Genomics

Geographical source of SARS-CoV-2 sequence data

The world map and table below provide a snapshot of the number of SARS-CoV-2 raw sequences submitted by country.
The original source of data is the COVID-19 Data Portal statistics section.

Raw sequences submitted by Country
Country Raw sequences submitted
1 USA 2,953,527
2 United Kingdom 2,651,771
3 Ireland 77,842
4 Switzerland 72,662
5 Portugal 43,860
6 Spain 41,545
7 Slovakia 39,140
8 Stonia 25,102
9 Norway 22,820
10 South Africa 17,981

VEO consortium reports

The VEO consortium (Versatile Emerging infectious disease Observatory) submits monthly reports to the European Commission on mutations and variation in publicly shared SARS-CoV-2 raw sequencing data.
You can browse all previous VEO reports in the table below.
If you would like to receive the VEO reports straight to your inbox, please send an email to veo.europe@erasmusmc.nl with ‘VEO COVID-19 Report’ in the subject line.

Report News Download
VEO Symposium 2022 report News Download report
14th report News Download report
13th report News Download report
12th report News Download report
11th report News Download report
10th report News Download report
9th report News Download report
8th report News Download report
7th report News Download report
6th report News Download report
5th report News Download report
4th report News Download report
3rd report News Download report
2nd report News Download report
1st report News Download report

Viral sequences

This section shows the samples sequenced from Severe acute respiratory syndrome coronavirus 2 (taxon: 2697049) in Spain.
These results are periodically retrieved from ENA.

Last update: 2024-02-24

Powered by ENA

Accession Collection date Country Host Isolate Description TAXON

Host sequences

This section shows studies related to COVID-19 containing host sequences sequenced in Spain and archived in the European Genome-Phenome Archive (EGA).
Note that each study can include more than one dataset.

These results are periodically manually retrieved from EGA.

Powered by EGA

EGA studies with Spanish partners

Download as CSV
Study accession Study title
EGAS00001005304 COVID19 Host Genetic Initiative
Accession Title
EGAD00010002171 Hostage_2_genotype
EGAD00010002172 BRACOVID_genotype
EGAD00010002173 Hostage_3_genotype
EGAD00010002174 INMUNGEN_CoV2_genotype
EGAD00010002175 SweCovid_genotype
EGAD00010002177 GEN_COVID_genotype
EGAD00010002178 Hostage_4_genotype
EGAD00010002179 BelCovid_2_genotype
EGAD00010002180 Hostage_1_genotype
EGAD00010002176 SPGRX_genotype
EGAD00001007837 GEN_COVID_phenotype_lab
EGAD00001007844 Hostage_4_phenotype_basic
EGAD00001007832 BRACOVID_phenotype_basic
EGAD00001007850 SweCovid_phenotype_lab
EGAD00001007848 SPGRX_phenotype_basic
EGAD00001007847 INMUNGEN_CoV2_phenotype_lab
EGAD00001007846 INMUNGEN_CoV2_phenotype_basic
EGAD00001007845 Hostage_4_phenotype_lab
EGAD00001007843 Hostage_3_phenotype_lab
EGAD00001007842 Hostage_3_phenotype_basic
EGAD00001007841 Hostage_2_phenotype_lab
EGAD00001007840 Hostage_2_phenotype_basic
EGAD00001007839 Hostage_1_phenotype_lab
EGAD00001007838 Hostage_1_phenotype_basic
EGAD00001007836 GEN_COVID_phenotype_basic
EGAD00001007835 BelCovid_2_phenotype_lab
EGAD00001007834 BelCovid_2_phenotype_basic
EGAD00001007833 BRACOVID_phenotype_lab
EGAD00001007849 SweCovid_phenotype_basic
EGAS00001005931 COVID-19 Severity of First Wave of Infection for Severe Patients in Madrid
Accession Title
EGAD00001008464 COVID-19 Severity First Wave of Infection for Severe Patients in Madrid

Other EGA Studies

Download as CSV
Study accession Study title
EGAS00001005465 Multi-omic single-cell profiling of peripheral blood immune cells from COVID-19 patients and controls.
Accession Title
EGAD00001007867 Cambridge COVID-19 Single-cell PBMC
EGAD00001007866 Newcastle COVID-19 Single-cell PBMC
EGAD00001007865 UCL COVID-19 Single-cell PBMC
EGAS00001005332 COVID-19 whole blood transcriptomic analysis
Accession Title
EGAD00001007776 Whole blood RNA-sequencing of covid-19 patients and healthy controls
EGAS00001005380 An analysis of humoral and cellular immune responses following COVID-19 vaccination.
Accession Title
EGAD00001007777 Covid vaccination BCR repertoire analysis
EGAS00001004571 ScRNA-seq of PBMC and whole blood samples reveals a dysregulated myeloid cell compartment in severe COVID-19
Accession Title
EGAD00001006550 ScRNA-seq of PBMC and whole blood samples reveales a dysregulated myeloid cell compartment in severe COVID-19
EGAS00001005060 SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes [10x]
Accession Title
EGAD00001008109 analysis of T cell receptor repertoirs
EGAD00001006995 Single-cell gene expression data from CD8+ T cells from two Austrian COVID19 patients stimulated with wildtype and mutant SARS-Cov-2 peptides
EGAS00001004508 Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2
Accession Title
EGAD00001006242 Single cell RNA sequencing data in "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2"
EGAD00001006241 Bulk RNA sequencing data in "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2"
EGAS00001004951 Upper respiratory microbiome of COVID-19 patients
Accession Title
EGAD00001006864 CONTAGIOUS trial - COVID-19 16S dataset
EGAD00001008006 CONTAGIOUS trial - COVID-19 16S metadata
EGAS00001004502 Swarm Learning to identify COVID-19 tuberculosis and leukemia patients based on blood transcriptomes
Accession Title
EGAD00001006231 Swarm Learning to identify COVID-19 tuberculosis and leukemia patients based on blood transcriptomes
EGAS00001005280 Impaired Humoral and Cellular Immunity after SARS-CoV2 BNT162b2 (Tozinameran) Prime-Boost Vaccination in Kidney Transplant Recipients
Accession Title
EGAD00001007689 RNA-Seq of response to Tozinameran vaccination in individuals with KTx/dialysis or healthy controls.
EGAS00001004689 COVID-19 Postmortem Lung snRNA-seq
Accession Title
EGAD00001006584 COVID-19 Postmortem Lung snRNA-seq
EGAS00001005039 SINGLE-CELL RNA SEQUENCING Single-cell RNA sequencing was performed on 13 ‘mild-moderate’ and 10 ‘critical’ COVID19 PBMC samples
Accession Title
EGAD00001006997 Single cell sequencing of mild and critical COVID19 PBMC
EGAS00001004717 Single-cell RNA sequencing of bronchoalveolar lavages from COVID-19 patients
Accession Title
EGAD00001006893 Single-cell RNA sequencing of bronchoalveolar lavages from COVID-19 patients
EGAS00001005461 Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
Accession Title
EGAD00001007969 Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
EGAS00001004716 Ancestry COVID-19 study
Accession Title
EGAD00010002011 Ancestry COVID-19 Study Phenotype
EGAD00010002012 Ancestry COVID-19 Study Genotype
EGAS00001005099 AncestryDNA COVID-19 GWAS with Eight Phenotypes
Accession Title
EGAD00010002104 AncestryDNA COVID-19 GWAS for Continuous_Severity_Score
EGAD00010002109 AncestryDNA COVID-19 GWAS for ExposedPositive_ExposedNegative
EGAD00010002111 AncestryDNA COVID-19 GWAS for Hospitalized_NotHosptialized
EGAD00010002120 AncestryDNA COVID-19 GWAS for Positive_Negative
EGAD00010002122 AncestryDNA COVID-19 GWAS for Symptomatic_Paucisymptomatic
EGAD00010002129 AncestryDNA COVID-19 GWAS for Hospitalized_Unscreened
EGAD00010002159 AncestryDNA COVID-19 GWAS for Positive_Unscreened
EGAD00010002162 AncestryDNA COVID-19 GWAS for Unscreened_ExposedNegative
EGAS00001005206 High titers and low fucosylation of early phase anti-SARS-CoV-2 IgG promote hyper-inflammation by alveolar macrophages
Accession Title
EGAD00001007512 anti-SARS-CoV-2 IgG and Fostamatinib treated human primary IL10-M2 macrophages
EGAS00001004503 Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures
Accession Title
EGAD00001006671 Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures
EGAD00001006326 Peripheral immunoprofiling of stratifies COVID-19 patients based on disease-specific neutrophil signatures
EGAS00001004391 Paediatric and adult nasal RNAseq COVID19
Accession Title
EGAD00001007718 The cellular immune and airway epithelial profile throughout childhood and in response to COVID-19 at multi-omic single cell level.
EGAS00001004772 Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
Accession Title
EGAD00001006828 Hypertension delays viral clearance and exacerbates airway hyperinflammation in patients with COVID-19
EGAS00001004481 Single-cell analysis of airway samples identifies immune cell activation correlating with COVID-19 disease severity
Accession Title
EGAD00001006339 COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis
EGAS00001004419 SARS‐CoV‐2 receptor ACE2 and TMPRSS2 are primarily expressed in bronchial transient secretory cells
Accession Title
EGAD00001006185 ALI culture bronchial cells and alveolar lung surgical resection scRNA-Seq
EGAS00001004412 Potent neutralizing antibodies against SARS-CoV-2
Accession Title
EGAD00001006130 Potent neutralizing antibodies against SARS-CoV-2

Genomic resources

NextSpain COVID-19 interactive epidemiological map
Developed by the Sequencing and Bioinformatics Services, FISABIO, and the Tuberculosis Genomics Unit, IBV-CSIC

NextSpain COVID-19 shows the results obtained from analysing complete genome sequences of SARS-CoV-2 deposited in GISAID or other publicly accessible databases. A large part of those sequences have been generated in the framework of the SeqCOVID genomic epidemiology of COVID-19 in Spain consortium. Still many others have been contributed by differnet groups across Spain with their resources. The analyses are performed with the NextStrain engine and the epidemiological map is built with this code.

Interactive epidemiological map of SARS-CoV-2 clinical circuit in Andalusia
Developed by the Clinical Bioinformatics Area, FPS

This map is part of the SARS-CoV-2 whole genome sequencing clinical circuit in Andalusia, which was created as a response by the Andalusian Health Service to a recommendation published by the Public Health Commission of the Interterritorial Council for the integration of genome sequencing in the SARS-CoV-2 surveillance in the approach to Personalised Medicine in COVID-19. The clinical circuit and the map is based upon a previous project funded by the Andalusian Health System: Sequencing of the SARS-CoV-2 virus genome for the monitoring and management of the Covid-19 epidemic in Andalusia and the rapid generation of prognostic and response to treatment biomarkers. The project included the 16 leading tertiary hospitals in Andalusia, three research centres with genome sequencing facilities (IBIS, Genyo and CABIMER) and the Bioinformatics Clinical Area of FPS.

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