Mary Wilson
Well-known member
24 May 2022
DOI: 10.1126/science.abm1208
FRITZ OBERMEYER, MARTIN JANKOWIAK, NIKOLAOS BARKAS, TEPHEN F. SCHAFFNER, JESSE D. PYLE, LEONID YURKOVETSKIY, MATTEO BOSSO, DANIEL J. PARK, MEHRTASH BABADI, BRONWYN L. MACINNIS, JEREMY LUBAN, PARDIS C. SABETI AND JACOB E. LEMIEUX
Abstract
Repeated emergence of 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 non-spike 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.
https://www.science.org/doi/10.1126/science.abm1208
DOI: 10.1126/science.abm1208
FRITZ OBERMEYER, MARTIN JANKOWIAK, NIKOLAOS BARKAS, TEPHEN F. SCHAFFNER, JESSE D. PYLE, LEONID YURKOVETSKIY, MATTEO BOSSO, DANIEL J. PARK, MEHRTASH BABADI, BRONWYN L. MACINNIS, JEREMY LUBAN, PARDIS C. SABETI AND JACOB E. LEMIEUX
Abstract
Repeated emergence of 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 non-spike 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.
https://www.science.org/doi/10.1126/science.abm1208
