The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), develops with wide clinical variability, ranging from asymptomatic infection to a life-threatening condition. Advanced age and the presence of comorbidities are well-known major risk factors of COVID-19 severity. In addition, male sex is another risk factor associated with COVID-19 severity, regardless of comorbidities. International genetic studies based on genome-wide association studies (GWAS) and/or comparative genome sequencing analyses have been conducted to identify genetic variants associated with COVID-19 severity. Through diverse nested sub-studies, the Spanish COalition to Unlock Research on host GEnetics on COVID-19 (SCOURGE) consortium was launched in May 2020 aiming to find biomarkers of evolution and prognosis that can have an immediate impact on clinical management and therapeutic decisions in SARS-CoV-2 infections. This consortium has recruited patients from hospitals across Spain and Latin America in close collaboration with the STOP-Coronavirus initiative and leverages a centralized genotyping and analysis platform (https://www.scourge-covid.org).
- Publicly available datasets
- A genome-wide association study of COVID-19 related hospitalization in Spain reveals genetic disparities among sexes (2022)
- Novel risk loci for COVID-19 hospitalization among admixed American populations (2024)
- Access to the results of SCOURGE studies
- Board of Directors
- References
A genome-wide association study of COVID-19 related hospitalization in Spain reveals genetic disparities among sexes (2022)
Here we describe the results of the first SCOURGE genome-wide studies of COVID-19 building up on the patients recruited in Spain from 34 centres in 25 cities [1]. The discovery stage of the study comprised up to 9,371 COVID-19 positive cases and 5,943 population controls. Replication was pursued in an additional 1,598 COVID-19 cases and 1,068 population controls and in other studies from the Host Genetics Initiative (COVID-19 HGI).
To help advance COVID-19 research and allow the wider research community to access to the genome-wide scale results of the SCOURGE study, the variant summary data resulting from the different SCOURGE analyses both for the overall and sex-disaggregated studies and with different outcomes (susceptibility to infection, hospitalization, severe illness, and critical illness) and control definitions (A1, A2 and C; following the COVID-19 HGI nomenclature) can be accessed after an internal assessment of formal requests received. Note that the individual file sizes are around 0.7 Gb each (approx. 7.5 Gb in total).
No individual level data will be made available. Granted requests will have access to a file with the GWAS meta-analysis variant summary data with information for the following descriptors:
• CHR [chromosome]
• POS [position, according to the GRCh38 reference]
• Allele1 [non effect allele]
• Allele2 [effect allele]
• AF_Allele2 [frequency of the effect allele in the study]
• Rsq [imputation r2 on the study. An NA is indicated for the genotyped variants]
• BETA [the beta (effect size) of Allele2 in the study]
• SE [the standard error of BETA]
• p.value [the p value from the study]
• SNP [includes the Affymetrix probesetID that may be necessary for downstream analyses or a chr:pos:allele1:allele2 identifier for all others]
• SNP2 [a chr:pos:allele1:allele2 identifier for all the variants]
Here we have conducted the largest GWAS meta-analysis for COVID-19 hospitalization in admixed Americans, comprising a total of 4,702 hospitalized cases recruited by SCOURGE and other seven participating studies in the COVID-19 Host Genetic Initiative (COVID-19 HGI) [2]. The main scripts used for this study are available here.
To help advance COVID-19 research and allow the wider research community to access to the genome-wide scale results of the SCOURGE study, the variant summary data resulting from the association study in SCOURGE samples can be accessed after an internal assessment of formal requests received.
No individual level data will be made available. Granted requests will have access to a file with the GWAS data of SCOURGE Latin-America (N=3,512) with information for the following descriptors:
• CHR [chromosome]
• POS [position, according to the GRCh38 reference]
• SNP2 [chr#:position:nea-ea, according to the GRCh38 reference]
• NEA [non effect allele]
• EA [effect allele]
• EAF [frequency of the effect allele in the study]
• N [count of individuals]
• beta [the beta (effect size) of EA in the study]
• SE [the standard error of beta]
• pval [the p value from the study]
• SNP [#:position:nea-ea, according to the GRCh38 reference]
Requesters should access the request form here: https://redcap.ciberisciii.es/surveys/?s=CMHFLDHXPALX3AAL
Requesters should provide the following information: full name and title of the PI, affiliation, and a brief description of the project and the aims where the data is to be used. They should also explicitly indicate that the data requester also agrees to: use the data only as part of that indicated research, not redistribute the data outside the project without permission, acknowledge the provenance of the data in any dissemination of results.
The SCOURGE Board of Directors will review the submitted request.
Within a few days, an email from formulariosScourge-CD[at]ciberer[dot]es with the instructions and the link for data downloading will be obtained in response.
Dr. Angel Carracedo - CIBERER, Instituto de Salud Carlos III - Centro Nacional de Genotipado (CEGEN), Universidade de Santiago de Compostela - Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS) - Instituto de Investigación Sanitaria de Santiago (IDIS) - Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Spain
Dr. Pablo Lapunzina - CIBERER, Instituto de Salud Carlos III - ERN-ITHACA-European Reference Network - Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz (IDIPAZ), Spain
Dr. Carlos Flores - CIBERES, Instituto de Salud Carlos III - Research Unit, Hospital Universitario N.S. de Candelaria - Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Spain
Dr. Jose Antonio Riancho - IDIVAL - Hospital U M Valdecilla - Universidad de Cantabria, Spain
Dr. Augusto Rojas-Martinez - Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Mexico
1: Cruz, R., Diz-de Almeida, S. et al. (2022). Novel genes and sex differences in COVID-19 severity. Human molecular genetics, 31(22), 3789–3806. doi: https://doi.org/10.1093/hmg/ddac132
2: Diz-de Almeida, S. et al. (2024). Novel risk loci for COVID-19 hospitalization among admixed American populations. eLife 13:RP93666. doi: https://doi.org/10.7554/eLife.93666.1