Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 35608456.
- Also identified by DOI 10.1126/science.abm1208 and PMC identifier 9161372.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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<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 identify numerous substitutions that increase fitness, including previously identified spike mutations and many nonspike mutations within the nucleocapsid and nonstructural proteins. PyR<sub>0</sub> 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.
Medical subject headings
- COVID-19
- Genetic Fitness
- SARS-CoV-2