This track shows rare variants associated with monogenic congenital defects of immunity to
the SARS-CoV-2 virus identified by the
COVID Human Genetic Effort.
This international consortium aims to discover truly causative variations: those underlying
severe forms of COVID-19 in previously healthy individuals, and those that make certain
individuals resistant to infection by the SARS-CoV2 virus despite repeated exposure.
The major feature of the small set of variants in this track is that they are functionally tested
to be deleterious and genetically tested to be disease-causing.
Specifically, rare variants were predicted to be loss-of-function at human loci known to govern
interferon (IFN) immunity to influenza virus in patients with life-threatening COVID-19 pneumonia,
relative to subjects with asymptomatic or benign infection.
These genetic defects display incomplete penetrance for influenza respiratory distress and only
appear clinically upon infection with the more virulent SARS-CoV-2.
Only eight genes with 23 variants are contained in this track.
Use the links below to navigate to the gene of interest or view
all eight genes together using the following sessions for
This track uses variant calls in autosomal IFN-related genes from whole exome and genome data
with a MAF lower than 0.001 (gnomAD v2.1.1) and experimental demonstration of loss-of-function.
The patient population studied consisted of 659 patients with life-threatening COVID-19 pneumonia
relative to 534 subjects with asymptomatic or benign infection of varying ethnicities.
Variants underlying autosomal-recessive or autosomal-dominant deficiencies were identified in
23 patients (3.5%) 17 to 77 years of age.
The proportion of individuals carrying at least one variant was compared between severe cases
and control cases by means of logistic regression with the likelihood ratio test.
Principal Component Analysis (PCA) was conducted with Plink v1.9 software on whole exome and
genome sequencing data with the 1000 Genomes (1kG) Project phase 3 public database as reference.
Analysis of enrichment in rare synonymous variants of the genes was performed to check the
calibration of the burden test.
The odds ratio was also estimated by logistic regression and adjusted for ethnic heterogeneity.
The raw data can be explored interactively with the
Table Browser, or the Data Integrator.
Please refer to
our mailing list archives for questions, or our Data Access FAQ for more information.
Thanks to the COVID Human Genetic Effort contributors for making these data available, and in
particular to Qian Zhang at the Rockefeller University for review and input during browser track
Zhang Q, Bastard P, Liu Z, Le Pen J, Moncada-Velez M, Chen J, Ogishi M, Sabli IKD, Hodeib S, Korol C
Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.
Science. 2020 Sep 24;.