Exome-wide association study for replication of rare variants affecting the severity of COVID-19 in the Russian population

Abstract

BACKGROUND: Human genetics is one of the factors determining the severity of COVID-19 disease. Previously, a large-scale whole-genome association study of the COVID-19 HG project (COVID-19 Host Genetics Initiative, 2021) investigated the association of genetic variants at multiple loci with COVID-19 severity. The genetic variants that have the greatest impact on COVID-19 severity are expected to have a low frequency in the population. Therefore, the study of rare variants may provide additional insights into the pathogenesis of the disease and thus help in the development of prevention and treatment options. AIM: The aim is to perform a replication analysis in search of genes with enrichment for rare genetic variants in relation to the severity of COVID-19 disease. METHODS: In this study, the clinical exome of a Russian cohort of patients was sequenced based on the St. Petersburg State Budgetary Institution "City Hospital No. 40" and St. Petersburg State University. The study used biomaterial from patients hospitalised at "City Hospital No. 40" with a diagnosis of COVID-19 and healthy individuals included in the population control group. The severity of the course of COVID-19 was determined according to the results of lung computed tomography. The list of genes for subsequent replication was generated by a literature review. Replication analysis of genes associated with COVID-19 severity was performed using burden test methods. RESULTS: In total, 701 clinical exomes were sequenced: 263 severe COVID-19 and 438 healthy individuals. A literature review identified 18 genes associated with severe COVID-19 that were included in the replication analysis. The replication analysis did not identify any genes whose association with severe COVID-19 was confirmed in the study cohort. CONCLUSION: Replication analysis did not identify any genes for which a significant association between functional variant enrichment and COVID-19 severity was found. However, the results demonstrated that the direction of the correlation was consistent with findings from previous studies. The small size of the sample analysed is an obvious limitation of our study. Expanding the study cohort would increase the power of the tests and allow us to detect additional rare variants that influence the severity of COVID-19 progression