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This site compiles COVID-19 genetic scan results for immediate public download and use from any source permitting such use. Users may cite this resource by referencing the HGG Advances publication Thibord et al. 2022. Right click links provided here and select “open link in a new tab” to stay on this webpage.
Format changes: 1) some variants have scientific format POS, i.e. 1.2e+07 for 12000000, now changed to integer, 2) 01, 02,…, 09 in CHR, now changed to 1, 2,.., 9. Changes are made from 01/04/2021 release.
Prior to 07/14/2020: The use of the term “positive” below denotes a positive or assumed positive COVID-19 case based on study definitions. “Negative” indicates someone who has tested negative or presumed negative based on study definitions for COVID-19.
“Unknown” indicates population control samples who may not have been tested or may not yet have results.
Between 07/14/2020 and 09/08/2020: COVID-19 deaths (ICD 10 U071) or inpatient diagnosis of COVID-19 (ICD 10 U071) were also added to “positive”. When new death data are released by UK BioBank, six COVID-19 death GWAS will be conducted in addition to COVID-19 GWAS.
From 10/16/2020 and on: COVID-19 deaths (ICD 10 U071), inpatient diagnosis of COVID-19 (ICD 10 U071), primary care clinical data indicating COVID-19 (both TPP/CTV3 and EMIS/SNOMED CT coding systems – see below) were also added to “positive”.
COVID-19 in TPP/CTV3 coding system (01/31/2020 or later)
Y228d: Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed by laboratory test (situation)
Y20d1: Severe acute respiratory syndrome coronavirus 2 detected (finding)
Y20fa: Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 (disorder)
Y210a: Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (disorder)
Y210b: Infection of upper respiratory tract caused by severe acute respiratory syndrome coronavirus 2 (disorder)
Y210e: Detection of severe acute respiratory syndrome coronavirus 2 using polymerase chain reaction technique (procedure)
Y23f7: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) detection result positive
COVID-19 in EMIS/SNOMED CT coding system (01/31/2020 or later)
EMISNQCO303: 2019-nCoV (Wuhan) infection
186747009: Coronavirus infection (disorder)
12802201000006101: Confirmed 2019-nCoV (novel coronavirus) infection
1240581000000104: 2019-nCoV (novel coronavirus) detected
1300721000000109: Coronavirus disease 19 caused by severe acute respiratory syndrome coronavirus 2 confirmed by laboratory test (situation)
1240751000000100: Disease caused by 2019-nCoV (novel coronavirus)
1240561000000108: Encephalopathy caused by 2019-nCoV (novel coronavirus)
1240571000000101: Gastroenteritis caused by 2019-nCoV (novel coronavirus)
1240531000000103: Myocarditis caused by 2019-nCoV (novel coronavirus)
1240521000000100: Otitis media caused by 2019-nCoV (novel coronavirus)
1240551000000105: Pneumonia caused by 2019-nCoV (novel coronavirus)
1240541000000107: Upper respiratory tract infection caused by 2019-nCoV (novel coronavirus)
1240511000000106: Detection of 2019-nCoV (novel coronavirus) using polymerase chain reaction technique
1240381000000105: Severe acute respiratory syndrome coronavirus 2 (organism)
1321541000000108: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgG detection result positive (added since 02/24/2021)
1321551000000106: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) IgM detection result positive (added since 02/24/2021)
1300731000000106: COVID-19 confirmed using clinical diagnostic criteria (added since 02/24/2021)
From 11/03/2020 and on: We added hospitalized COVID-19 GWAS and severe COVID-19 GWAS with primary care data (both TPP/CTV3 and EMIS/SNOMED CT) being released by UKBB. A hospitalized COVID-19 case is defined by a sample with inpatient diagnosis of
COVID-19 (ICD 10 U071). A severe COVID-19 case is defined by a sample with COVID-19 death (ICD 10 U071) or with inpatient diagnosis of both COVID-19 and dependence on respirator (ICD 10 Z991 and Z9911) in the same instance index, or
a COVID-10 case with advanced respiratory support (from inpatient critical care data). Due to limited case samples, currently we only conducted both hospitalized and sever COVID-19 GWAS for European and overall samples in UKBB – with
3 additional non-European GWAS for hospitalized COVID-19.
From 02/24/2021 and on: We added two COVID-19 GWAS in UKBB EAS samples, and three hospitalized COVID-19 GWAS for each of the UKBB AFR, SAS and OTHERS samples.
Note OTHERS samples include samples that are not EUR, AFR and SAS, thus EAS are included in OTHERS.
After each COVID-19 release of UK Biobank data (https://biobank.ctsu.ox.ac.uk/crystal/exinfo.cgi?src=timelines_all) we are calculating GWAS summary statistics and releasing them to this site. GWAS were conducted
with SAIGE (https://github.com/weizhouUMICH/SAIGE) adjusted for baseline age, sex and 10 principal components.
Summary statistics are for UK Biobank (v.3) imputed genome-wide association (GWAS) studies of COVID-19 test positives with variant filters of imputation quality INFO score >0.3,
minor allele count (MAC) > 2, minor allele frequency > 0.0001.
Note allele2 is coded allele.
See SAIGE output description here: https://github.com/weizhouUMICH/SAIGE/wiki/Genetic-association-tests-using-SAIGE.
Ellinghaus, Degenhardt et al.
Meta-analysis of Spanish and Italian COVID19 cases with respiratory failure
NOTE: full GWAS files are GRCh38 build position whereas top results and annotated files have been Lifted Over to GRCh37.
COVID-19 Host Genetics initiative results provided under Creative Commons License. This includes meta-analyses of international case/control samples with a larger sample size than UKBB alone. These analyses may also have greater test/population ascertainment and genetic heterogeneity effects. If you have samples to contribute we urge you to consider joining.
See also https://www.covid19hg.org/blog/ and https://www.nature.com/articles/s41431-020-0636-6
GWAS of critically ill COVID patients. See also: https://genomicc.org/ and https://pubmed.ncbi.nlm.nih.gov/33307546/
Dube et al.
GWAS of time to remission of symptoms in the COVID colchicine trial COLCORONA. Before using data please see their terms and conditions here: https://pheweb.statgen.org/terms/pheweb/terms.html
Annotation of all top results P<1E-5 was done from several sources:
All files are in compressed Gzip format.
Send questions, comments or requests to add data or analysis to: firstname.lastname@example.org, email@example.com,
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