Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness.

ABSTRACT: Repeated emergence of SARS-CoV-2 variants with increased fitness necessitates rapid detection and characterization of new lineages. To address this need, we developed PyR ₀ , a hierarchical Bayesian multinomial logistic regression model that infers relative prevalence of all viral lineages across geographic regions, detects lineages increasing in prevalence, and identifies mutations relevant to fitness. Applying PyR ₀ to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many non-spike mutations within the nucleocapsid and nonstructural proteins. PyR ₀ forecasts growth of new lineages from their mutational profile, identifies viral lineages of concern as th

SUBMITTER: Obermeyer F 

PROVIDER: S-EPMC8863165 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature