Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness.
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ABSTRACT: One sentence summary
A Bayesian hierarchical model of all SARS-CoV-2 viral genomes predicts lineage fitness and identifies associated mutations.
SUBMITTER: Obermeyer F
PROVIDER: S-EPMC8863165 | biostudies-literature | 2022 Feb
REPOSITORIES: biostudies-literature
Publications
Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness.
Obermeyer Fritz F Jankowiak Martin M Barkas Nikolaos N Schaffner Stephen F SF Pyle Jesse D JD Yurkovetskiy Lonya L Bosso Matteo M Park Daniel J DJ Babadi Mehrtash M MacInnis Bronwyn L BL Luban Jeremy J Sabeti Pardis C PC Lemieux Jacob E JE
medRxiv : the preprint server for health sciences 20220216
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 <sub>0</sub> , 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 <sub>0</sub> to all publicly available SARS-CoV-2 genomes, we identif ...[more]
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