基因组
生物
进化生物学
遗传学
突变
计算生物学
2019年冠状病毒病(COVID-19)
遗传适应性
严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)
冠状病毒
基因
疾病
医学
传染病(医学专业)
病理
作者
Fritz Obermeyer,Martin Jankowiak,Nikolaos Barkas,S. F. Schaffner,Jesse D. Pyle,Leonid Yurkovetskiy,Matteo Bosso,Daniel J. Park,Mehrtash Babadi,Bronwyn MacInnis,Jeremy Luban,Pardis C. Sabeti,Jacob E. Lemieux
出处
期刊:Science
[American Association for the Advancement of Science (AAAS)]
日期:2022-05-24
卷期号:376 (6599): 1327-1332
被引量:250
标识
DOI:10.1126/science.abm1208
摘要
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 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 nonspike mutations within the nucleocapsid and nonstructural proteins. PyR 0 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.
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