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Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness
Ist Teil von
Science (American Association for the Advancement of Science), 2022-06, Vol.376 (6599), p.1327-1332
Ort / Verlag
United States: The American Association for the Advancement of Science
Erscheinungsjahr
2022
Quelle
American Association for the Advancement of Science
Beschreibungen/Notizen
Repeated emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased fitness underscores the value of rapid detection and characterization of new lineages. We have developed PyR
, 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
to all publicly available SARS-CoV-2 genomes, we identify numerous substitutions that increase fitness, including previously identified spike mutations and many nonspike mutations within the nucleocapsid and nonstructural proteins. PyR
forecasts growth of new lineages from their mutational profile, ranks the fitness of lineages as new sequences become available, and prioritizes mutations of biological and public health concern for functional characterization.