Genetic Risk Prediction of COVID-19 Susceptibility and Severity in the Indian Population

P. Prakrithi, Priya Lakra, Durai Sundar, Manav Kapoor, Mitali Mukerji, Ishaan Gupta, Indian Genome Variation Consortium The Indian Genome Variation Consortium

Research output: Contribution to journalArticlepeer-review

4 Scopus citations


Host genetic variants can determine their susceptibility to COVID-19 infection and severity as noted in a recent Genome-wide Association Study (GWAS). Given the prominent genetic differences in Indian sub-populations as well as differential prevalence of COVID-19, here, we compute genetic risk scores in diverse Indian sub-populations that may predict differences in the severity of COVID-19 outcomes. We utilized the top 100 most significantly associated single-nucleotide polymorphisms (SNPs) from a GWAS by Pairo-Castineira et al. determining the genetic susceptibility to severe COVID-19 infection, to compute population-wise polygenic risk scores (PRS) for populations represented in the Indian Genome Variation Consortium (IGVC) database. Using a generalized linear model accounting for confounding variables, we found that median PRS was significantly associated (p < 2 x 10−16) with COVID-19 mortality in each district corresponding to the population studied and had the largest effect on mortality (regression coefficient = 10.25). As a control we repeated our analysis on randomly selected 100 non-associated SNPs several times and did not find significant association. Therefore, we conclude that genetic susceptibility may play a major role in determining the differences in COVID-19 outcomes and mortality across the Indian sub-continent. We suggest that combining PRS with other observed risk-factors in a Bayesian framework may provide a better prediction model for ascertaining high COVID-19 risk groups and to design more effective public health resource allocation and vaccine distribution schemes.

Original languageEnglish
Article number714185
JournalFrontiers in Genetics
StatePublished - 11 Oct 2021
Externally publishedYes


  • COVID-19
  • Indian population
  • genetic risk prediction
  • genetics
  • polygenic risk score
  • suscepibility


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