Trait: Orthocoronavirinae infectious disease

Trait Information
Identifier MONDO_0020753
Description Infectious disease causes by viruses in the subfamily Orthocoronavirinae (coronaviruses). In humans, coronaviruses cause respiratory tract infections that can be mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), and others that can be lethal, such as SARS, MERS, and COVID-19. [Wikipedia: Coronavirus]
Trait category
Other trait
Synonyms 2 synonyms
  • Coronavinae infectious disease
  • coronavirus infectious disease
Child trait(s) COVID-19

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Note: This table shows PGS for child terms of "Orthocoronavirinae infectious disease" in the EFO hierarchy.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS002272
(GRS6_COVID)
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 COVID-19 infection COVID-19 6
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002272/ScoringFiles/PGS002272.txt.gz
PGS002273
(GRS12_COVID)
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 COVID-19 infection COVID-19 12
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002273/ScoringFiles/PGS002273.txt.gz
PGS004938
(pgs_data_ldpred)
 PGP000666 |
Kovalenko E et al. Front Med (Lausanne) (2024)
 Severe COVID-19 course COVID-19 955,503
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004938/ScoringFiles/PGS004938.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM012926 PGS002272
(GRS6_COVID)
 PSS009624|
European Ancestry|
44,958 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of hospitalization (COVID-19) — — OR (top 10% vs rest of population): 1.38 [1.26, 1.53] Age, sex, age-by-sex interaction and ten ancestry-informative PCs —
PPM012927 PGS002272
(GRS6_COVID)
 PSS009624|
European Ancestry|
44,958 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of severe disease (COVID-19) — — OR (top 10% vs rest of population): 1.58 [1.36, 1.82] Age, sex, age-by-sex interaction and ten ancestry-informative PCs —
PPM012928 PGS002272
(GRS6_COVID)
 PSS009623|
African Ancestry|
2,598 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of hospitalization (COVID-19) — — OR (top 10% vs rest of population): 1.7 [1.03, 2.82] Age, sex, age-by-sex interaction and ten ancestry-informative PCs —
PPM012929 PGS002272
(GRS6_COVID)
 PSS009625|
Hispanic or Latin American Ancestry|
3,752 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of hospitalization (COVID-19) — — OR (top 10% vs rest of population): 1.56 [1.0, 2.43] Age, sex, age-by-sex interaction and ten ancestry-informative PCs —
PPM012930 PGS002272
(GRS6_COVID)
 PSS009626|
South Asian Ancestry|
760 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of hospitalization (COVID-19) — — OR (top 10% vs rest of population): 1.42 [0.72, 2.82] Age, sex, age-by-sex interaction and ten ancestry-informative PCs —
PPM012933 PGS002272
(GRS6_COVID)
 PSS009624|
European Ancestry|
44,958 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of hospitalization (COVID-19) in those with high clinical risk — — OR (top 10% vs rest of population): 1.39 [1.23, 1.56] — High clinical risk included indiviiduals with any of the following criteria: age≥65, BMI≥35, chronic kidney disease, diabetes, immunosuppressive disease, or age ≥55 and presence of chronic obstructive pulmonary disease, cardiovascular disease, or hypertension
PPM012934 PGS002272
(GRS6_COVID)
 PSS009624|
European Ancestry|
44,958 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of severe disease (COVID-19) in those with high clinical risk — — OR (top 10% vs rest of population): 1.65 [1.39, 1.96] — High clinical risk included indiviiduals with any of the following criteria: age≥65, BMI≥35, chronic kidney disease, diabetes, immunosuppressive disease, or age ≥55 and presence of chronic obstructive pulmonary disease, cardiovascular disease, or hypertension
PPM012935 PGS002272
(GRS6_COVID)
 PSS009625|
Hispanic or Latin American Ancestry|
3,752 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of severe disease (COVID-19) in those with high clinical risk — — OR (top 10% vs rest of population): 3.35 [1.56, 7.2] — —
PPM012936 PGS002272
(GRS6_COVID)
 PSS009622|
European Ancestry|
14,320 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of hospitalization (COVID-19) — AUROC: 0.659 [0.639, 0.679] — age, sex, PCs —
PPM012937 PGS002272
(GRS6_COVID)
 PSS009622|
European Ancestry|
14,320 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of hospitalization (COVID-19) — AUROC: 0.708 [0.688, 0.727] — age, sex, PCs, BMI, CVD, hypertension, diabetes, CKD, COPD, Autoimmune —
PPM012938 PGS002272
(GRS6_COVID)
 PSS009622|
European Ancestry|
14,320 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of severe disease (COVID-19) — AUROC: 0.696 [0.668, 0.723] — age, sex, PCs —
PPM012939 PGS002272
(GRS6_COVID)
 PSS009622|
European Ancestry|
14,320 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of severe disease (COVID-19) — AUROC: 0.75 [0.723, 0.776] — age, sex, PCs, BMI, CVD, hypertension, diabetes, CKD, COPD, Autoimmune —
PPM012940 PGS002272
(GRS6_COVID)
 PSS009621|
European Ancestry|
25,353 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of hospitalization (COVID-19) — AUROC: 0.744 [0.731, 0.756] — age, sex, PCs —
PPM012941 PGS002272
(GRS6_COVID)
 PSS009621|
European Ancestry|
25,353 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of hospitalization (COVID-19) — AUROC: 0.766 [0.753, 0.778] — age, sex, PCs, BMI, CVD, hypertension, diabetes, CKD, COPD, Autoimmune —
PPM012942 PGS002272
(GRS6_COVID)
 PSS009621|
European Ancestry|
25,353 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of severe disease (COVID-19) — AUROC: 0.796 [0.777, 0.815] — age, sex, PCs —
PPM012943 PGS002272
(GRS6_COVID)
 PSS009621|
European Ancestry|
25,353 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of severe disease (COVID-19) — AUROC: 0.814 [0.769, 0.832] — age, sex, PCs, BMI, CVD, hypertension, diabetes, CKD, COPD, Autoimmune —
PPM012931 PGS002273
(GRS12_COVID)
 PSS009624|
European Ancestry|
44,958 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of hospitalization (COVID-19) — — OR (top 10% vs rest of population): 1.38 [1.26, 1.52] Age, sex, age-by-sex interaction and ten ancestry-informative PCs —
PPM012932 PGS002273
(GRS12_COVID)
 PSS009624|
European Ancestry|
44,958 individuals
 PGP000302 |
Horowitz JE et al. Nat Genet (2022)
 Reported Trait: Risk of severe disease (COVID-19) — — OR (top 10% vs rest of population): 1.64 [1.43, 1.9] Age, sex, age-by-sex interaction and ten ancestry-informative PCs —
PPM021730 PGS004938
(pgs_data_ldpred)
 PSS011763|
European Ancestry|
7,124 individuals
 PGP000666 |
Kovalenko E et al. Front Med (Lausanne) (2024)
 Reported Trait: Severe COVID-19 course — AUROC: 0.6 Odds ratio (OR, high vs low tertile): 2.25 PC1-20, sex, gender —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS009621 COVID-19 positive, that is, those with a positive qPCR orserology test for SARS-CoV-2 or with a COVID-19-related ICD-10 code (U07), hospitalization or death — 25,353 individuals — European — AncestryDNA —
PSS009622 COVID-19 positive, that is, those with a positive qPCR orserology test for SARS-CoV-2 or with a COVID-19-related ICD-10 code (U07), hospitalization or death — 14,320 individuals — European — UKB —
PSS009623 COVID-19 positive, that is, those with a positive qPCR orserology test for SARS-CoV-2 or with a COVID-19-related ICD-10 code (U07), hospitalization or death — 2,598 individuals — African unspecified — AncestryDNA, MyCode, UKB Meta-analysis
PSS009624 COVID-19 positive, that is, those with a positive qPCR orserology test for SARS-CoV-2 or with a COVID-19-related ICD-10 code (U07), hospitalization or death — 44,958 individuals — European — AncestryDNA, MyCode, UKB Meta-analysis
PSS009625 COVID-19 positive, that is, those with a positive qPCR orserology test for SARS-CoV-2 or with a COVID-19-related ICD-10 code (U07), hospitalization or death — 3,752 individuals — Hispanic or Latin American — AncestryDNA, MyCode, UKB Meta-analysis
PSS009626 COVID-19 positive, that is, those with a positive qPCR orserology test for SARS-CoV-2 or with a COVID-19-related ICD-10 code (U07), hospitalization or death — 760 individuals — South Asian — AncestryDNA, MyCode, UKB Meta-analysis
PSS011763 Very severe respiratory confirmed covid vs. not severe respiratory confirmed covid —
[
  • 724 cases
  • , 6,400 controls
]
 — European — Genotek —