functionalized chitosan sulfates that mimic heparan sulfate in cellular membranes for inhibition of SARS-CoV-2 and respiratory syncytial virus (RSV) entry. An array of compounds blocking SARS-CoV-2 and RSV were identified, with the lead compound displaying broad-spectrum activity against multiple viral strains and clinical isolates. Mechanism of action studies showed the drug to block viral entry irreversibly, likely via a virucidal mechanism. Importantly, the drug was non-toxic in vivo and showed potent post-exposure therapeutic activity against both SARS-CoV-2 and RSV. Together, these results highlight the potential of functionalized carbohydrates as broad-spectrum antivirals targeting respiratory viruses.

Background

Schizophrenia, affecting approximately 1 % of the population worldwide, is associated with increased mortality rates and a reduced life expectancy of 10-20 years. Approximately 30 % of cases are resistant to conventional antipsychotic treatments, necessitating the use of clozapine. Recent evidence suggests that clozapine exerts immunomodulatory effects, with individuals undergoing chronic clozapine treatment exhibiting immune profiles resembling primary immunodeficiencies.

Objective

To evaluate the immune response to vaccination with the spike protein of SARS-CoV-2 in schizophrenia patients treated with clozapine, compared to those receiving other antipsychotics.

Methods

The study included 98 patients diagnosed with schizophrenia or schizoaffective disorder, of whom 69 were treated with clozapine. Demographic, clinical, and laboratory data were collected for all participants. Anti-spike protein antibodies were measured using the Elecsys® Anti-SARS-CoV-2 S assay.

Results

No significant differences were observed in demographic, clinical, or laboratory parameters between the groups. Univariate analysis revealed that spike antibody levels were positively associated with smoking habits and more than two exposures to the virus, while they were negatively associated with the time elapsed since vaccination and clozapine dosage.In multivariate analysis, patients receiving clozapine doses >350 mg/day exhibited a significant reduction in anti-spike antibody levels compared to those not treated with clozapine (fold change = 0.49 [0.24-0.97], p = 0.041) and those receiving <200 mg/day of clozapine (fold change = 0.39 [0.17-0.88], p = 0.024).

Conclusion

High doses of clozapine (>350 mg/day) in patients with schizophrenia and schizoaffective disorders are associated with a diminished immune response to SARS-CoV-2 spike protein vaccination.

Background and Objectives: The pulmonary sequelae of COVID-19 and their evolution are of interest to the scientific community. We aimed to determine the radiological changes at 6 and 12 months after COVID-19 pneumonia, its evolution and its risk factors. Materials and Methods: This retrospective longitudinal study included adults admitted for COVID-19 pneumonia from 1 March 2020 to 30 April 2021 who had a high-resolution computed tomography (HRCT) scan at 6 months and 12 months after hospital discharge. The primary outcome was the appearance of radiological abnormalities on HRCT and the number of lung segments affected by them at 6 and 12 months, while the main explanatory variables were about the disease course, analytical parameters and treatment. Results: This study included n = 108 patients, with a mean age of 64 years. There was a decrease in the percentage of patients presenting parenchymal (93.5% to 88.9%, p < 0.001) and reticular (63% to 62%, p < 0.001) patterns on HRCT at 12 months compared to 6, and an increase in those presenting a fibrotic pattern (62% to 63.9%, p < 0.001). Ground-glass opacities were the most frequent radiological change at 6 and 12 months (91.7% and 87%, respectively). There was a significant reduction in the total number of lung segments with ground-glass opacities (445 to 382, p < 0.001) and consolidation (158 to 136, p = 0.019) and an increase in those with bronchiectasis (66 to 80, p = 0.033) between the two moments. After multivariate analysis, high-flow oxygen therapy (HFOT), highest ferritin levels, hypertension and ≥71 years showed an association with the development of subpleural parenchymal bands, consolidation, bronchiectasis and septal thickening at 6 and 12 months. Conclusions: Parenchymal patterns seem to be more frequent than reticular and fibrotic patterns after COVID-19 pneumonia. The fibrotic pattern was the only one that worsened significantly over time, with bronchiectasis being the only change that increased at 12 months. Older age, hypertension, the need for HFOT, and high levels of ferritin may be directly associated with worse radiological outcomes after COVID-19 pneumonia.

Background

The COVID-19 pandemic, caused by SARS-CoV-2, has highlighted the need for vaccines targeting both neutralizing antibodies (NAbs) and long-lasting cross-reactive T cells covering multiple viral proteins to provide broad and durable protection against emerging variants.

Methods

To address this, here we developed two vaccine candidates, namely (i) DNA-CoV2-TMEP, expressing the multiepitopic CoV2-TMEP protein containing immunodominant and conserved T cell regions from SARS-CoV-2 structural proteins, and (ii) MVA-CoV2-B2AT, encoding a bi-cistronic multiepitopic construct that combines conserved B and T cell overlapping regions from SARS-CoV-2 structural proteins.

Results

Both candidates were assessed in vitro and in vivo demonstrating their ability to induce robust immune responses. In C57BL/6 mice, DNA-CoV2-TMEP enhanced the recruitment of innate immune cells and stimulated SARS-CoV-2-specific polyfunctional T cells targeting multiple viral proteins. MVA-CoV2-B2AT elicited NAbs against various SARS-CoV-2 variants of concern (VoCs) and reduced viral replication and viral yields against the Beta variant in susceptible K18-hACE2 mice. The combination of MVA-CoV2-B2AT with a mutated ISG15 form as an adjuvant further increased the magnitude, breadth and polyfunctional profile of the response.

Conclusion

These findings underscore the potential of these multiepitopic proteins when expressed from DNA or MVA vectors to provide protection against SARS-CoV-2 and its variants, supporting their further development as next-generation COVID-19 vaccines.

Sepsis is a life-threatening condition caused by the body's overwhelming response to an infection, such as pneumonia or urinary tract infection. It occurs when the immune system releases cytokines into the bloodstream, triggering widespread inflammation. If not treated, it can lead to organ failure and death. Unfortunately, sepsis has a high mortality rate, with studies reporting rates ranging from 20% to over 50%, depending on the severity and promptness of treatment. According to the World Health Organization (WHO), the annual death toll in the world is about 11 million. One of the main toxins responsible for inflammation induction are lipopolysaccharides (LPS, endotoxin) from Gram-negative bacteria, which ranks among the most potent immunostimulants found in nature. Antibiotics are consistently prescribed as a part of anti-sepsis-therapy. However, antibiotic therapy (i) is increasingly ineffective due to resistance development and (ii) most antibiotics are unable to bind and neutralize LPS, a prerequisite to inhibit the interaction of endotoxin with its cellular receptor complex, namely Toll-like receptor 4 (TLR4)/MD-2, responsible for the intracellular cascade leading to pro-inflammatory cytokine secretion. The pandemic virus SARS-CoV-2 has infected hundreds of millions of humans worldwide since its emergence in 2019. The COVID-19 (Coronavirus disease-19) caused by this virus is associated with high lethality, particularly for elderly and immunocompromised people. As of August 2023, nearly 7 million deaths were reported worldwide due to this disease. According to some reported studies, upregulation of TLR4 and the subsequent inflammatory signaling detected in COVID-19 patients “mimics bacterial sepsis”. Furthermore, the immune response to SARS-CoV-2 was described by others as “mirror image of sepsis”. Similarly, the cytokine profile in sera from severe COVID-19 patients was very similar to those suffering from the acute respiratory distress syndrome (ARDS) and sepsis. Finally, the severe COVID-19 infection was frequently accompanied by bacterial co-infections, as well as by the presence of significant LPS concentrations. These data indicate similarity and interdependences of both syndromes, but also significant differences which will be discussed in the present review.

Introduction

While the general immune response to Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is well-understood, the long-term effects of Human Immunodeficiency Virus-1/Severe Acute Respiratory Syndrome-Coronavirus-2 (HIV-1/SARS-CoV-2) co-infection on the immune system remain unclear. This study investigates the immune response in people with HIV-1 (PWH) co-infected with SARS-CoV-2 to understand its long-term health consequences.

Methods

A retrospective longitudinal study of PWH with suppressed viral load and SARS-CoV-2 infection was conducted. Cryopreserved peripheral blood mononuclear cells and plasma samples were collected at three time-points: HIV-1/pre-SARS-CoV-2 (n = 18), HIV-1/SARS-CoV-2 (n = 46), and HIV-1/post-SARS-CoV-2 (n = 36). Plasma levels of 25 soluble cytokines and chemokines, and anti-S/anti-N-IgG-SARS-CoV-2 antibodies were measured. Immunophenotyping of innate and adaptive immune components and HIV-1 and SARS-CoV-2-specific T/B-cell responses were assessed by flow cytometry.

Results

HIV-1/SARS-CoV-2 co-infection was associated with long-lasting immune dysfunction, characterized by elevated levels of pro-inflammatory cytokines and a decrease in the MIG-IP10-ITAC chemokine axis at the HIV/SARS-CoV-2 time-point, which persisted one year later. Additionally, alterations in the distribution of subsets and increased activation (NKG2D/NKG2C) and maturation (TIM3) markers of NK and dendritic cells were observed at the HIV-1/SARS-CoV-2 time-point, persisting throughout the study. Effector memory CD4 T-cell subsets were decreased, while exhaustion/senescence (PD1/TIM3/CD57) markers were elevated at all three time-points. SARS-CoV-2-specific T/B-cell responses remained stable throughout the study, while HIV-1-specific T-cell responses decreased at the HIV-1/SARS-CoV-2 time-point and remained so.

Conclusions

Persistent immune dysfunction in HIV-1/SARS-CoV-2 co-infection increases the risk of future complications, even in PWH with mild symptoms. Exacerbated inflammation and alterations in immune cells may contribute to reduce vaccine efficacy and potential reinfections.

Objectives

To study the prevalence and timing of neurological manifestations, including cognitive involvement, in patients hospitalized for Coronavirus disease 2019 (COVID-19). To analyze the pathogenic mechanisms and any association they have with disease severity.

Methods

Longitudinal cohort study with prospective follow-up of patients who required hospitalization. Patients under 65 who had no pre-existing cognitive impairment and did not require an ICU stay were evaluated 3 and 12 months after discharge using a battery of neuropsychological tests.

Results

Of 205 patients hospitalized for COVID-19, 153 (74.6%) presented with neurological manifestations. The most frequent were myalgia (32.7%), headache (31.7%), dysgeusia (29.2%), and anosmia (24.9%). Patients with more severe illness at the time of hospitalization presented fewer neurological manifestations. Of the 62 patients who underwent neuropsychological examination 3 months after discharge, 22.6% had impaired attention, 19.4% impaired working memory, 16.1% impaired learning and retrieval, 9.7% impaired executive functions, and 8.2% impaired processing speed. Patients with anosmia also presented with more headache (OR 5.45; p < 0.001) and greater risk of working memory impairment (OR 5.87; p 0.03). At follow-up 12 months after hospital discharge, 14.3% of patients still showed impaired attention, 2.4% impaired working memory, 2.5% impaired executive functions, and 2.5% impaired processing speed.

Discussion

Neurological manifestations are common in patients hospitalized for COVID-19 regardless of severity. The high prevalence of anosmia and its association with headache and working memory impairment at 3 months, suggest potential direct or indirect damage to the prefrontal cortex via invasion of the olfactory bulb by COVID-19.

The COVID-19 pandemic has underscored the importance of swift responses and the necessity of dependable technologies for vaccine development. Our team previously developed a fast cloning system for the modified vaccinia virus Ankara (MVA) vaccine platform. In this study, we report the construction and preclinical testing of a recombinant MVA vaccine obtained using this system. We obtained recombinant MVA expressing the unmodified full-length SARS-CoV-2 spike (S) protein containing the D614G amino acid substitution (MVA-Sdg) and a version expressing a modified S protein containing amino acid substitutions designed to stabilize the protein a in a pre-fusion conformation (MVA-Spf). S protein expressed by MVA-Sdg was found to be expressed and correctly processed and transported to the cell surface, where it efficiently produced cell-cell fusion. Version Spf, however, was not proteolytically processed and despite being transported to the plasma membrane, it failed to induce cell-cell fusion. We assessed both vaccine candidates in prime-boost regimens in the susceptible transgenic K18-human angiotensin converting enzyme 2 (K18-hACE2) mice and in golden Syrian hamsters. Robust immunity and protection from disease was induced with either vaccine in both animal models. Remarkably, the MVA-Spf vaccine candidate produced higher levels of antibodies, a stronger T cell response, and a higher degree of protection from challenge. In addition, the levels of SARS-CoV-2 in the brain of MVA-Spf inoculated mice was decreased to undetectable levels. Those results add to our current experience and range of vaccine vectors and technologies for developing a safe and effective COVID-19 vaccine

The global impact of the SARS-CoV-2 pandemic has underscored the need for a deeper understanding of viral evolution to anticipate new viruses or variants. Genetic recombination is a fundamental mechanism in viral evolution, yet it remains poorly understood. In this study, we conducted a comprehensive research on the genetic regions associated with genetic recombination features in SARS-CoV-2. With this aim, we implemented a two-phase transfer learning approach using genomic spectrograms of complete SARS-CoV-2 sequences. In the first phase, we utilized a pre-trained VGG-16 model with genomic spectrograms of HIV-1, and in the second phase, we applied HIV-1 VGG-16 model to SARS-CoV-2 spectrograms. The identification of key recombination hot zones was achieved using the Grad-CAM interpretability tool, and the results were analyzed by mathematical and image processing techniques. Our findings unequivocally identify the SARS-CoV-2 Spike protein (S protein) as the pivotal region in the genetic recombination feature. For non-recombinant sequences, the relevant frequencies clustered around 1/6 and 1/12. In recombinant sequences, the sharp prominence of the main hot zone in the Spike protein prominently indicated a frequency of 1/6. These findings suggest that in the arithmetic series, every 6 nucleotides (two triplets) in S may encode crucial information, potentially concealing essential details about viral characteristics, in this case, recombinant feature of a SARS-CoV-2 genetic sequence. This insight further underscores the potential presence of multifaceted information within the genome, including mathematical signatures that define an organism's unique attributes.

SUMMARY

Several viruses hijack various forms of endocytosis in order to infect host cells. Here, we report the discovery of a new molecule with antiviral properties that we named virapinib, which limits viral entry by macropinocytosis. The identification of virapinib derives from a chemical screen using High-Throughput Microscopy, where we identified new chemical entities capable of preventing infection with a pseudotype virus expressing the spike (S) protein from SARS-CoV-2. Subsequent experiments confirmed the capacity of virapinib to inhibit infection by SARS-CoV-2, as well as by additional viruses, such as Monkeypox virus and TBEV. Mechanistic analyses revealed that the compound inhibited macropinocytosis, limiting this entry route for the viruses. Importantly, virapinib has no significant toxicity to host cells. In summary, we present a new molecule that inhibits viral entry via the endocytic route, offering a new alternative to prevent viral infection.

Introduction

AZD7442 (tixagevimab/cilgavimab) comprises neutralising monoclonal antibodies (mAbs) that bind to distinct non-overlapping epitopes on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. Viral evolution during mAb therapy can select for variants with reduced neutralisation susceptibility. We examined treatment-emergent SARS-CoV-2 variants during TACKLE (NCT04723394), a phase 3 study of AZD7442 for early outpatient treatment of coronavirus disease 2019 (COVID-19).

Methods

Non-hospitalised adults with mild-to-moderate COVID-19 were randomised and dosed ≤ 7 days from symptom onset with AZD7442 (n = 452) or placebo (n = 451). Next-generation sequencing of the spike gene was performed on SARS-CoV-2 reverse-transcription polymerase chain reaction-positive nasopharyngeal swabs at baseline and study days 3, 6, and 15 post dosing. SARS-CoV-2 lineages were assigned using spike nucleotide sequences. Amino acid substitutions were analysed at allele fractions (AF; % of sequence reads represented by substitution) ≥ 25% and 3% to 25%. In vitro susceptibility to tixagevimab, cilgavimab, and AZD7442 was evaluated for all identified treatment-emergent variants using a pseudotyped microneutralisation assay.

Results

Longitudinal spike sequences were available for 461 participants (AZD7442, n = 235; placebo, n = 226) and showed that treatment-emergent variants at any time were rare, with 5 (2.1%) AZD7442 participants presenting ≥ 1 substitution in tixagevimab/cilgavimab binding sites at AF ≥ 25%. At AF 3% to 25%, treatment-emergent variants were observed in 15 (6.4%) AZD7442 and 12 (5.3%) placebo participants. All treatment-emergent variants showed in vitro susceptibility to AZD7442.

Conclusion

These data indicate that AZD7442 creates a high genetic barrier for resistance and is a feasible option for COVID-19 treatment.

COVID-19 is characterized by a wide range of clinical manifestations, where aging, underlying diseases, and genetic background are related to worse outcomes. In the present study, the differential expression of seven genes related to immunity, IRF9, CCL5, IFI6, TGFB1, IL1B, OAS1, and TFRC, was analyzed in individuals with COVID-19 diagnoses of different disease severities. Two-step RT-qPCR was performed to determine the relative gene expression in whole-blood samples from 160 individuals. The expression of OAS1 (p < 0.05) and IFI6 (p < 0.05) was higher in moderate hospitalized cases than in severe ones. Increased gene expression of OAS1 (OR = 0.64, CI = 0.52-0.79; p = 0.001), IRF9 (OR = 0.581, CI = 0.43-0.79; p = 0.001), and IFI6 (OR = 0.544, CI = 0.39-0.69; p < 0.001) was associated with a lower risk of requiring IMV. Moreover, TGFB1 (OR = 0.646, CI = 0.50-0.83; p = 0.001), CCL5 (OR = 0.57, CI = 0.39-0.83; p = 0.003), IRF9 (OR = 0.80, CI = 0.653-0.979; p = 0.03), and IFI6 (OR = 0.827, CI = 0.69-0.991; p = 0.039) expression was associated with patient survival. In conclusion, the relevance of OAS1, IRF9, and IFI6 in controlling the viral infection was confirmed.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10^-3-10^-4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.

Most COVID-19 vaccines are based on the SARS-CoV-2 Spike glycoprotein (S) or their subunits. However, S shows some structural instability that limits its immunogenicity and production, hampering the development of recombinant S-based vaccines. The introduction of the K986P and V987P (S-2P) mutations increases the production and immunogenicity of the recombinant S trimer, suggesting that these two parameters are related. Nevertheless, S-2P still shows some molecular instability and it is produced with low yield. Here we described a novel set of mutations identified by molecular modeling and located in the S2 region of the S-2P that increase its production up to five-fold. Besides their immunogenicity, the efficacy of two representative S-2P-based mutants, S-29 and S-21, protecting from a heterologous SARS-CoV-2 Beta variant challenge was assayed in K18-hACE2 mice (an animal model of severe SARS-CoV-2 disease) and golden Syrian hamsters (GSH) (a moderate disease model). S-21 induced higher level of WH1 and Delta variants neutralizing antibodies than S-2P in K18-hACE2 mice three days after challenge. Viral load in nasal turbinate and oropharyngeal samples were reduced in S-21 and S-29 vaccinated mice. Despite that, only the S-29 protein protected 100% of K18-hACE2 mice from severe disease. When GSH were analyzed, all immunized animals were protected from disease development irrespectively of the immunogen they received. Therefore, the higher yield of S-29, as well as its improved immunogenicity and efficacy protecting from the highly pathogenic SARS-CoV-2 Beta variant, pinpoint the S-29 mutant as an alternative to the S-2P protein for future SARS-CoV-2 vaccine development.

The development of novel tools to tackle viral processes has become a central focus in global health, during the COVID-19 pandemic. The spike protein is currently one of the main SARS-CoV-2 targets, owing to its key roles in infectivity and virion formation. In this context, exploring innovative strategies to block the activity of essential factors of SARS-CoV-2, such as spike proteins, will strengthen the capacity to respond to current and future threats. In the present work, we developed and tested novel bispecific molecules that encompass: (i) oligonucleotide aptamers S901 and S702, which bind to the spike protein through its S1 domain, and (ii) hydrophobic tags, such as adamantane and tert-butyl-carbamate-based ligands. Hydrophobic tags have the capacity to trigger the degradation of targets recruited in the context of a proteolytic chimera by activating quality control pathways. We observed that S901-adamantyl conjugates promote the degradation of the S1 spike domain, stably expressed in human cells by genomic insertion. These results highlight the suitability of aptamers as target-recognition molecules and the robustness of protein quality control pathways triggered by hydrophobic signals, and place aptamer-Hytacs as promising tools for counteracting coronavirus progression in human cells.

Acute respiratory infections are a significant challenge in primary care and hospital settings. Viruses are the most common etiology and the overlapping symptomatology among major respiratory viruses, such as influenza, severe acute respiratory syndrome coronavirus 2, and respiratory syncytial virus, requires the use of diagnostic tests that deliver early and accurate results. With the increasing availability of rapid antigen tests (RATS), it is tempting to prefer them over polymerase chain reaction (PCR) tests. However, compelling arguments support the existing recommendations in some European countries to maintain PCR testing for patient management throughout the year. RATs show sensitivities below 30% with lower viral loads, which are common and can have significant clinical implications. RATs perform well at lower cycle threshold (Ct) values, with sensitivity reaching 97.9% for Ct values below 20, which drops significantly for values above 25. Factors affecting viral load include disease stage, vaccination status, and viral variants, all of which can compromise the accuracy of antigen tests. Multi-target PCR tests effectively overcome these issues, ensuring reliable diagnosis. Additionally, the early detection of paucisymptomatic cases is essential in primary care and hospital settings to facilitate isolation and prevent secondary infections. Economic analyses support the use of comprehensive PCR tests, such as triplex-type tests, detecting SARS-CoV-2, influenza viruses, and RSV, as a first-line approach, as they can reduce case numbers and healthcare resource utilization. Maintaining PCR testing year-round is therefore crucial for the effective management of respiratory infections.

Background

We aimed to describe respiratory sequelae up to 4 years after discharge in COVID-19 patients with severe pneumonia having required non-invasive respiratory support therapies.

Methods

This study was conducted between March 2020 and June 2020 at University Hospital Doctor Josep Trueta (Girona, Spain). We assessed the patient's dyspnoea and performed, pulmonary function tests, a high-resolution CT (HRCT), a 6-minute walking test, a blood test, and the Saint George's respiratory questionnaire 3 months after discharge. At the 6-month, 1-year, and 4-year follow-up, we repeated all tests except for pulmonary function, 6-min walking test, and HRCT, which were only performed if abnormal findings had been previously detected.

Results

94 patients were enrolled 3 months after discharge; 73% were male, the median age was 62.9 years, and most were non-smokers (58%). 56 patients (59.6%) completed the 4-year follow-up. When comparing data 3 months and 4 years after discharge, the percentage of patients presenting dyspnoea ≥ 2 decreased (19.5% vs. 7.9%), the quality-of-life total score improved (22.8% vs. 18.1%), diffusing capacity for carbon monoxide improved (75.9% vs. 81.4%), the 6-min walking test distance was enhanced (368.0 m vs. 436.6 m), ground glass opacities findings waned (56.6% vs. 0.8%), and traction bronchiectasis increased (2.7% vs. 9.2%). Age was the only parameter that exhibited significant differences between patients with and without pulmonary fibrotic-like changes.

Conclusion

Most patients, 4 years after discharge, improved their pulmonary function, exercise capacity, clinical condition, and quality of life. Although pulmonary fibrotic-like changes were observed during the follow-ups, its disparity with clinical-functional improvement pointed to non-progressive and non-clinically relevant lung scars.

COVID-19 pandemic, caused by the novel SARS-CoV-2 virus, has raised significant interest in understanding potential cross-immunity mechanisms. Recent evidence suggests that T-cells associated with common cold coronaviruses (229E, NL63, OC43, HKU1) may provide some level of cross-immunity against SARS-CoV-2. It is also known that the prevalence of smokers among patients admitted to hospital for COVID-19 is lower than expected according to the corresponding country's smoking prevalence, which is known as smoker's paradox in COVID-19. No clear consensus to explain it has yet been reached. This phenomenon suggests a complex interaction between smoking and immune response. Nonetheless, very few works have studied the prevalence of smokers in those infected by common cold coronaviruses, and its relation to COVID-19 has not been investigated. We performed a systematic review and meta-analysis to study the prevalence of smokers among patients infected by common cold coronaviruses, and to compare them to the corresponding country's smoking prevalence. L'Abbé plots were used to visually assess the consistency of the observed effects across the different studies included in the meta-analysis. Additionally, significant differences were found in smoking prevalence among the various types of ccCoV, indicating the need for further research into the biological mechanisms driving these disparities. The results show that smoking prevalence is higher among those patients infected by these coronaviruses than in the general population (OR = 1.37, 95% CI: 0.81-2.33). A study was separately done for the four coronavirus types, and the prevalence of smokers was higher in three of the four than that corresponding to country, gender and study year: OC43 (OR = 1.93, 95% CI: 0.64-5.82); HKU1 (OR = 3.62, 95% CI: 1.21-10.85); NL63 (OR = 1.93, 95% CI: 0.64-5.82); 229E (OR = 0.97, 95% CI: 0.50-1.90). The heterogeneity of the studies was assessed using the Cochrane Chi-squared test, I-squared (I2), and Tau-squared (τ2). This detailed statistical analysis enhances the robustness of our findings and highlights the variations in smoking prevalence among different ccCoVs. Our data suggest that COVID-19 might be less prevalent among smokers due to greater cross-immunity from a larger number or more recent infections by common cold coronaviruses than the non-smoking population, which would explain smoker's paradox in COVID-19. IMPLICATIONS. The low prevalence of current smokers among SARS-CoV-2 patients is a finding recurrently repeated, even leading to postulate the "smoker's paradox" in COVID-19. This fact compelled us to study the prevalence of smokers among patients infected by common cold coronaviruses, and to compare them to the corresponding country's smoking prevalence. Our data could explain smoker's paradox in COVID-19 by a greater cross immunity due to a larger number, or more recent infections by common cold coronaviruses than the non-smoking population. This manuscript allow understand potential unrevealed mechanism for low prevalence of current smokers among SARS-CoV-2 patients.

Patients surviving coronavirus disease of 2019 (COVID-19) often complain of skeletal muscle weakness that may be very limiting and long-lasting. There are almost no studies on the skeletal muscle of these patients, and electron microscopic data are scarce. We assessed the ultrastructural changes in the quadriceps of eight patients with COVID-19 and found a combination of features different from those reported in corticosteroid myopathy and acute relaxant-steroid myopathy. The most remarkable and constant changes involved the endothelial cells and consisted of massive amounts of pinocytotic vesicles, degenerative changes, platelet aggregates and, most characteristic of all, an increase in the external lamina thickness that seems to stem from reduplication due to successive bouts of endothelial cell damage and subsequent regeneration. Viral particles were not found in any of the cases. This distinct and quite common set of alterations defines the myopathy associated with infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This association seems to be the result of an inflammatory process that would arise in infected cells but could damage non-infected endomysial blood vessels, thus resulting in persistent changes of the microvasculature that would be related to long-standing myopathic clinical features.

Although many studies have associated changes in the nasopharyngeal microbiota to patient's susceptibility to COVID-19, their results are highly variable and contradictory. Addressing the limitations in previous research responsible for that variability, this study uses 16S rRNA gene sequencing to analyze the nasopharyngeal microbiota of 395 subjects, 117 controls, and 278 COVID-19 patients, of different age groups that cover the entire lifespan and across varying disease severities. This revealed that bacterial alpha diversity decreases progressively throughout life but only in severely ill COVID-19 patients, in whose nasopharynx, moreover, several opportunistic pathogen bacterial genera are overrepresented. Notably, Scardovia wiggsiae appears only in severe COVID-19 patients over 60 years of age, suggesting its potential utility as a COVID-19 severity biomarker in the elderly, who are the most susceptible individuals to suffer from serious forms of the disease. Thus, our results provide valuable insights into age-associated dynamics within nasopharyngeal microbiota during severe COVID-19.

In the wake of the COVID-19 pandemic caused by SARS-CoV-2, questions emerged about the potential effects of Bacillus Calmette-Guérin (BCG) vaccine on the immune response to SARS-CoV-2 infection, including the neurodegenerative diseases it may contribute to. To explore this, an experimental study was carried out in BCG-stimulated and non-stimulated k18-hACE2 mice challenged with SARS-CoV-2. Viral loads in tissues determined by RT-qPCR, histopathology in brain and lungs, immunohistochemical study in brain (IHC) as well as mortality rates, clinical signs and plasma inflammatory and coagulation biomarkers were assessed. Our results showed BCG-SARS-CoV-2 challenged mice presented higher viral loads in the brain and an increased frequency of neuroinvasion, with the greatest differences observed between groups at 3-4 days post-infection (dpi). Histopathological examination showed a higher severity of brain lesions in BCG-SARS-CoV-2 challenged mice, mainly consisting of neuroinflammation, increased glial cell population and neuronal degeneration, from 5 dpi onwards. This group also presented higher interstitial pneumonia and vascular thrombosis in lungs (3-4 dpi), BCG-SARS-CoV-2 mice showed higher values for TNF-α and D-dimer values, while iNOS values were higher in SARS-CoV-2 mice at 3-4 dpi. Results presented in this study indicate that BCG stimulation could have intensified the inflammatory and neurodegenerative lesions promoting virus neuroinvasion and dissemination in this experimental model. Although k18-hACE2 mice show higher hACE2 expression and neurodissemination, this study suggests that, although the benefits of BCG on enhancing heterologous protection against pathogens and tumour cells have been broadly demonstrated, potential adverse outcomes due to the non-specific effects of BCG should be considered.

Background

To provide a detailed understanding and apply a comprehensive strategy, this study examines the association between COVID-19 vaccination and cardiovascular events. We conducted a Bayesian multivariate meta-analysis using summary data across multiple outcomes including myocardial infarction, stroke, arrhythmia, and CAD, considering potential dependencies in the data. Markov chain Monte Carlo (MCMC) methods were detected for easy implementation of the Bayesian approach. Also, the sensitivity analysis of the model was done by using different priors.

Methods

Fifteen studies were included in the systematic review, with eleven studies comparing the results between the vaccine group and the unvaccinated group. Additionally, six studies were used for further analysis to compare mRNA COVID-19 Vaccines (Pfizer-BioNTech and Moderna).

Results

Bayesian meta-analysis revealed a link between vaccines and CAD risk (OR, 1.70; 95% CrI: 1.11-2.57), particularly after BNT162b2 (OR, 1.64; 95% CrI: 1.06-2.55) and second dose (OR, 3.44; 95% CrI: 1.99-5.98). No increased risk of heart attack, arrhythmia, or stroke was observed post-COVID-19 vaccination. As the only noteworthy point, a protective effect on stroke (OR, 0.19; 95% CrI: 0.10-0.39) and myocardial infarction (OR, 0.003; 95% CrI: 0.001-0.006) was observed after the third dose of the vaccine.

Conclusions

Secondary analysis showed no notable disparity in cardiovascular outcomes between BNT162b2 and mRNA vaccines. The association of COVID-19 vaccination with the risk of coronary artery disease should be considered in future vaccine technologies for the next pandemic.

Background

Children are less susceptible than adults to symptomatic COVID-19 infection, but very few studies addressed their underlying cause. Moreover, very few studies analyzed why children highly exposed to the virus remain uninfected.

Methods

We analyzed the serum levels of ACE2, angiotensin II, anti-spike and anti-N antibodies, cytokine profiles, and virus neutralization in a cohort of children at high risk of viral exposure, cohabiting with infected close relatives during the lockdown in Spain.

Results

We analyzed 40 children who were highly exposed to the virus since they lived with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected relatives during the lockdown for several months without taking preventive measures. Of those, 26 reported mild or very mild symptoms. The induced immune response to the virus was analyzed 3 months after the household infection. Surprisingly, only 15 children had IgG anti-S (IgG⁺) determined by a sensitive method indicative of a past infection. The rest, negative for IgG anti-N or S in various tests, could be further subdivided, according to IgM antibodies, into those having IgM anti-S and IgM anti-N (IgG^-IgM^high) and those having only IgM anti-N (IgG^-IgM^low). Interestingly, those two subgroups of children with IgM antibodies have strikingly different patterns of cytokines. The IgM^high group had significantly higher IFN-α2 and IFN-γ levels as well as IL-10 and GM-CSF than the IgM^low group. In contrast, the IgM^low group had low levels of ACE2 in the serum. Both groups have a weaker but significant capacity to neutralize the virus in the serum than the IgG⁺ group. Two children were negative in all immunological antibody tests.

Conclusions

A significant proportion of children highly exposed to SARS-CoV-2 did not develop a classical adaptive immune response, defined by the production of IgG, despite being in close contact with infected relatives. A large proportion of those children show immunological signs compatible with innate immune responses (as secretion of natural antibodies and cytokines), and others displayed very low levels of the viral receptor ACE2 that may have protected them from the virus spreading in the body despite high and constant viral exposure.

Background/Objectives: SARS-CoV-2 infection increases thrombotic events in hospitalized patients, especially those of greater severity. It has been associated with the cytokine storm and worsening renal and liver function, increased inflammatory markers, and altered coagulation markers. This study analyzes differences in inflammatory, hepatic, renal, and coagulation markers between hospitalized patients with and without COVID-19 who experienced thromboembolic events during the last three years of the pandemic. Methods: This single-center, retrospective observational study, with an inferential component and biomarker analysis, included 663 patients (600 without COVID-19, 63 with COVID-19) admitted between December 2022 and January 2023. Results: Patients with COVID-19 exhibited significantly higher mean glomerular filtration rate (GFR) (100.5 mL/min/1.73 m²; p < 0.01) and alanine aminotransferase (ALT) levels (33.0 IU/L; p < 0.01) compared to those without COVID-19. Ferritin levels were also significantly elevated in COVID-19 patients (441.1; p < 0.01), particularly those with severe disease. Conversely, troponin I was significantly higher in patients without COVID-19 (22.6 × 10⁴ pg/mL; p < 0.001). Among COVID-19 patients, D-dimer levels were significantly higher in those not requiring intensive care unit (ICU) admission (9.0 × 10³ ng/mL; p = 0.023). Multivariate analysis revealed a significant association between COVID-19 and sex. Conclusions: Overall, renal function did not differ significantly between COVID-19 and non-COVID-19 patients. However, renal function was better in patients admitted to the ICU, regardless of COVID-19 status. Troponin I levels were elevated in non-COVID-19 patients, while ferritin and ALT levels were higher in COVID-19 patients. D-dimer levels showed no significant difference between the two groups.

The impact on immunogenicity and efficacy of SARS-CoV-2 vaccination in people with prior COVID-19 could differ depending on timing of vaccination and number of doses. The VATICO study randomized 66 hospitalized recovered COVID-19 individuals to receive either immediate or deferred vaccination, with one or two doses of mRNA SARS-CoV-2 vaccines. We measured binding and neutralizing antibodies against SARS-CoV-2 at enrollment and longitudinally. Median (IQR) time from SARS-CoV-2 infection to first vaccination was 68 (53-75) days in the immediate group, and 151 (137-173) days in the deferred group. At week 48, timing or number of vaccine doses did not influence the change in antibody levels relative to baseline. Adherence to the assigned vaccine regimen was lower in the deferred group, particularly in participants receiving two doses. Although the study ultimately lacked adequate power to draw firm conclusions, these results suggest possible benefits of prompt vaccination after recovery from COVID-19.

The impact of SARS-CoV-2 infection remains substantial on a global scale, despite widespread vaccination efforts, early therapeutic interventions, and an enhanced understanding of the disease's underlying mechanisms. At the same time, a significant number of patients continue to develop severe COVID-19, necessitating admission to intensive care units (ICUs). This study aimed to provide evidence concerning the most influential predictors of mortality among critically ill patients with severe COVID-19, employing machine learning (ML) techniques. To accomplish this, we conducted a retrospective multicenter investigation involving 684 patients with severe COVID-19, spanning from 1 June 2020 to 31 March 2023, wherein we scrutinized sociodemographic, clinical, and analytical data. These data were extracted from electronic health records. Out of the six supervised ML methods scrutinized, the extreme gradient boosting (XGB) method exhibited the highest balanced accuracy at 96.61%. The variables that exerted the greatest influence on mortality prediction encompassed ferritin, fibrinogen, D-dimer, platelet count, C-reactive protein (CRP), prothrombin time (PT), invasive mechanical ventilation (IMV), PaFi (PaO₂/FiO₂), lactate dehydrogenase (LDH), lymphocyte levels, activated partial thromboplastin time (aPTT), body mass index (BMI), creatinine, and age. These findings underscore XGB as a robust candidate for accurately classifying patients with COVID-19.

SARS-CoV-19 infection provokes a variety of symptoms; most patients present mild/moderate symptoms, whereas a small proportion of patients progress to severe illness with multiorgan failure accompanied by metabolic disturbances requiring ICU-level care. Given the importance of the disease, researchers focused on identifying severity-associated biomarkers in infected patients as well as markers associated with patients suffering long-COVID. However, little is known about the presence of biomarkers that remain a few years after SARS-CoV-2 infection once the patients fully recover of the symptoms. In this study, we evaluated the presence of persistent biomarkers in the nasopharyngeal tract two years after SARS-Cov-2 infection in fully asymptomatic patients, taking into account the severity of their infection (mild/moderate and severe infections). In addition to the direct identification of several components of the Coronavirus Infection Pathway in those individuals that suffered severe infections, we describe herein 371 proteins and their associated canonical pathways that define the different adverse effects of SARS-CoV-2 infections. The persistence of these biomarkers for up to two years after infection, along with their ability to distinguish the severity of the infection endured, highlights the surprising presence of persistent nasopharyngeal exudate changes in fully recovered patients.

Immune memory is essential for the effectiveness of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination. In the current context of the pandemic, with a diminished vaccine efficacy against emerging variants, it remains crucial to perform long-term studies to evaluate the durability and quality of immune responses. Here, we examined the antibody and memory B-cell responses in a cohort of 113 healthcare workers with distinct exposure histories over a 3-year period. Previously infected and naive participants developed comparable humoral responses by 17 months after receiving a full three-dose mRNA vaccination. In addition, both maintained a substantial SARS-CoV-2-reactive memory B-cell pool, associated with a lower incidence of breakthrough infections in naive participants. Of note, previously infected participants developed an expanded SARS-CoV-2-reactive CD27^-CD21^- atypical B-cell population that remained stable throughout the follow-up period. Thus, previous SARS-CoV-2 infection differentially imprints the memory B-cell compartment without compromising the development of long-lasting humoral responses.

The COVID-19 pandemic has underscored the importance of swift responses and the necessity of dependable technologies for vaccine development. Our team previously developed a fast cloning system for the modified vaccinia virus Ankara (MVA) vaccine platform. In this study, we reported on the construction and preclinical testing of a recombinant MVA vaccine obtained using this system. We obtained recombinant MVA expressing the unmodified full-length SARS-CoV-2 spike (S) protein containing the D614G amino-acid substitution (MVA-Sdg) and a version expressing a modified S protein containing amino-acid substitutions designed to stabilize the protein a in a pre-fusion conformation (MVA-Spf). S protein expressed by MVA-Sdg was found to be expressed and was correctly processed and transported to the cell surface, where it efficiently produced cell-cell fusion. Version Spf, however, was not proteolytically processed, and despite being transported to the plasma membrane, it failed to induce cell-cell fusion. We assessed both vaccine candidates in prime-boost regimens in the susceptible transgenic K18-human angiotensin-converting enzyme 2 (K18-hACE2) in mice and in golden Syrian hamsters. Robust immunity and protection from disease was induced with either vaccine in both animal models. Remarkably, the MVA-Spf vaccine candidate produced higher levels of antibodies, a stronger T cell response, and a higher degree of protection from challenge. In addition, the level of SARS-CoV-2 in the brain of MVA-Spf inoculated mice was decreased to undetectable levels. Those results add to our current experience and range of vaccine vectors and technologies for developing a safe and effective COVID-19 vaccine.

Importance

The relevance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF8 in the pathogenesis of COVID-19 is unclear. Virus natural isolates with deletions in ORF8 were associated with wild milder disease, suggesting that ORF8 might contribute to SARS-CoV-2 virulence. This manuscript shows that ORF8 is involved in inflammation and in the activation of macrophages in two experimental systems: humanized K18-hACE2 transgenic mice and organoid-derived human airway cells. These results identify ORF8 protein as a potential target for COVID-19 therapies.

Background

Remdesivir (RDV) was the first antiviral approved for mild-to-moderate COVID-19 and for those patients at risk for progression to severe disease after clinical trials supported its association with improved outcomes. Real-world evidence (RWE) generated by artificial intelligence techniques could potentially expedite the validation of new treatments in future health crises. We aimed to use natural language processing (NLP) and machine learning (ML) to assess the impact of RDV on COVID19-associated outcomes including time to discharge and in-hospital mortality.

Methods

Using EHRead®, an NLP technology including SNOMED-CT terminology that extracts unstructured clinical information from electronic health records (EHR), we retrospectively examined hospitalized COVID-19 patients with moderate-to-severe pneumonia in three Spanish hospitals between January 2021 and March 2022. Among RDV eligible patients, treated (RDV+) vs untreated (RDV‒) patients were compared after propensity score matching (PSM; 1:3.3 ratio) based on age, sex, Charlson comorbidity index, COVID-19 vaccination status, other COVID-19 treatment, hospital, and variant period. Cox proportional hazards models and Kaplan-Meier plots were used to assess statistical differences between groups.

Results

Among 7,651,773 EHRs from 84,408 patients, 6,756 patients were detected with moderate-to-severe COVID-19 pneumonia during the study period. The study population was defined with 4,882 (72.3%) RDV eligible patients. The median age was 72 years and 57.3% were male. A total of 812 (16.6%) patients were classified as RDV+ and were matched to 2,703 RDV‒ patients (from a total of 4,070 RDV‒). After PSM, all covariates had an absolute mean standardized difference of less than 10%. The hazard ratio for in-hospital mortality at 28 days was 0.73 (95% confidence interval, CI, 0.56 to 0.96, p = 0.022) with RDV‒ as the reference group. Risk difference and risk ratio at 28 days was 2.7% and 0.76, respectively, both favoring the RDV+ group. No differences were found in length of hospital stay since RDV eligibility between groups.

Conclusions

Using NLP and ML we were able to generate RWE on the effectiveness of RDV in COVID-19 patients, confirming the potential of using this methodology to measure the effectiveness of treatments in pandemics. Our results show that using RDV in hospitalized patients with moderate-to-severe pneumonia is associated with significantly reduced inpatient mortality. Adherence to clinical guideline recommendations has prognostic implications and emerging technologies in identifying eligible patients for treatment and avoiding missed opportunities during public health crises are needed.

Abstract

Autopsy followed by histopathological examination is foundational in clinical and forensic medicine for discovering and understanding pathological changes in disease, their underlying processes, and cause of death. Imaging technology has become increasingly important for advancing clinical research and practice, given its noninvasive, in vivo and ex vivo applicability. Medical and forensic autopsy can benefit greatly from advances in imaging technology that lead toward minimally invasive, whole-brain virtual autopsy. Brain autopsy followed by histopathological examination is still the hallmark for understanding disease and a fundamental modus operandi in forensic pathology and forensic medicine, despite the fact that its practice has become progressively less frequent in medical settings. This situation is especially relevant with respect to new diseases such as COVID-19 caused by the SARS-CoV-2 virus, for which our neuroanatomical knowledge is sparse. In this narrative review, we show that ad hoc clinical autopsies and histopathological analyses combined with neuroimaging of the principal circumventricular organs are critical to gaining insight into the reconstruction of the pathophysiological mechanisms and the explanation of cause of death (ie, atrium mortis) related to the cardiovascular effects of SARS-CoV-2 infection in forensic and clinical medicine.

Background

Epigenetics and clinical observations referring to Betacoronavirus lead to the conjecture that Sarbecovirus may have the ability to infect lymphocytes using a different way than the spike protein. In addition to inducing the death of lymphocytes, thus drastically reducing their population and causing a serious immune deficiency, allows it to remain hidden for long periods of latency using them as a viral reservoir in what is named Long-Covid Disease. Exploring possibilities, the hypothesis is focused on that N protein may be the key of infecting lymphocytes.

Method

The present article exhibits a computational assay for the latest complete sequences reported to GISAID, correlating N genotypes with an enhancement in the affinity of the complex that causes immune deficiency in order to determine a good docking with the N protein and some receptors in lymphocytes.

Results

A novel high-interaction coupling of N-RBD and CD147 is presented as the main way of infecting lymphocytes, allowing to define those genotypes involved in their affinity enhancement.

Conclusion

The hypothesis is consistent with the mutagenic deriving observed on the in-silico assay, which reveals that genotypes N/120 and N/152 are determinant to reduce the Immune Response of the host infecting lymphocytes, allowing the virus persists indefinitely and causing an Acquire Immune Deficiency Syndrome.

Background

Up to 30% of people infected with SARS-CoV-2 report disabling symptoms 2 years after the infection. Over 100 persistent symptoms have been associated with Post-Acute COVID-19 Symptoms (PACS) and/or long-COVID, showing a significant clinical heterogeneity. To develop effective, patient-targeted treatment, a better understanding of underlying mechanisms is needed. Epigenetics has helped elucidating the pathophysiology of several health conditions and it might help unravelling inter-individual differences in patients with PACS and long-COVID. As accumulating research is exploring epigenetic mechanisms in PACS and long-COVID, we systematically summarized the available literature on the topic.

Methods

We interrogated five databases (Medline, Embase, Web of Science, Scopus and medXriv/bioXriv) and followed PRISMA and SWiM guidelines to report our results.

Results

Eight studies were included in our review. Six studies explored DNA methylation in PACS and/or long-COVID, while two studies explored miRNA expression in long-COVID associated with lung complications. Sample sizes were mostly small and study quality was low or fair. The main limitation of the included studies was a poor characterization of the patient population that made a homogeneous synthesis of the literature challenging. However, studies on DNA methylation showed that mechanisms related to the immune and the autonomic nervous system, and cell metabolism might be implicated in the pathophysiology of PACS and long-COVID.

Conclusion

Epigenetic changes might help elucidating PACS and long-COVID underlying mechanisms, aid subgrouping, and point towards tailored treatments. Preliminary evidence is promising but scarce. Biological and epigenetic research on long-COVID will benefit millions of people suffering from long-COVID and has the potential to be transferable and benefit other conditions as well, such as Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). We urge future research to employ longitudinal designs and provide a better characterization of included patients.

Background/Objectives: The clinical forms of coronavirus disease 2019 (COVID-19) vary widely in severity, ranging from asymptomatic or moderate cases to severe pneumonia that can lead to acute respiratory failure, acute respiratory distress syndrome, multiple organ dysfunction syndrome, and death. Our main objective was to determine the prevalence of bacterial and fungal secondary infections in an intensive care unit (ICU). Secondary objectives included analyzing the impact of these infections on mortality and medical resource utilization, as well as assessing antimicrobial resistance in this context. Methods: We conducted a retrospective cohort study that included critically ill severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) patients treated in an ICU and analyzed the prevalence of co-infections and superinfections. Results: A multivariate analysis of mortality found that the presence of superinfections increased the odds of death by more than 15-fold, while the Sequential Organ Failure Assessment (SOFA) score and C-reactive protein (adjusted for confounders) increased the odds of mortality by 51% and 13%, respectively. The antibiotic resistance profile of microorganisms indicated a high prevalence of resistant strains. Carbapenems, glycopeptides, and oxazolidinones were the most frequently used classes of antibiotics. Among patients, 27.9% received a single antibiotic, 47.5% received two from different classes, and 24.4% were treated with three or more. Conclusions: The incidence and spectrum of bacterial and fungal superinfections are higher in critically ill ICU patients, leading to worse outcomes in COVID-19 cases. Multidrug-resistant pathogens present significant challenges for ICU and public health settings. Early screening, accurate diagnosis, and minimal use of invasive devices are essential to reduce risks and improve patient outcomes.

The gut microbiota plays a key role in shaping immune responses, including those induced by vaccination. Its impact on the humoral response to mRNA-based SARS-CoV-2 vaccines, however, remains underexplored. We analyzed gut microbiota composition and anti-Spike (S) IgG levels in 50 healthcare workers vaccinated with the mRNA-1273 SARS-CoV-2 vaccine. Participants were stratified into low, medium, and high responders based on IgG titers 30 days post-vaccination. Stool samples were collected at baseline, and 16 S rRNA sequencing was used to assess microbiota diversity and taxonomic profiles. Alpha diversity indices showed no significant differences across response groups. However, specific microbial signatures were associated with vaccine response. Higher relative abundance of Clostridia, Clostridiales, Ruminococcaceae, and Odoribacter splanchnicus correlated with stronger IgG responses. Functional microbiome analysis revealed enrichment of acetate-producing pathways in high responders (p = 0.012), suggesting a role for short-chain fatty acids in enhancing vaccine-induced immunity. Logistic regression and Random Forest models identified these taxa as predictors of strong antibody responses. The area under the ROC curve (AUC) for individual taxa ranged from 0.70 to 0.76, indicating moderate predictive performance. Conversely, taxa such as Hallella and Sutterella wadsworthensis were linked to lower responses. These findings support a modulatory role of the gut microbiota in mRNA vaccine immunogenicity and highlight microbial metabolic functions as potential targets to boost vaccine efficacy in personalized immunization strategies.

Background

Understanding the COVID-19 patient characteristics that impact environmental SARS-CoV-2 load is essential for improving infection risk management. In this study, we analyzed the influence of patient variables on airborne SARS-CoV-2 genome detection.

Methods

Sixty-nine COVID-19 patients were recruited across three independent studies with airborne SARS-CoV-2 genome assessed in individual hospital rooms using droplet digital PCR.

Results

In the bivariate analysis, the odds of airborne SARS-CoV-2 detection were significantly higher for patients with obesity, chronic respiratory diseases, pneumonia at admission, sampling, and discharge, and lower lymphocytes count. No significant associations were found between airborne SARS-CoV-2 detection and symptoms presence or duration, nor with the results of the most recent positive nasopharyngeal PCR test prior to air sampling. In the multivariate analysis, the best-fit model included patient age, type of admission, and symptoms duration. Patient age significantly contributed to the risk of airborne SARS-CoV-2 detection in the multivariate analysis.

Conclusions

Our findings highlight the variability in individual responses to SARS-CoV-2 infection and suggest that factors linked to COVID-19 severity, symptomatology, and immunocompetence influence the airborne SARS-CoV-2 detection. Our results may support the development of more precise preventive measures in healthcare settings.

Protein kinase R (PKR) expression is induced by interferons. This protein is activated by double-stranded (ds) RNAs or RNAs containing duplex regions, produced after different stimuli, such as after viral infections, leading to the phosphorylation of the eukaryotic translation initiation factor 2α (eIF2α), and subsequently inhibiting cellular and viral protein translation. This function may lead to different effects such as to impairing the replication of RNA viruses by inhibiting viral protein translation, and to modulating the innate immune responses after viral infections by affecting the translation of effector proteins. In this work, we identify, for the first time, an interaction of IFN alpha inducible protein 27 (IFI27) with PKR-activating protein (PACT or PRKRA) and with PKR, showing that the interaction of IFI27 with PACT is likely mediated by dsRNAs or RNAs containing duplex regions, and that the interaction of IFI27 with PKR is PACT-dependent. Interestingly, using IFI27 knocked-down, knocked-out and overexpressing tumour-derived, established cells, we show that these interactions trigger a potentiation of the activity of PKR and, therefore, a decrease in protein translation. Moreover, we find that IFI27 increases PKR function in cells infected with different RNA viruses such as Severe Acute Respiratory virus 2 (SARS-CoV-2), and Vesicular Stomatitis virus (VSV), and in cells transfected with the dsRNA analog poly(I:C), suggesting a broad effect of IFI27 on PKR activation. Moreover, we show that IFI27 expression increases the formation of stress granules (SGs) at the cell cytoplasm, correlating with the increased PKR activation mediated by IFI27, as it has been shown that the translational arrest induced by activated PKR leads to the formation of SGs. Mechanistically, we describe that this ability of IFI27 to activate PKR is dependent on its interaction with PACT. Further understanding of the regulation of PKR activity will allow us to develop new antiviral drugs to modulate this signalling axis, which is crucial in RNA virus infections.

Vaccines are a fundamental public health tool, particularly effective in preventing respiratory infections. Their importance is amplified in patients with chronic respiratory diseases, who are more susceptible to acute infections such as influenza, pneumococcus, COVID-19, respiratory syncytial virus (RSV), pertussis, and herpes zoster. These individuals face an increased risk of severe infections, exacerbations, hospitalizations, and mortality. Vaccination against influenza, pneumococcus, and SARS-CoV-2 significantly reduces these adverse outcomes. Evidence also supports the use of vaccines against RSV, pertussis, and herpes zoster in this population. In specific cases, tailored immunization strategies are warranted. The Spanish Society of Pulmonology and Thoracic Surgery (SEPAR) strongly advocates for systematic vaccination in patients with chronic respiratory diseases. This document provides clear and up-to-date recommendations based on the available evidence to support clinical practice and standardize vaccination strategies. These recommendations aim to reduce complications, improve quality of life, and enhance public health outcomes in this vulnerable population.

Introduction

One of the causes of congenital hearing loss are infections suffered by the mother during pregnancy. The objective of this study was to investigate the effects on hearing in newborns to SARS-CoV-2 seropositive mothers during pregnancy. We also studied the hearing impact in the first year of life of the newborns to investigate whether neonatal infection produced a risk of infantile sensorineural hearing loss.

Material and methods

All children born in our center whose mother had been infected with SARS-CoV-2 positive COVID were included and were audiologically studied at two and a half months and at one year of life. All infants were evaluated by brainstem evoked response audiometry (BERA) and auditory steady-state responses (ASSR).

Results

The range of the latencies for BERA founded were inside the desired ranges of normality both at two and a half months and at one year of life No significant differences by sex and ears were found in the BERA performed (p > 0,05). The mean ASSR values were found to be significantly below 30 dB in all frequencies studied both at two and a half months, and at one year of life (p < 0,05).

Conclusion

There is no association between COVID-19 infection during pregnancy and neonatal hearing loss. Further studies are needed to clarify this field since it is still unclear whether pregnant women infected with SARS-CoV-2 can produce hearing alterations in their newborns according to the current evidence in the literature.

Introduction

As the SARS-CoV-2 virus continues to evolve and new variants emerge, it becomes crucial to understand the comparative pathological and immunological responses elicited by different strains. This study focuses on the original Wuhan strain and the Omicron variant, which have demonstrated significant differences in clinical outcomes and immune responses.

Methods

We employed ferrets as an experimental model to assess the D614G variant (a derivative of the Wuhan strain) and the Omicron BA.5 variant. Each variant was inoculated into separate groups of ferrets to compare disease severity, viral dissemination, and immune responses.

Results

The D614G variant induced more severe disease and greater viral spread than the Omicron variant. Notably, ferrets infected with the D614G variant exhibited a robust neutralizing antibody response, whereas those infected with the Omicron variant failed to produce a detectable neutralizing antibody response. Despite the clearance of the virus from nearly all tissues by 7 days post-infection, an increase in pathological lesions was observed from 14 to 21 days, particularly in those infected with the D614G variant, suggesting a sustained immune response even after viral clearance.

Discussion

These findings underscore the adaptability of SARS-CoV-2 and illuminate how susceptibility and clinical manifestations vary across different strains and species. The results emphasize the necessity of considering both the direct effects of viral infection and the indirect, often prolonged, impacts of the immune response in evaluating the outcomes of SARS-CoV-2 infections.

This study aimed to investigate the association between saliva soluble angiotensin-converting enzyme 2 (sACE2) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adults. We selected a convenience sample of adults with post-acute SARS-CoV-2 infection and their household children living in quarantined family households of the metropolitan Barcelona region (Spain) during the spring 2020 pandemic national lockdown. Participants were tested for saliva sACE2 quantification by western blot and nasopharyngeal SARS-CoV-2 RT-PCR detection. A total of 161 saliva samples [82 (50.9%) from children; 79 (49.1%) from females] yielded valid western blot and RT-PCR results. Saliva sACE2 was detected in 79 (96.3%) children and 76 (96.2%) convalescent adults. Twenty (24.4%) children and 20 (25.3%) convalescent adults were positive for SARS-CoV-2 in nasopharynx by RT-PCR. SARS-CoV-2 RT-PCR-negative children had a significantly higher mean proportional level of saliva sACE2 (0.540 × 10^-3%) than RT-PCR-positive children (0.192 × 10^-3%, p < 0.001) and convalescent adults (0.173 × 10^-3%, p < 0.001). In conclusion, children negative for nasopharyngeal SARS-CoV-2 RT-PCR appear to exhibit a higher concentration of saliva sACE2 than SARS-CoV-2 RT-PCR-positive children and convalescent adults. Release of adequate levels of sACE2 in saliva could play a protective role against SARS-CoV-2.

Background

This study aimed to validate the role of the D-dimer to lymphocyte ratio (DLR) for mortality prediction in a large national cohort of hospitalized coronavirus disease 2019 (COVID-19) patients.

Methods

A retrospective, multicenter, observational study that included hospitalized patients due to SARS-CoV-2 infection in Spain was conducted from March 2020 to March 2022. All biomarkers and laboratory indices analyzed were measured once at admission.

Results

A total of 10,575 COVID-19 patients were included in this study. The mean age of participants was 66.9 (±16) years, and 58.6% (6202 patients) of them were male. The overall mortality rate was 16.3% (n = 1726 patients). Intensive care unit admission was needed in 10.5% (n = 1106 patients), non-invasive mechanical ventilation was required in 8.8% (n = 923 patients), and orotracheal intubation was required in 7.5% (789 patients). DLR presented a c-statistic of 0.69 (95% CI, 0.68-0.71) for in-hospital mortality with an optimal cut-off above 1. Multivariate analysis showed an independent association for in-hospital mortality for DLR > 1 (adjusted OR 2.09, 95% CI 1.09-4.04; p = 0.03); in the same way, survival analysis showed a higher mortality risk for DLR > 1 (HR 2.24; 95% CI 2.03-2.47; p < 0.01). Further, no other laboratory indices showed an independent association for mortality in multivariate analysis.

Conclusions

This study confirmed the usefulness of DLR as a prognostic biomarker for mortality associated with SARS-CoV-2 infection, being an accessible, cost-effective, and easy-to-use biomarker in daily clinical practice.

Research publications aimed at understanding the various aspects of Coronaviruses, particularly COVID-19, have significantly shaped our knowledge base. While the urgency to monitor COVID-19 in real-time has decreased, the continual influx of new research of monthly articles underscores the importance of systematic review and analysis to deepen our understanding of the pandemic's broad impact. To explore research trends and innovations in this space, we developed a pipeline using natural language processing techniques. This pipeline systematically catalogues and synthesises the vast array of research articles, leading to the creation of a dataset with more than eight hundred thousand articles from July 2002 to May 2024. This paper describes the content of this dataset and provides the necessary information to make this dataset accessible and reusable for future research. Our approach aggregates and organises global research related to Coronaviruses into thematic clusters such as vaccine development, public health strategies, infection mechanisms, mental health issues, and economic consequences. Also, we have leveraged the contribution of health experts to review and revise the dataset.

Introduction

Solid organ transplant (SOT) recipients display weak seroconversion and neutralizing antibody (NAb) responses after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination and remain at risk of severe coronavirus disease 2019 (COVID-19). While B-cell memory is the hallmark of serological immunity, its role in driving successful vaccine responses and providing immune protection in SOT patients remains unclear.

Methods

We investigated the function and interplay of SARS-CoV-2-specific memory B cells (mBc), different cytokineproducing T cells, and cross-reactive NAb in driving seroconversion and protection against COVID-19 in two cohorts. First, we studied a large cohort of 148 SOT recipients and 32 immunocompetent individuals who underwent several vaccinations. Subsequently, we assessed 25 SOT patients participating in a randomized controlled trial to compare two different immunosuppressive strategies for allowing successful seroconversion and memory-cell responses after booster vaccination.

Results

We corroborate previous findings that B- and T-cell memory responses are weaker and more delayed in SOT patients than in immunocompetent (IC) individuals; however, within the SOT cohort, we found that these responses are relatively stronger and more robust in patients not receiving mycophenolate mofetil (MMF)-based therapies. Anti- spike IgG titers strongly correlated with RBD-specific IgG-producing mBc, with both displaying broad viral cross reactivity. Prebooster SARS-CoV-2-specific mBc and IL-2- producing T cells accurately predicted Nab seroconversion (AUC, 0.828) and protection against severe COVID-19. While switching unresponsive SOT patients from calcineurin inhibitors (CNI)/MMF to a low-exposure CNI/mTOR-i regimen favored wider SARS-CoV-2-specific immune responses after a fourth booster vaccination, preformed RBD-specific mBc predicted NAb seroconversion.

Discussion

Our study adds new insights into the pathobiology of immune memory and highlights the pivotal role of SARS-CoV-2-specific mBc in promoting immune protection inSOT patients.

In a patient on immunosuppressant treatment, SARS-CoV-2 RNA was documented in different extra-respiratory samples over several months in the absence of positive determinations in upper respiratory samples. Whole-genome sequencing of these samples showed the acquisition of different single-nucleotide polymorphisms over time, suggesting viral evolution and thus viral viability.

Aim

This study aims to investigate the influence of fatigue and mood disturbances in Spanish long-COVID patients and to establish relationships between these factors and other clinical manifestations.

Method

A descriptive correlational study was conducted using a self-administered online questionnaire. The sample was obtained through non-random convenience sampling, comprising 374 participants from various regions of Spain. Data collection occurred between July 2, 2022, and November 30, 2022. The questionnaire collected demographic information and inquired about symptomatology as well as self-perception of health status. Validated scales, namely the Fatigue Severity Scale (FSS) and the Scale for Mood Assessment (EVEA), were utilized.

Results

The non-random sample consisted of 374 participants from diverse regions of Spain, of whom 79.9% were women. Over 70% of participants reported fatigue, while the EVEA revealed high scores in sadness-depression (4.94 ± 2.82) and anxiety (4.57 ± 2.88). Significant relationships were identified between fatigue and mood disturbances and neurological, psychological, locomotive, and pain symptoms.

Conclusions

Given the impact of the syndrome on psychological, social and economic spheres, regular monitoring of patients with long COVID is crucial. This study corroborates previous research findings and is notable for demonstrating the persistence of symptoms for over a year. Mood disorders, such as anxiety and depression, are closely related to physical symptoms, highlighting the need for holistic healthcare approaches.

Abstract

Endotheliopathy has been increasingly recognized as a key feature of critical illness. Different diseases and syndromes manifest endothelial dysfunction in their severe forms. Septic syndrome, SARS-CoV-2 disease spectrum, and cell therapy-associated toxicities represent paradigmatic examples of endotheliopathy, in intensive care units. As common features, and in response to the environment associated with these conditions, endothelial cells develop a proinflammatory and prothrombotic phenotype, switching its secretion behavior of anticoagulant and profibrinolytic factors toward a hypercoagulative and hypofibrinolytic state. Intravascular microthrombi, release of neutrophil extracellular traps, detached endothelial cells, and exposure of a highly reactive extracellular matrix toward platelets result in turbulent blood flow and agglutination of circulating cells, ultimately leading to tissue hypoperfusion. Levels of endothelial damage biomarkers correlate with disease severity and, therefore, implementation of biomarkers panels could enhance prediction, differential diagnosis, and severity stratification in critical illness conditions. Development of strategies to protect the endothelium could mitigate proinflammatory and procoagulant responses, offering therapeutic potential for the endotheliopathy-associated conditions of critically ill patients.

Background: IgG4 is the least immunogenic subclass of IgG. Immunization with mRNA vaccines against SARS-CoV-2, unlike other vaccines, induces an increase in IgG4 against the spike protein in healthy populations. This study investigated whether immunosuppressive therapy affects the immune response, focusing on IgG subclass changes, to four doses of mRNA vaccine in kidney transplant recipients (KTRs). Methods: This study includes 146 KTRs and 23 dialysis patients (DPs) who received three mRNA-1273 vaccine doses and a BNT162b2 booster. We evaluated anti-spike IgG titers and subclasses, T-CD4+ and T-CD8+ cellular responses, and serum neutralizing activity (SNA). Results: At the fourth dose, 75.8% of COVID-19 naïve KTRs developed humoral and cellular responses (vs. 95.7% in DPs). There was a correlation between anti-spike IgG titers/subclasses and SNA (p < 0.001). IgG subclass kinetics after the third/fourth dose differed between COVID-19 naïve KTRs and DPs. Immunosuppressive therapy influenced IgG subclasses: mTOR inhibitors (mTORi) positively influenced IgG1 and IgG3 (p < 0.05), while mycophenolic acid negatively affected IgG1, IgG3, and IgG4 (p < 0.05). SNA is correlated with breakthrough infections after four doses of vaccine in KTRs. mTORi was the only factor associated with SNA > 65% in naïve KTRs [4.29 (1.21-15.17), p = 0.024]. Conclusions: KTRs show weaker cellular and humoral immune responses to mRNA vaccines and a class shift towards non-inflammatory anti-S IgG4 upon booster doses. IgG subclasses show a positive correlation with SNA and are influenced by immunosuppression. Increased SNA after four doses of vaccine is protective against infection. mTORi may benefit non-responding KTRs.

Objective

The aim of this study was to evaluate humoral and cellular immune responses in people living with HIV (PLWH) following successive COVID-19 vaccine booster doses, to determine immune correlates associated with clinical outcomes (avoiding severe infections) and epidemiological impacts (preventing new infections), a topic of growing controversy in this vulnerable population.

Methods

A prospective study followed 151 PLWH on suppressive antiretroviral therapy who completed initial COVID-19 vaccination and received two additional vaccine doses. The study evaluated changes in SARS-CoV-2-specific antibodies, SARS-CoV-2-ACE2 binding inhibition rates, spike-specific memory B cells, and CD4/CD8 cell responses to variants (Ancestral, Delta, and Omicron), considering initial vaccine type, prior infections, and levels of immunosuppression.

Results

Vaccine doses progressively enhanced antibody levels, memory B cells, and T-cell responses. PLWH with CD4 counts ≤350 cells/mm³ showed impaired memory B cell production vs. those with CD4 >500 cells/mm³ after the third dose (0.39% [0.29-0.55] vs. 0.68% [0.49-0.86]; p < 0.001). Immune responses remained consistent across variants. Non-infected PLWH receiving plasmid vector vaccines demonstrated lower antibody levels against Delta and Omicron (10 930 ng/mL [9623-12 511] vs. 13 340 ng/mL [10 602-14 724], p 0.018; 399 ng/mL [335-702] vs. 615 ng/mL [492-924], p 0.041) compared with infected PLWH. IgA-producing memory B cells increased after the third booster, particularly with mRNA vaccines (0.05% [0.0-0.09] vs. 0.11 [0.07-0.17], p < 0.001 in non-infected individuals). Post-booster infection rates were higher in previously uninfected individuals (25% vs. 4% after the second booster, p < 0.001), especially among vector vaccine recipients (34.6% vs. 14.5%, p 0.028).

Discussion

This study reveals that successive vaccine doses significantly enhance immune responses in PLWH, improving antibody levels, IgA⁺ memory B cells, and T-cell responses, thereby reducing the risk of severe infections and potentially new infections. Nevertheless, low CD4 counts result in reduced memory B cells, necessitating tailored vaccination strategies. mRNA vaccines also offer superior protection against breakthrough infections during variant surges.

The current clinical management of SARS-CoV-2 disease control and immunity may be not optimal anymore. Reverse transcription polymerase chain reaction (RT-PCR) of genomic viral RNA is broadly used for diagnosis, even though the virus may still be detectable when it is already non-infectious. Regarding serology, commercial assays mostly still rely on ancestral spike detection despite significant changes in the genetic sequence of the current circulating variants. We followed a group of 105 non-vaccinated individuals, measuring their viral shedding until negativity and antibody response up to six months. The mean viral detection period until a negative RT-PCR result was 2.2 weeks when using subgenomic RNA-E as a detection target, and 5.2 weeks when using genomic RNA as a detection target. Our neutralising antibody results suggest that, when challenged against a variant different from the variant of first exposure, commercial immunoassays are suboptimal at predicting the neutralising capacity of sera. Additionally, anti-Alpha and anti-Delta antibodies showed very low cross-reactivity between variants. This study provides insights into viral shedding and immune response in pre-Omicron variants like Alpha and Delta, which have been understudied in the published literature. These conclusions point to potential improvements in the clinical management of SARS-CoV-2 cases in order to organise vaccination campaigns and select monoclonal antibody treatments.

Background

Long-COVID has mostly been investigated in clinical settings. We aimed to assess the risk, subtypes, persistence, and determinants of long-COVID in a prospective population-based study of adults with a history of SARS-CoV-2 infection in Catalonia.

Methods

We examined 2764 infected individuals from a population-based cohort (COVICAT) established before the pandemic and followed up three times across the pandemic (2020, 2021, 2023). We assessed immunoglobulin (Ig)G levels against SARS-CoV-2, clinical, vaccination, sociodemographic, and lifestyle factors. Long-COVID risk and subtypes were defined based on participant-reported symptoms and electronic health records. We identified a total of 647 long-COVID cases and compared them with 2117 infected individuals without the condition.

Results

Between 2021 and 2023, 23% of infected subjects developed long-COVID symptoms. In 56% of long-COVID cases in 2021, symptoms persisted for 2 years. Long-COVID presented clinically in three subtypes, mild neuromuscular, mild respiratory, and severe multi-organ. The latter was associated with persistent long-COVID. Risk was higher among females, participants under 50 years, of low socioeconomic status, severe COVID-19 infection, elevated pre-vaccination IgG levels, obesity, and prior chronic disease, particularly asthma/chronic obstructive pulmonary disease and mental health conditions. A lower risk was associated to pre-infection vaccination, infection after omicron became the dominant variant, higher physical activity levels, and sleeping 6-8 h. Vaccination during the 3 months post-infection was also protective against long-COVID.

Conclusions

Long-COVID persisted for up to 2 years in half of the cases, and risk was influenced by multiple factors.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the causative agent of the recent COVID-19 pandemic, continues representing one of the main health concerns worldwide. Autophagy, in addition to its role in cellular homeostasis and metabolism, plays an important part for the host antiviral immunity. However, viruses including SARS-CoV-2 have evolved diverse mechanisms to not only overcome autophagy's antiviral pressure but also manipulate its machinery in order to enhance viral replication and propagation. Here, we discuss our current knowledge on the impact that autophagy exerts on SARS-CoV-2 replication, as well as the different counteracting measures that this virus has developed to manipulate autophagy's complex machinery. Some of the elements regarding this interplay may become future therapeutic targets in the fight against SARS-CoV-2.

Heterologous vaccines, which induce immunity against several related pathogens, can be a very useful and rapid way to deal with new pandemics. In this study, the potential impact of licensed COVID-19 vaccines on cytotoxic and helper cell immune responses against Khosta-2, a novel sarbecovirus that productively infects human cells, was analyzed for the 567 and 41 most common HLA class I and II alleles, respectively. Computational predictions indicated that most of these 608 alleles, covering more than 90% of the human population, contain sufficient fully conserved T-cell epitopes between the Khosta-2 and SARS-CoV-2 spike-in proteins. Ninety percent of these fully conserved peptides for class I and 93% for class II HLA molecules were verified as epitopes recognized by CD8⁺ or CD4⁺ T lymphocytes, respectively. These results show a very high correlation between bioinformatic prediction and experimental assays, which strongly validates this study. This immunoinformatics analysis allowed a broader assessment of the alleles that recognize these peptides, a global approach at the population level that is not possible with experimental assays. In summary, these findings suggest that both cytotoxic and helper cell immune protection elicited by currently licensed COVID-19 vaccines should be effective against Khosta-2 virus infection. Finally, by being rapidly adaptable to future coronavirus pandemics, this study has potential public health implications.

Coronavirus disease 2019 (COVID-19) has been a major public health burden. We hypothesised that circulating extracellular vesicles (cEVs), key players in health and disease, could trace the cell changes during COVID-19 infection and recovery. Therefore, we studied the temporal trend of cEV and inflammatory marker levels in plasma samples of COVID-19 patients that were collected within 24 h of patient admission (baseline, n = 80) and after hospital discharge at day-90 post-admission (n = 59). Inflammatory markers were measured by standard biochemical methods. cEVs were quantitatively and phenotypically characterized by high-sensitivity nano flow cytometry. In patients recovered from COVID-19 lower levels of inflammatory markers were detected. cEVs from vascular (endothelial cells) and blood (platelets, distinct immune subsets) cells were significantly reduced at day-90 compared to admission levels, a pattern also observed for cEVs from progenitor, perivascular and epithelial cells. The best discriminatory power for COVID-19 severity was found for inflammatory markers lactate dehydrogenase and neutrophil-to-lymphocyte ratio and for granulocyte/macrophage-released CD66b⁺/CD68⁺-cEVs. Albeit inflammatory markers were good indicators of systemic inflammatory response and discriminators of COVID-19 remission, they do not completely reveal cell stress and organ damage states. cEVs reaching baseline pre-infection levels at 90 days post-infection in recovered patients discriminate parental cells affected by disease.

Despite multiple research efforts to characterize coronavirus disease 2019 (COVID-19) in humans, there is no clear data on the specific role of mucosal immunity on COVID-19 disease. Here, we longitudinally profile the antibody response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and seasonal HCoV-OC43 S proteins in serum and nasopharyngeal swabs from COVID-19 patients. Results showed that specific antibody responses against SARS-CoV-2 and HCoV-OC43 S proteins can be detected in the upper respiratory tract. We found that COVID-19 patients mounted a robust mucosal antibody response against SARS-CoV-2 S with specific secretory immunoglobulin A (sIgA), IgA, IgG, and IgM antibody subtypes detected in the nasal swabs. Additionally, COVID-19 patients showed IgG, IgA, and sIgA responses against HCoV-OC43 S in the local mucosa, whereas no specific IgM was detected. Interestingly, mucosal antibody titers against SARS-CoV-2 peaked at day 7, whereas HCoV-OC43 titers peaked earlier at day 3 post-recruitment, suggesting an immune memory recall to conserved epitopes of beta-HCoVs in the upper respiratory tract.

Background

The spread of SARS-CoV-2 has been influenced by multiple factors, from the inherent transmission capabilities of the different variants to the control measurements put in place. Understanding how new variants enter a country is essential for managing future outbreaks. This study investigates how three major variants-Alpha, Delta, and Omicron (BA.1)-entered Spain and how different restrictions potentially affected their introduction.

Methods

We collected Spanish and international SARS-CoV-2 genomes from the GISAID database. Leveraging connectivity data from different countries with Spain, we performed a phylodynamic Bayesian analysis of the SARS-CoV-2 introductions into Spain.

Results

Most introductions of the Alpha variant originated from France. As travel restrictions eased, the number of introductions from different countries increased. During the Delta and Omicron waves, the United Kingdom and Germany became important sources of the virus. The highest number of introductions occurred during the Delta wave, coinciding with fewer travel restrictions and the summer season, when Spain receives a considerable number of tourists.

Conclusions

Our findings highlight the role of international travel in the spread of new variants. They underscore the importance of monitoring travel patterns and implementing targeted public health measures to manage the spread of SARS-CoV-2.

Background

Demonstrating the capability to isolate biological material from the environment was fundamental to supporting any transmission route. Various and inconsistent methodologies have been used to address this issue; however, the debate in scientific societies about the possibility of airborne transmission as a source of SARS-CoV-2 spread remained open.

Objective

To analyze SARS-CoV-2 contamination in the air and on surfaces in a hospital setting during the COVID-19 pandemic.

Methods

This study involved air and surface sampling in the emergency, hospitalization, and intensive care unit areas of the Ramón y Cajal University Hospital. A consistent methodology was used for all samples, and clinical and environmental parameters and characterization of each location were recorded.

Results

A total of 234 samples were collected, comprising 160 surface samples and 74 air samples, of which 6.84 % tested positive (13/160 surface samples and 3/74 air samples). High-contact surfaces had the highest proportion of positive samples (12/13). All positive air samples were identified within 2 m of patients who had recently developed symptoms (<5 days). High dependency and elevated temperatures seemed to indicate a higher risk of environmental biocontamination. Additionally, there was a higher risk of contamination in the intensive care units than in the hospitalization or emergency units.

Aprotinin is a broad-spectrum inhibitor of human proteases that has been approved for the treatment of bleeding in single coronary artery bypass surgery because of its potent antifibrinolytic actions. Following the outbreak of the COVID-19 pandemic, there was an urgent need to find new antiviral drugs. Aprotinin is a good candidate for therapeutic repositioning as a broad-spectrum antiviral drug and for treating the symptomatic processes that characterise viral respiratory diseases, including COVID-19. This is due to its strong pharmacological ability to inhibit a plethora of host proteases used by respiratory viruses in their infective mechanisms. The proteases allow the cleavage and conformational change of proteins that make up their viral capsid, and thus enable them to anchor themselves by recognition of their target in the epithelial cell. In addition, the activation of these proteases initiates the inflammatory process that triggers the infection. The attraction of the drug is not only its pharmacodynamic characteristics but also the possibility of administration by the inhalation route, avoiding unwanted systemic effects. This, together with the low cost of treatment (≈2 Euro/dose), makes it a good candidate to reach countries with lower economic means. In this article, we will discuss the pharmacodynamic, pharmacokinetic, and toxicological characteristics of aprotinin administered by the inhalation route; analyse the main advances in our knowledge of this medication; and the future directions that should be taken in research in order to reposition this medication in therapeutics.

The pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 instigated the most serious global health crisis. Clinical presentation of COVID-19 frequently includes severe neurological and neuropsychiatric symptoms. However, it is presently unknown whether and to which extent pathological impairment of blood-brain barrier (BBB) contributes to the development of neuropathology during COVID-19 progression. In the present study, we used human induced pluripotent stem cells-derived brain endothelial cells (iBECs) to study the effects of blood plasma derived from COVID-19 patients on the BBB integrity in vitro. We also performed a comprehensive analysis of the cytokine and chemokine profiles in the plasma of COVID-19 patients, healthy and recovered individuals. We found significantly increased levels of interferon γ-induced protein 10 kDa, hepatocyte growth factor, and interleukin-18 in the plasma of COVID-19 patients. However, blood plasma from COVID-19 patients did not affect transendothelial electrical resistance in iBEC monolayers. Our results demonstrate that COVID-19-associated blood plasma inflammatory factors do not affect BBB paracellular pathway directly and suggest that pathological remodeling (if any) of BBB during COVID-19 may occur through indirect or yet unknown mechanisms.

Background: COVID-19, caused by SARS-CoV-2, has posed significant challenge to global healthcare systems, necessitating reliable biomarkers to predict disease severity and mortality. This systematic review and meta-analysis evaluated the prognostic value of novel biomarkers in COVID-19 patients. The aim of this study was to identify and prioritize the most prognostically relevant novel biomarkers associated with COVID-19 outcomes. Methods: We conducted a systematic review and meta-analysis of the available evidence. A systematic search of PubMed and Web of Science was performed to identify studies on the COVID-19 biomarkers. Observational studies that compared poor (severe disease/mortality) and good outcomes were included. For continuous measures, standard mean differences (SMDs) with 95% confidence intervals (CIs) were calculated. Pooled sensitivity, specificity, diagnostic odds ratio (DOR), and summary receiver operating characteristic (SROC) curve analyses for the biomarkers were used. The risk of bias was assessed using the Newcastle-Ottawa scale. Results: Of the 2907 screened studies, 38 were included (21 in the meta-analysis). MR-proADM showed higher levels of prediction for poor outcomes (SMD = 1.40, 95% CI: 1.11-1.69; AUC 0.74-0.96; sensitivity, 85%; specificity, 71%). The neutrophil-to-lymphocyte ratio (NLR) showed a high correlation with disease severity (SMD = 1.07, 95% CI: 0.79-1.35; AUC 0.73-0.98; sensitivity, 86%; specificity, 78%). Increased KL-6 levels were associated with lung injury (SMD = 1.22, 95% CI: 0.24-2.19; AUC 0.85-0.95). Other biomarkers (suPAR, miR-155, Galectin-3) showed promise but lacked sufficient data for pooled analysis. Heterogeneity was observed among the included studies in terms of diagnostic accuracy. These findings indicate that elevated levels of MR-proADM, NLR, and KL-6 are significantly associated with COVID-19 prognostic accuracy to guide patient management. Conclusions: MR-proADM, NLR, and KL-6 levels demonstrated strong prognostic value for COVID-19 severity and mortality. These biomarkers can enhance clinical decision-making.

It is known that SARS-CoV-2 can translocate via membrane ACE2 exopeptidase into the host cells, and thus hypomethylation of ACE2 possibly upregulates its expression, enhancing the risk of SARS-CoV-2 infection. This study investigated if DNA methylation levels of the ACE2 promoter are associated with the development of post-COVID-19 symptomatology in a cohort of COVID-19 survivors who had been previously hospitalized. Non-stimulated saliva samples were obtained from 279 (51.5 male, mean age: 56.5 ± 13.0 years old) COVID-19 survivors who were hospitalized during the first wave of the pandemic. A face-to-face interview in which patients described the presence of post-COVID-19 symptoms (defined as a symptom that started no later than three months after SARS-CoV-2 infection) that they suffered from to an experienced healthcare trainer was conducted. Methylation of five CpG dinucleotides in the ACE2 promoter was quantified using bisulfite pyrosequencing. The percentage of methylation (%) was associated with the presence of the following reported post-COVID-19 symptoms: fatigue, dyspnea at rest, dyspnea at exertion, brain fog, memory loss, concentration loss, or gastrointestinal problems. Participants were assessed a mean of 17.8 (SD: 5.3) months after hospitalization. At that time, 88.1% of the patients experienced at least one post-COVID-19 symptom (mean number for each patient: 3.0; SD: 1.9 post-COVID-19 symptoms). Dyspnea at exertion (67.3%), fatigue (62.3%), and memory loss (31.2%) were the most frequent post-COVID-19 symptoms in the sample. Overall, the analysis did not reveal any difference in the methylation of the ACE2 promoter in any of the CpG locations according to the presence or absence of fatigue, dyspnea at rest, dyspnea at exertion, memory loss, brain fog, concentration loss, and gastrointestinal problems. This study did not find an association between methylation of ACE2 promoter and the presence of post-COVID-19 fatigue, dyspnea, cognitive or gastrointestinal problems in previously hospitalized COVID-19 survivors.

ABSTRACT

Several coronavirus (CoV) encoded proteins are being evaluated as targets for antiviral therapies for COVID-19. Included in this set of proteins is the conserved macrodomain, or Mac1, an ADP-ribosylhydrolase and ADP-ribose binding protein. Utilizing point mutant recombinant viruses, Mac1 was shown to be critical for both murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-CoV virulence. However, as a potential drug target, it is imperative to understand how a complete Mac1 deletion impacts the replication and pathogenesis of different CoVs. To this end, we created recombinant bacterial artificial chromosomes (BACs) containing complete Mac1 deletions (ΔMac1) in MHV, MERS-CoV, and SARS-CoV-2. While we were unable to recover infectious virus from MHV or MERS-CoV ΔMac1 BACs, SARS-CoV-2 ΔMac1 was readily recovered from BAC transfection, indicating a stark difference in the requirement for Mac1 between different CoVs. Furthermore, SARS-CoV-2 ΔMac1 replicated at or near wild-type levels in multiple cell lines susceptible to infection. However, in a mouse model of severe infection, ΔMac1 was quickly cleared causing minimal pathology without any morbidity. ΔMac1 SARS-CoV-2 induced increased levels of interferon (IFN) and interferon-stimulated gene (ISG) expression in cell culture and mice, indicating that Mac1 blocks IFN responses which may contribute to its attenuation. ΔMac1 infection also led to a stark reduction in inflammatory monocytes and neutrophils. These results demonstrate that Mac1 only minimally impacts SARS-CoV-2 replication, unlike MHV and MERS-CoV, but is required for SARS-CoV-2 pathogenesis and is a unique antiviral drug target.

SIGNIFICANCE

All CoVs, including SARS-CoV-2, encode for a conserved macrodomain (Mac1) that counters host ADP-ribosylation. Prior studies with SARS-CoV-1 and MHV found that Mac1 blocks IFN production and promotes CoV pathogenesis, which has prompted the development of SARS-CoV-2 Mac1 inhibitors. However, development of these compounds into antivirals requires that we understand how SARS-CoV-2 lacking Mac1 replicates and causes disease in vitro and in vivo . Here we found that SARS-CoV-2 containing a complete Mac1 deletion replicates normally in cell culture but induces an elevated IFN response, has reduced viral loads in vivo , and does not cause significant disease in mice. These results will provide a roadmap for testing Mac1 inhibitors, help identify Mac1 functions, and open additional avenues for coronavirus therapies.

Objectives

To determine the prevalence of persistent COVID-19 symptoms in SARS-CoV-2 patients 15 months after ICU discharge,their impact on physical, psychological, and neurocognitive domains, and the burden on primary caregivers.

Design

Descriptive, ambispective observational study.

Setting

Intensive Care Unit from a tertiary-level hospital.

Patients

SARS-CoV-2 patients discharged from ICU.

Main variables of interest

demographics and hospitalization data. Questionnaires assesing persistent COVID symptoms, functional tests (6-Minute Walk Test), anxiety (Beck Anxiety Inventory), PTSD and Zarit Caregiver Burden scales. Statistical analysis was performed using Stata for Mac, version 14.2.

Results

85 patients were evaluated, with a median age of 60.3 years (IQR 54.0-68.9), 70.6% males. A high percentage of patients reported musculoskeletal disorders such as arthralgia (44.7%) and myalgia (38.2%), cognitive impairments (52.9%), sleep disturbances (34.1%), asthenia (44.5%) and anxiety (34.5%). The overall BAI score was 2 (0-9), with paraesthesia being the most common symptom. Additionally, 29.4% of patients reported "fear of the worst", 35% had unpleasant or recurrent memories of their ICU stay, and 16.4% were unable to relax (moderate/severe degree). Interviews with primary caregivers revealed that 22.2% reported caregiving as a significant burden.

Conclusions

persistent COVID affects three primary functional domains: physical, cognitive and psychological, as well as on primary caregivers concerns and burdens.

Background

The aim of the study was to evaluate the humoral and cellular immunity after SARS-CoV-2 infection and/or vaccination according to the type of vaccine, number of doses and combination of vaccines.

Methods

Volunteer subjects were sampled between September 2021 and July 2022 in Hospital Clínico San Carlos, Madrid (Spain). Participants had different immunological status against SARS-CoV-2: vaccinated and unvaccinated, with or without previous COVID-19 infection, including healthy and immunocompromised individuals. Determination of IgG against the spike protein S1 subunit receptor-binding domain (RBD) was performed by chemiluminescence microparticle immunoassay (CMIA) using the Architect i10000sr platform (Abbott). The SARS-CoV-2-specific T-cell responses were assessed by quantification of interferon gamma release using QuantiFERON SARS-CoV-2 assay (Qiagen).

Results

A total of 181 samples were collected, 170 were from vaccinated individuals and 11 from unvaccinated. Among the participants, 41 were aware of having previously been infected by SARS-CoV-2. Vaccinated people received one or two doses of the following vaccines against SARS-CoV-2: ChAdOx1-S (University of Oxford-AstraZeneca) (AZ) and/orBNT162b2 (Pfizer-BioNTech)(PZ). Subjects immunized with a third-booster dose received PZ or mRNA-1273 (Moderna-NIAID)(MD) vaccines. All vaccinees developed a positive humoral response (>7.1 BAU/ml), but the cellular response varied depending on the vaccination regimen. Only AZ/PZ combination and 3 doses of vaccination elicited a positive cellular response (median concentration of IFN- γ > 0.3 IU/ml). Regarding a two-dose vaccination regimen, AZ/PZ combination induced the highest humoral and cellular immunity. A booster with mRNA vaccine resulted in increases in median levels of IgG-Spike antibodies and IFN-γ as compared to those of two-dose of any vaccine. Humoral and cellular immunity levels were significantly higher in participants with previous infection compared to those without infection.

Conclusion

Heterologous vaccination (AZ/PZ) elicited the strongest immunity among the two-dose vaccination regimens. The immunity offered by the third-booster dose of SARS-CoV-2 vaccine depends not only on the type of vaccine administered but also on previous doses and prior infection. Previous exposure to SARS-CoV-2 antigens by infection strongly affect immunity of vaccinated individuals.

On 11 February 2020, the prevalent outbreak of COVID-19, a coronavirus illness, was declared a global pandemic. Since then, nearly seven million people have died and over 765 million confirmed cases of COVID-19 have been reported. The goal of this study is to develop a diagnostic tool for detecting COVID-19 infections more efficiently. Currently, the most widely used method is Reverse Transcription Polymerase Chain Reaction (RT-PCR), a clinical technique for infection identification. However, RT-PCR is expensive, has limited sensitivity, and requires specialized medical expertise. One of the major challenges in the rapid diagnosis of COVID-19 is the need for reliable imaging, particularly X-ray imaging. This work takes advantage of artificial intelligence (AI) techniques to enhance diagnostic accuracy by automating the detection of COVID-19 infections from chest X-ray (CXR) images. We obtained and analyzed CXR images from the Kaggle public database (4035 images in total), including cases of COVID-19, viral pneumonia, pulmonary opacity, and healthy controls. By integrating advanced techniques with transfer learning from pre-trained convolutional neural networks (CNNs), specifically InceptionV3, ResNet50, and Xception, we achieved an accuracy of 95%, significantly higher than the 85.5% achieved with ResNet50 alone. Additionally, our proposed method, CXR-DNNs, can accurately distinguish between three different types of chest X-ray images for the first time. This computer-assisted diagnostic tool has the potential to significantly enhance the speed and accuracy of COVID-19 diagnoses.

SARS-CoV-2 infection represents a new challenge for solid organ transplantation (SOT) with evolving recommendations. A cross-sectional survey was performed (February-June 2024) to describe practices among Member States of the Council of Europe (COE) on the use of organs from deceased donors with resolved or active SARS-CoV-2 infection. Overall, 32 out of 47 Member States with a transplant program participated in the study. Four (12.5%) countries did not use organs from deceased donors either with resolved or with active SARS-CoV-2 infection and 8 (25%) countries accepted organs only from deceased donors with resolved SARS-CoV-2 infection. Donor evaluation for SARS-CoV-2 included universal screening with standard PCR testing on respiratory specimens generally (61.4%) performed within 24 h prior to organ recovery. Further microbiological, immunological and radiological investigations varied. Most waitlisted patients receiving organs from a deceased donor with active (94.5%) or resolved (61.5%) SARS-CoV-2 infection were preferred to have natural, vaccine-induced or hybrid SARS-CoV-2 immunity. Most countries did not require recipients to undergo specific anti-SARS-CoV-2 treatment as pre-exposure (0%), post-exposure prophylaxis (15.4%) or modification of immunosuppression regimen (24%). This study highlights similarities and heterogeneities in the management of SARS-CoV-2 positive donors between COE countries, and a potential to safely expand donors' pool.

Millions of people worldwide have chronic kidney disease (CKD). Affected patients are at high risk for cardiovascular (CV) disease for several reasons. Among various comorbidities, CKD is associated with the more severe forms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. This is particularly true for patients receiving dialysis or for kidney recipients. From the start of the SARS-CoV-2 pandemic, several CV complications have been observed in affected subjects, spanning acute inflammatory manifestations, CV events, thrombotic episodes and arrythmias. Several pathogenetic mechanisms have been hypothesized, including direct cytopathic viral effects on the myocardium, endothelial damage and hypercoagulability. This spectrum of disease can occur during the acute phase of the infection, but also months after recovery. This review is focussed on the CV complications of coronavirus disease 2019 (COVID-19) with particular interest in their implications for the CKD population.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the Coronavirus Disease 2019 (COVID-19) pandemic, which is still a health issue worldwide mostly due to a high rate of contagiousness conferred by the high-affinity binding between cell viral receptors, Angiotensin-Converting Enzyme 2 (ACE2) and SARS-CoV-2 Spike protein. Therapies have been developed that rely on the use of antibodies or the induction of their production (vaccination), but despite vaccination being still largely protective, the efficacy of antibody-based therapies wanes with the advent of new viral variants. Chimeric Antigen Receptor (CAR) therapy has shown promise for tumors and has also been proposed for COVID-19 treatment, but as recognition of CARs still relies on antibody-derived sequences, they will still be hampered by the high evasion capacity of the virus. In this manuscript, we show the results from CAR-like constructs with a recognition domain based on the ACE2 viral receptor, whose ability to bind the virus will not wane, as Spike/ACE2 interaction is pivotal for viral entry. Moreover, we have developed a CAR construct based on an affinity-optimized ACE2 and showed that both wild-type and affinity-optimized ACE2 CARs drive activation of a T cell line in response to SARS-CoV-2 Spike protein expressed on a pulmonary cell line. Our work sets the stage for the development of CAR-like constructs against infectious agents that would not be affected by viral escape mutations and could be developed as soon as the receptor is identified.

Recent years have witnessed the emergence of several viruses and other pathogens. Some of these infectious diseases have spread globally, resulting in pandemics. Although biosensors of various types have been utilized for virus detection, their limited sensitivity remains an issue. Therefore, the development of better diagnostic tools that facilitate the more efficient detection of viruses and other pathogens has become important. Nanotechnology has been recognized as a powerful tool for the detection of viruses, and it is expected to change the landscape of virus detection and analysis. Recently, nanomaterials have gained enormous attention for their value in improving biosensor performance owing to their high surface-to-volume ratio and quantum size effects. This article reviews the impact of nanotechnology on the design, development, and performance of sensors for the detection of viruses. Special attention has been paid to nanoscale materials, various types of nanobiosensors, the internet of medical things, and artificial intelligence-based viral diagnostic techniques.

Several coronavirus (CoV) encoded proteins are being evaluated as targets for antiviral therapies for COVID-19. Included in these drug targets is the conserved macrodomain, or Mac1, an ADP-ribosylhydrolase and ADP-ribose binding protein encoded as a small domain at the N terminus of nonstructural protein 3. Utilizing point mutant recombinant viruses, Mac1 was shown to be critical for both murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-CoV virulence. However, as a potential drug target, it is imperative to understand how a complete Mac1 deletion impacts the replication and pathogenesis of different CoVs. To this end, we created recombinant bacterial artificial chromosomes (BACs) containing complete Mac1 deletions (ΔMac1) in MHV, MERS-CoV, and SARS-CoV-2. While we were unable to recover infectious virus from MHV or MERS-CoV ΔMac1 BACs, SARS-CoV-2 ΔMac1 was readily recovered from BAC transfection, indicating a stark difference in the requirement for Mac1 between different CoVs. Furthermore, SARS-CoV-2 ΔMac1 replicated at or near wild-type levels in multiple cell lines susceptible to infection. However, in a mouse model of severe infection, ΔMac1 was quickly cleared causing minimal pathology without any morbidity. ΔMac1 SARS-CoV-2 induced increased levels of interferon (IFN) and IFN-stimulated gene expression in cell culture and mice, indicating that Mac1 blocks IFN responses which may contribute to its attenuation. ΔMac1 infection also led to a stark reduction in inflammatory monocytes and neutrophils. These results demonstrate that Mac1 only minimally impacts SARS-CoV-2 replication, unlike MHV and MERS-CoV, but is required for SARS-CoV-2 pathogenesis and is a unique antiviral drug target.

SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state involves the activation of the innate immune response by viral patterns and coincides with the biosynthesis of the biomass required for viral replication, which may overwhelm the capacity of the endoplasmic reticulum and drive the unfolded protein response (UPR). The UPR is a signal transduction pathway composed of three branches that is initiated by a set of sensors: inositol-requiring protein 1 (IRE1), protein kinase RNA-like ER kinase (PERK), and activating transcription factor 6 (ATF6). These sensors control adaptive processes, including the transcriptional regulation of proinflammatory cytokines. Based on this background, the role of the UPR in SARS-CoV-2 replication and the ensuing inflammatory response was investigated using in vivo and in vitro models of infection. Mice and Syrian hamsters infected with SARS-CoV-2 showed a sole activation of the Ire1α-Xbp1 arm of the UPR associated with a robust production of proinflammatory cytokines. Human lung epithelial cells showed the dependence of viral replication on the expression of UPR-target proteins branching on the IRE1α-XBP1 arm and to a lower extent on the PERK route. Likewise, activation of the IRE1α-XBP1 branch by Spike (S) proteins from different variants of concern was a uniform finding. These results show that the IRE1α-XBP1 system enhances viral replication and cytokine expression and may represent a potential therapeutic target in SARS-CoV-2 severe pneumonia.

Animals have been involved in the three known outbreaks of severe respiratory syndromes due to coronaviruses (years 2005, 2012, and 2019). The pandemic nature of the SARS-CoV-2 outbreak increases the likelihood of infection from humans of susceptible animal species that, thus, could become secondary viral hosts and even disease reservoirs. We present evidence of spillover infection of wild mustelids by reporting the presence of SARS-CoV-2 in a Eurasian river otter found near a water reservoir in the Valencian Community (Spain). We detected the virus using two different commercial RTqPCR assays on RNA extracted from the nasopharynx (swabbing) and from lung tissue and mediastinal lymph node homogenates. The corresponding samples from two additional otters from distant sites tested negative in identical assays. The diagnosis in the positive otter was confirmed by two-tube RT-PCR assay in which RNA was first retrotranscribed, and then specific regions of the spike (S), nucleocapsid (N), and ORF10 genes were separately amplified from the produced cDNA, followed by electrophoretic visualization and Sanger sequencing. The sequences of the amplified products revealed some non-synonymous changes in the N and ORF10 partial sequences, relative to the consensus sequence. These changes, identified already in human patient samples, point to human origin of the virus, although their specific combination was unique. These findings, together with our previous report of SARS-CoV-2 infection of feral American mink, highlight the need for SARS-CoV-2 surveillance of wild or feral mustelids to evaluate the risk that these animals could become SARS-CoV-2 reservoirs.

The dysregulated immune response and inflammation resulting in severe COVID-19 are still incompletely understood. Having recently determined that aberrant death-ligand-induced cell death can cause lethal inflammation, we hypothesized that this process might also cause or contribute to inflammatory disease and lung failure following SARS-CoV-2 infection. To test this hypothesis, we developed a novel mouse-adapted SARS-CoV-2 model (MA20) that recapitulates key pathological features of COVID-19. Concomitantly with occurrence of cell death and inflammation, FasL expression was significantly increased on inflammatory monocytic macrophages and NK cells in the lungs of MA20-infected mice. Importantly, therapeutic FasL inhibition markedly increased survival of both, young and old MA20-infected mice coincident with substantially reduced cell death and inflammation in their lungs. Intriguingly, FasL was also increased in the bronchoalveolar lavage fluid of critically-ill COVID-19 patients. Together, these results identify FasL as a crucial host factor driving the immuno-pathology that underlies COVID-19 severity and lethality, and imply that patients with severe COVID-19 may significantly benefit from therapeutic inhibition of FasL.

Aim

Since the first cases of the COVID-19 pandemic, caused by the SARS-CoV-2 virus, described in 2019, numerous drugs have been proposed for the treatment of the disease. However, studies have given contradictory or inconclusive results, making it difficult to determine which treatments are truly effective. The objective was to carry out a systematic review of the literature analyzing the effectiveness (mortality, hospitalization and clinical improvement) of COVID-19 treatments initially proposed and finally authorized in the European Union.

Methods

PubMed and other electronic databases were systematically searched for meta-analyses published between January 2020 and December 2022, as well as two additional searches: one of individual clinical studies published until October 2023 and another of those drugs that were considered at the beginning and that were discarded early because the clinical results were unfavorable.

Results

In the synthesis, 85 meta-analyses and 19 additional clinical studies were included (base case). All medications indicated in the treatment of COVID-19 have favorable efficacy results (mortality, hospitalization rate, clinical improvement) but these results were not confirmed in all studies carried out, being frequently contradictory (confirming or not confirming the impact of treatment on mortality). According to meta-analysis with the largest sample size, the drugs with the greatest evidence of effectiveness in reducing mortality are remdesivir (HR= 0.79; 95% CI 0.73-0.85) and tocilizumab (OR= 0.73; 95% CI 0.56-0.93). Regarding the composite of Covid-19-related hospitalization or death from any cause, the drugs with the greatest evidence of efficacy are remdesivir, nirmatrelvir/ritonavir and sotrovimab (although, currently the effectiveness of monoclonal antibodies against the new variants of the virus has not been demonstrated).

Conclusion

According to this systematic review, the treatments with the greatest evidence of reducing mortality in patients with COVID-19 are remdesivir and tocilizumab.

Classical epidemiology relies on incidence, mortality rates, and clinical data from individual testing, which can be challenging for many countries. Therefore, innovative, flexible, cost-effective, and scalable surveillance techniques are needed. Wastewater-based epidemiology (WBE) has emerged as a highly powerful tool in this regard. WBE analyses substances excreted in human fluids and faeces that enter the sewer system. This approach provides insights into community health status and lifestyle habits. WBE serves as an early warning system for viral surveillance, detecting the emergence of new pathogens, changes in incidence rates, identifying future trends, studying outbreaks, and informing the performance of action plans. While WBE has long been used to study different viruses such as poliovirus and norovirus, its implementation has surged due to the pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2. This has led to the establishment of wastewater surveillance programmes at international, national, and community levels, many of which remain operational. Furthermore, WBE is increasingly applied to study other pathogens, including antibiotic resistance bacteria, parasites, fungi, and emerging viruses, with new methodologies being developed. Consequently, the primary focus now is on creating international frameworks to enhance states' preparedness against future health risks. However, there remains considerable work to be done, particularly in integrating the principles of One Health into epidemiological surveillance to acknowledge the interconnectedness of humans, animals, and the environment in pathogen transmission. Thus, a broader approach to analysing the three pillars of One Health must be developed, transitioning from WBE to wastewater and environmental surveillance, and establishing this approach as a routine practice in public health.

Background

Chronic kidney disease (CKD), especially diabetic CKD, is the condition that most increases the risk of lethal coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the underlying molecular mechanisms are unclear. SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs) regulate coronavirus cell entry and/or replication. We hypothesized that CKD may alter the expression of SCARF genes.

Methods

A literature search identified 34 SCARF genes of which we selected 21 involved in interactions between SARS-CoV/SARS-CoV-2 and host cells, and assessed their mRNA expression in target tissues of COVID-19 (kidneys, lungs, aorta and heart) in mice with adenine-induced CKD.

Results

Twenty genes were differentially expressed in at least one organ in mice with CKD. For 15 genes, the differential expression would be expected to favor SARS-CoV-2 infection and/or severity. Of these 15 genes, 13 were differentially expressed in the kidney and 8 were validated in human CKD kidney transcriptomics datasets, including those for the most common cause of CKD, diabetic nephropathy. Two genes reported to protect from SARS-CoV-2 were downregulated in at least two non-kidney target organs: Ifitm3 encoding interferon-induced transmembrane protein 3 (IFITM3) in lung and Ly6e encoding lymphocyte antigen 6 family member 6 (LY6E) in aorta.

Conclusion

CKD, including diabetic CKD, is associated with the differential expression of multiple SCARF genes in target organs of COVID-19, some of which may sensitize to SARS-CoV-2 infection. This information may facilitate developing therapeutic strategies aimed at decreasing COVID-19 severity in patients with CKD.

Several anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monoclonal antibodies (mAbs) have received emergency authorization for coronavirus disease 2019 (COVID-19) treatment. However, most of these mAbs are not active against the highly mutated Omicron SARS-CoV-2 subvariants. We have tested a polyclonal approach of equine anti-SARS-CoV-2 F(ab')2 antibodies that achieved a high level of neutralizing potency against all SARS-CoV-2 variants of concern tested including Omicron BA.1, BA.2, BA.2.12 and BA.4/5. A repertoire of antibodies targeting conserved epitopes in different regions of the spike protein could plausibly account for this remarkable breadth of neutralization. These results warrant the clinical investigation of equine polyclonal F(ab')2 antibodies as a novel therapeutic strategy against COVID-19.

We investigated whether antibody concentrations measured in plasma using the Roche Elecsys® Anti-SARS-CoV-2 S assay (targeting the receptor binding domain, RBD) could estimate levels of Wuhan-Hu-1 and Omicron XBB.1.5 spike-directed antibodies with neutralizing ability (NtAb) or those mediating NK-cell activity. We analyzed 135 plasma samples from 39 vaccinated elderly nursing home residents. A strong correlation was found for NtAb against both Wuhan-Hu-1 (Rho = 0.73, p < 0.001) and Omicron XBB.1.5 (sub)variants (Rho = 0.73, p < 0.001). Moderate positive correlations were observed for NK-cell activity, based on lysosome-associated membrane protein 1 (LAMP1)-producing NK cells stimulated with Wuhan-Hu-1 (Rho = 0.43, p < 0.001) and Omicron XBB.1.5 spike proteins (Rho = 0.50, p < 0.001). Similarly, interferon-gamma (IFN-γ)-producing NK-cell frequencies showed moderate correlations (Wuhan-Hu-1: Rho = 0.43, p < 0.001; Omicron XBB.1.5: Rho = 0.50, p < 0.001). Random Forest models accurately predicted NtAb levels against Wuhan-Hu-1 (R² = 0.72), though models for Omicron XBB.1.5 were less robust. Anti-RBD antibody concentrations of 4.73 and 5.02 log₁₀ BAU/mL predicted high NtAb levels for Wuhan-Hu-1 and Omicron XBB.1.5, respectively. Antibody thresholds for predicting functional NK cell-mediated responses were 4.73 log₁₀ and 4.54 log₁₀ BAU/mL for Wuhan-Hu-1 and Omicron XBB.1.5, respectively. For LAMP1-producing NK cells, the thresholds were 4.94 and 4.75 log₁₀ BAU/mL for Wuhan-Hu-1 and Omicron XBB.1.5, respectively. In summary, total anti-RBD antibody levels measured by the Roche assay may allow inference of NtAb levels and, to a lesser extent, Fc-mediated NK-cell responses against Omicron XBB.1.5.

Coronavirus disease (COVID-19) causes various vascular and blood-related reactions, including exacerbated responses. The role of endothelial cells in this acute response is remarkable and may remain important beyond the acute phase. As we move into a post-COVID-19 era (where most people have been or will be infected by the SARS-CoV-2 virus), it is crucial to define the vascular consequences of COVID-19, including the long-term effects on the cardiovascular system. Research is needed to determine whether chronic endothelial dysfunction following COVID-19 could lead to an increased risk of cardiovascular and thrombotic events. Endothelial dysfunction could also serve as a diagnostic and therapeutic target for post-COVID-19. This review covers these topics and examines the potential of emerging vessel-on-a-chip technology to address these needs. Vessel-on-a-chip would allow for the study of COVID-19 pathophysiology in endothelial cells, including the analysis of SARS-CoV-2 interactions with endothelial function, leukocyte recruitment, and platelet activation. "Personalization" could be implemented in the models through induced pluripotent stem cells, patient-specific characteristics, or genetic modified cells. Adaptation for massive testing under standardized protocols is now possible, so the chips could be incorporated for the personalized follow-up of the disease or its sequalae (long COVID) and for the research of new drugs against COVID-19.

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has significantly impacted global health, stressing the necessity of basic understanding of the host response to this viral infection. In this study, we investigated how SARS-CoV-2 remodels the landscape of small non-coding RNAs (sncRNA) from a large collection of nasopharyngeal swab samples taken at various time points from patients with distinct symptom severity. High-throughput RNA sequencing analysis revealed a global alteration of the sncRNA landscape, with abundance peaks related to species of 21-23 and 32-33 nucleotides. Principal component analysis successfully discriminated infected patients based on the sncRNA profiles. Host-derived sncRNAs, including microRNAs (miRNAs), transfer RNA-derived small RNAs (tsRNAs), and small nucleolar RNAs (sdRNAs) exhibited significant differential expression in infected patients compared to controls. Importantly, miRNA expression was predominantly down-regulated in response to SARS-CoV-2 infection, especially in patients with severe symptoms. Furthermore, we identified specific tsRNAs derived from Glu- and Gly-tRNAs as major altered elements upon infection, with 5’ tRNA halves being the most abundant species and suggesting their potential as biomarkers for viral presence and disease severity prediction. Additionally, down-regulation of C/D-box sdRNAs and altered expression of tyRNAs were observed in infected patients. These findings provide valuable insights into the host sncRNA response to SARS-CoV-2 infection and may contribute to the development of further diagnostic and therapeutic strategies in the clinic.

An accurate spatial representation of protein-protein interaction networks is needed to achieve a realistic and biologically relevant representation of interactomes. Here, we leveraged the spatial information included in Proximity-Dependent Biotin Identification (BioID) interactomes of SARS-CoV-2 proteins to calculate weighted distances and model the organization of the SARS-CoV-2-human interactome in three dimensions (3D) within a cell-like volume. Cell regions with viral occupancy were highlighted, along with the coordination of viral proteins exploiting the cellular machinery. Profiling physical intra-virus and virus-host contacts enabled us to demonstrate both the accuracy and the predictive value of our 3D map for direct interactions, meaning that proteins in closer proximity tend to interact physically. Several functionally important virus-host complexes were detected, and robust structural models were obtained, opening the way to structure-directed drug discovery screens. This PPI discovery pipeline approach brings us closer to a realistic spatial representation of interactomes, which, when applied to viruses or other pathogens, can provide significant information for infection. Thus, it represents a promising tool for coping with emerging infectious diseases.

The robustness, safety, versatility, and high immunogenicity of virus-like particles (VLPs) make them a promising approach for the generation of vaccines against a broad range of pathogens. VLPs are recombinant macromolecular structures that closely mimic the native conformation of viruses without carrying viral genetic material. Particularly, HIV-1 Gag-based VLPs are a suitable platform for the presentation of the SARS-CoV-2 Spike (S) protein on their surface. In this context, this work studies the effect of different rationally engineered mutations of the S protein to improve some of its characteristics. The studied variants harbored mutations such as proline substitutions for S stabilization, D614G from the early dominant pandemic form, the elimination of the S1/S2 furin cleavage site to improve S homogeneity, the suppression of a retention motif to favor its membrane localization, and cysteine substitutions to increase its immunogenicity and avoid potential undesired antibody-dependent enhancement (ADE) effects. The influence of the mutations on VLP expression was studied, as well as their immunogenic potential, by testing the recognition of the generated VLP variants by COVID-19 convalescent patients' sera. The results of this work are conceived to give insights on the selection of S protein candidates for their use as immunogens and to showcase the potential of VLPs as carriers for antigen presentation.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) studies usually rely on cross-sectional data of large cohorts but limited repeated samples, overlooking significant inter-individual antibody kinetic differences. By combining Luminex, activation-induced marker (AIM) and IFN-γ/IL-2 Fluorospot assays, we characterized the IgM, IgA, and IgG antibody kinetics using 610 samples from 31 healthy adults over two years after COVID-19 vaccination, and the T-cell responses six months post-booster. Antibody trajectories varied among isotypes: IgG decayed slowly, IgA exhibited an initial sharp decline, which gradually slowed down and stabilized above the seropositivity threshold. Contrarily, IgM rapidly dropped to undetectable levels after primary vaccination. Importantly, three vaccine doses induced higher and more durable anti-spike IgG and IgA levels compared to two doses, whereas infection led to the highest antibody peak and slowest antibody decay rate compared to vaccination. Comparing with ancestral virus, antibody levels recognizing Omicron subvariants had a faster antibody decay. Finally, polyfunctional T cells were positively associated with subsequent IgA responses. These results revealed distinctive antibody patterns by isotype and highlight the benefits of booster doses in enhancing and sustaining antibody responses.

Background: Despite advancements in vaccination, early treatments, and understanding of SARS-CoV-2, its impact remains significant worldwide. Many patients require intensive care due to severe COVID-19. Remdesivir, a key treatment option among viral RNA polymerase inhibitors, lacks comprehensive studies on factors associated with its effectiveness. Methods: We conducted a retrospective study in 2022, analyzing data from 252 hospitalized COVID-19 patients treated with remdesivir. Six machine learning algorithms were compared to predict factors influencing remdesivir's clinical benefits regarding mortality and hospital stay. Results: The extreme gradient boost (XGB) method showed the highest accuracy for both mortality (95.45%) and hospital stay (94.24%). Factors associated with worse outcomes in terms of mortality included limitations in life support, ventilatory support needs, lymphopenia, low albumin and hemoglobin levels, flu and/or coinfection, and cough. For hospital stay, factors included vaccine doses, lung density, pulmonary radiological status, comorbidities, oxygen therapy, troponin, lactate dehydrogenase levels, and asthenia. Conclusions: These findings underscore XGB's effectiveness in accurately categorizing COVID-19 patients undergoing remdesivir treatment.

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has infected several animal species, including dogs, presumably via human-to-animal transmission. Most infected dogs reported were asymptomatic, with low viral loads. However, in this case we detected SARS-CoV-2 in a dog from the North African coastal Spanish city of Ceuta presenting hemorrhagic diarrhea, a disease also reported earlier on in an infected dog from the USA.

Case presentation

In early January 2021, a West Highland Terrier pet dog from Ceuta (Spain) presented hemorrhagic diarrhea with negative tests for candidate microbial pathogens. Since the animal was in a household whose members suffered SARS-CoV-2 in December 2020, dog feces were analyzed for SARS-CoV-2, proving positive in a two-tube RT-PCR test, with confirmation by sequencing a 399-nucleotide region of the spike (S) gene. Furthermore, next-generation sequencing (NGS) covered > 90% SARS-CoV-2 genome sequence, allowing to classify it as variant B.1.177. Remarkably, the sequence revealed the Ile402Val substitution in the spike protein (S), of potential concern because it mapped in the receptor binding domain (RBD) that mediates virus interaction with the cell. NGS reads mapping to bacterial genomes showed that the dog fecal microbiome fitted best the characteristic microbiome of dog's acute hemorrhagic diarrhea.

Conclusion

Our findings exemplify dog infection stemming from the human SARS-CoV-2 pandemic, providing nearly complete-genome sequencing of the virus, which is recognized as belonging to the B.1.177 variant, adding knowledge on variant circulation in a geographic region and period for which there was little viral variant characterization. A single amino acid substitution found in the S protein that could have been of concern is excluded to belong to this category given its rarity and intrinsic nature. The dog's pathology suggests that SARS-CoV-2 could affect the gastrointestinal tract of the dog.

Introduction

SARS-CoV-2 variants are defined by specific genome-wide mutations compared to the Wuhan genome. However, non-clade-defining mutations may also impact protein structure and function, potentially leading to reduced vaccine effectiveness. Our objective is to identify mutations across the entire viral genome rather than focus on individual mutations that may be associated with vaccine failure and to examine the physicochemical properties of the resulting amino acid changes.

Materials and methods

Whole-genome consensus sequences of SARS-CoV-2 from COVID-19 patients were retrieved from the GISAID database. Analysis focused on Dataset_1 (7,154 genomes from Italy) and Dataset_2 (8,819 sequences from Spain). Bioinformatic tools identified amino acid changes resulting from codon mutations with frequencies of 10% or higher, and sequences were organized into sets based on identical amino acid combinations.

Results

Non-defining mutations in SARS-CoV-2 genomes belonging to clades 21 L (Omicron), 22B/22E (Omicron), 22F/23A (Omicron) and 21J (Delta) were associated with vaccine failure. Four sets of sequences from Dataset_1 were significantly linked to low vaccine coverage: one from clade 21L with mutations L3201F (ORF1a), A27- (S) and G30- (N); two sets shared by clades 22B and 22E with changes A27- (S), I68- (S), R346T (S) and G30- (N); and one set shared by clades 22F and 23A containing changes A27- (S), F486P (S) and G30- (N). Booster doses showed a slight improvement in protection against Omicron clades. Regarding 21J (Delta) two sets of sequences from Dataset_2 exhibited the combination of non-clade mutations P2046L (ORF1a), P2287S (ORF1a), L829I (ORF1b), T95I (S), Y145H (S), R158- (S) and Q9L (N), that was associated with vaccine failure.

Discussion

Vaccine coverage associations appear to be influenced by the mutations harbored by marketed vaccines. An analysis of the physicochemical properties of amino acid revealed that primarily hydrophobic and polar amino acid substitutions occurred. Our results suggest that non-defining mutations across the proteome of SARS-CoV-2 variants could affect the extent of protection of the COVID-19 vaccine. In addition, alteration of the physicochemical characteristics of viral amino acids could potentially disrupt protein structure or function or both.

The constant appearance of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VoCs) has jeopardized the protective capacity of approved vaccines against coronavirus disease-19 (COVID-19). For this reason, the generation of new vaccine candidates adapted to the emerging VoCs is of special importance. Here, we developed an optimized COVID-19 vaccine candidate using the modified vaccinia virus Ankara (MVA) vector to express a full-length prefusion-stabilized SARS-CoV-2 spike (S) protein, containing 3 proline (3P) substitutions in the S protein derived from the beta (B.1.351) variant, termed MVA-S(3Pbeta). Preclinical evaluation of MVA-S(3Pbeta) in head-to-head comparison to the previously generated MVA-S(3P) vaccine candidate, expressing a full-length prefusion-stabilized Wuhan S protein (with also 3P substitutions), demonstrated that two intramuscular doses of both vaccine candidates fully protected transgenic K18-hACE2 mice from a lethal challenge with SARS-CoV-2 beta variant, reducing mRNA and infectious viral loads in the lungs and in bronchoalveolar lavages, decreasing lung histopathological lesions and levels of proinflammatory cytokines in the lungs. Vaccination also elicited high titers of anti-S Th1-biased IgGs and neutralizing antibodies against ancestral SARS-CoV-2 Wuhan strain and VoCs alpha, beta, gamma, delta, and omicron. In addition, similar systemic and local SARS-CoV-2 S-specific CD4⁺ and CD8⁺ T-cell immune responses were elicited by both vaccine candidates after a single intranasal immunization in C57BL/6 mice. These preclinical data support clinical evaluation of MVA-S(3Pbeta) and MVA-S(3P), to explore whether they can diversify and potentially increase recognition and protection of SARS-CoV-2 VoCs.

The protein sequence space is vast. This fact, together with the prevalence of epistasis, hampers the engineering of novel enzymes through library screening and is a major obstacle to any attempt to predict natural protein evolution. Recently, specialized methodologies have been used to determine fitness data on ~260,000 sequences for the gene of the enzyme dihydrofolate reductase and antibody affinity data for all combinations of the mutations present in the receptor-binding domain (RBD) of the Omicron strain of SARS-CoV-2 (~30,000 variants). We show that upon iterative training on a total of just a few hundred variants, various state-of-the-art AI tools (multi-layer perceptron, random forest, and XGBoost algorithms) find very high fitness variants of the enzyme and predict the antibody evasion patterns of the RBD. This work provides a basis for efficient, widely applicable, low-throughput experimental approaches to assess viral protein evolution and to engineer enzymes for biotechnological applications.

Background/Objectives: Long-term studies on the immune response following multiple doses of SARS-CoV-2 mRNA vaccines remain limited. Methods: Secondary analyses of data from a cohort of non-immunocompromised subjects who received two doses of BNT162b2 (primary vaccination) and a booster with mRNA-1273 nine months later. Antibodies targeting the receptor-binding domain of the S1 subunit of the SARS-CoV-2 spike (anti-RBD) were measured at eight time points during follow-up; the SARS-CoV-2-specific T cell response was measured 16 and 25 months after primary vaccination using an interferon-γ release assay. Results: During the 9-month follow up period after primary vaccination and before the mRNA-1273 booster, anti-RBD were significantly higher at all time points in subjects with documented SARS-CoV-2 infection before the first study time point (previously infected subjects; n = 50) compared to naïve subjects (n = 208; p < 0.05). During a 16-month follow up period following the mRNA-1273 booster, anti-RBD were lower at all time points in previously infected subjects (n = 21) compared to naïve subjects (n = 109), although the differences were non-significant. Breakthrough SARS-CoV-2 infections increased over time in both groups, particularly after the mRNA-1273 booster. Most participants had a persistent SARS-CoV-2 specific T cell response regardless of prior infection. Conclusions: These findings suggest a modulating effect of previous SARS-CoV-2 infection on the humoral immune response to mRNA vaccination, a non-durable hybrid immunity following mRNA vaccination in previously infected subjects, and attenuation of the humoral immune response (immune damping) after repeated exposure to SARS-CoV-2 antigens through mRNA vaccination and/or infection.

The emergence of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) posed a serious worldwide threat and emphasized the urgency to find efficient solutions to combat the spread of the virus. Drug repurposing has attracted more attention than traditional approaches due to its potential for a time- and cost-effective discovery of new applications for the existing FDA-approved drugs. Given the reported success of machine learning (ML) in virtual drug screening, it is warranted as a promising approach to identify potential SARS-CoV-2 inhibitors. The implementation of ML in drug repurposing requires the presence of reliable digital databases for the extraction of the data of interest. Numerous databases archive research data from studies so that it can be used for different purposes. This article reviews two aspects: the frequently used databases in ML-based drug repurposing studies for SARS-CoV-2, and the recent ML models that have been developed for the prospective prediction of potential inhibitors against the new virus. Both types of ML models, Deep Learning models and conventional ML models, are reviewed in terms of introduction, methodology, and its recent applications in the prospective predictions of SARS-CoV-2 inhibitors. Furthermore, the features and limitations of the databases are provided to guide researchers in choosing suitable databases according to their research interests.

Background

The COVID-19 pandemic drastically disrupted usual seasonal mortality patterns, creating challenges in assessing temperature-related mortality. While previous studies explored the effect of temperature on SARS-CoV-2 transmission, few examined its relationship with mortality during the pandemic, often excluding COVID-19 deaths or relying on pre-pandemic models. In this study, we developed an innovative methodological framework that accounts for COVID-19 waves, allowing us to estimate changes in the short-term effects of temperature on mortality and assess the role of adaptation and maladaptation before and after the onset of the pandemic.

Methods

We analyzed pre- (2015-2019) and pandemic (2020-2023) mortality data from Eurostat, covering 805 contiguous regions across 32 European countries. To adjust for COVID-19 deaths, we selected specific time windows during COVID-19 waves, and increased the degrees of freedom (d.f.) for these windows as necessary until achieving well-behaved residuals.

Findings

Adjusting for COVID-19 deaths reduced uncertainty in the pandemic association, providing more precise estimates. When adjusting for COVID-19 deaths, we observed a significant reduction in cold and heat-related mortality risks in all sub-regions except in the southern regions for heat, which experienced a significant increase. When assessing the role of adaptation between pre- and pandemic periods, we observed significant changes for heat risks in southern and western regions with higher risks in the pandemic period than in the pre-pandemic one. For cold, all sub-regions except the southern ones had higher risks in the pre-pandemic period.

Interpretation

Our work defines a new innovative methodological framework for future epidemiological studies using data from the pandemic period. The proposed methodology demonstrates the importance of using pandemic data and adjusting for COVID-19 deaths to accurately capture current vulnerabilities. The findings highlight different regional adaptation processes and underscore the need for enhanced heat adaptation measures, particularly in vulnerable regions.

Plitidepsin is a host-targeted compound known for inducing a strong anti-SARS-CoV-2 activity, as well as for having the capacity of reducing lung inflammation. Because IL-6 is one of the main cytokines involved in acute respiratory distress syndrome, the effect of plitidepsin in IL-6 secretion in different in vitro and in vivo experimental models was studied. A strong plitidepsin-mediated reduction of IL-6 was found in human monocyte-derived macrophages exposed to nonproductive SARS-CoV-2. In resiquimod (a ligand of TLR7/8)-stimulated THP1 human monocytes, plitidepsin-mediated reductions of IL-6 mRNA and IL-6 levels were also noticed. Additionally, although resiquimod-induced binding to DNA of NF-κB family members was unaffected by plitidepsin, a decrease in the regulated transcription by NF-κB (a key transcription factor involved in the inflammatory cascade) was observed. Furthermore, the phosphorylation of p65 that is required for full transcriptional NF-κB activity was significantly reduced by plitidepsin. Moreover, decreases of IL-6 levels and other proinflammatory cytokines were also seen in either SARS-CoV-2 or H1N1 influenza virus-infected mice, which were treated at low enough plitidepsin doses to not induce antiviral effects. In summary, plitidepsin is a promising therapeutic agent for the treatment of viral infections, not only because of its host-targeted antiviral effect, but also for its immunomodulatory effect, both of which were evidenced in vitro and in vivo by the decrease of proinflammatory cytokines.

People with Post-Covid Condition (PCC) may demonstrate aberrant immune responses post-infection; however, serological follow-up studies are limited. We aim to compare SARS-CoV-2 serological responses to infection and vaccination in people who develop PCC versus those with an acute infection only. Participants (n = 2010) are a sub-cohort of the Virus Watch community cohort in England who provided monthly finger-prick serological samples. We compare the likelihood of post-infection seroconversion using logistic mixed models and the trajectories of anti-nucleocapsid (anti-N) and anti-spike (anti-S) antibodies using linear mixed models. Participants who developed PCC (n = 394) have 1.8x the odds of post-infection seroconversion for anti-N antibodies compared to those with an acute infection only (n = 1616) (odds ratio= 1.81 (95% confidence interval (CI) 1.16-2.90); however, these results are moderated by vaccination status and variant - with differences observed in pre-Omicron, unvaccinated participants. Anti-N levels, however, were elevated within 200 days post-infection in people with PCC compared to those without, after accounting for variant and vaccination status. Vaccination response (anti-S) pre- or post-infection did not systematically differ between groups. People with PCC demonstrate persistently higher anti-N antibody levels following primary infection compared to those with an acute infection only. These findings extend emerging evidence around infection-related immune activation and PCC.

We present 2 clinical cases of central retinal vein occlusion (CRVO) combined with cilioretinal artery occlusion (CRAO) in young patients with no cardiovascular risk factors (CVRF) or medical history of interest. An extensive etiological study with analytical and imaging tests was performed without finding relevant alterations. Finally, in the first case, the intake of 1 postcoital contraceptive pill was considered the triggering cause while, in the second case, the etiology was attributed to a previous infection by the SARS-Cov-2 virus. On both cases, antiplatelet treatment was initiated. In both patients the evolution was favorable, with good visual recovery.

Motivation

Understanding the host response to SARS-CoV-2 infection is crucial for deciding on the correct treatment of this epidemic disease. Although several recent studies reported the comparative transcriptome analyses of the three coronaviridae (CoV) members; namely SARS-CoV, MERS-CoV, and SARS-CoV-2, there is yet to exist a web-tool to compare increasing number of host transcriptome response datasets against the pre-processed CoV member datasets. Therefore, we developed a web application called CompCorona, which allows users to compare their own transcriptome data of infected host cells with our pre-built datasets of the three epidemic CoVs, as well as perform functional enrichment and principal component analyses (PCA).

Results

Comparative analyses of the transcriptome profiles of the three CoVs revealed that numerous differentially regulated genes directly or indirectly related to several diseases (e.g., hypertension, male fertility, ALS, and epithelial dysfunction) are altered in response to CoV infections. Transcriptome similarities and differences between the host PBMC and lung tissue infected by SARS-CoV-2 are presented. Most of our findings are congruent with the clinical cases recorded in the literature. Hence, we anticipate that our results will significantly contribute to ongoing studies investigating the pre-and/or post-implications of SARS-CoV-2 infection. In addition, we implemented a user-friendly public website, CompCorona for biomedical researchers to compare users own CoV-infected host transcriptome data against the built-in CoV datasets and visualize their results via interactive PCA, UpSet and Pathway plots.

Availability

CompCorona is freely available on the web at http://compcorona.mu.edu.tr

Contact

tugbasuzek@mu.edu.tr

Introduction

The aim of this study was to compare the histopathological findings in the resected tracheal ring of tracheotomized critically ill patients with or without severe SARS-CoV-2 infection.

Material and methods

This is a prospective case-control study. The data collection period was between May 2020 and 2022. Eighty tracheostomies were performed on patients with long intubation, and the resected tracheal ring was examined by standard microscopy. Forty consecutive tracheotomies were carried out in COVID-19-positive and -negative patients.

Results

The mean age was 67.1 (6.9 SD) years in the COVID-19 group and 67.8 (9.6 SD) in the control group (p = 0.3). The number of men in each group was 30 (75.0%) versus 27 (67.5%), respectively (p = 0.5). No relevant histological alterations were found in 82.5% of samples. Chronic subepithelial inflammation was found in 13.8% of cases. Two cases presented with vasculitis (2.5%), and one case presented with thrombotic microangiopathy (1.2%), all of them in the COVID-19 group. We found no statistically significant dependence between relevant histologic findings versus no alterations (X² = 0.779, p= 0.377) and no significant risk indices (RR = 1.8, OR = 2.032, PAR = 44%).

Conclusion

There is no evidence of increased risk of histopathological findings in the resected tracheal ring of patients with long intubation and COVID-19 disease.