Stochastic processes constrain the within and between host evolution of influenza virus

eLife

Emily T Martin¹  Arnold S Monto¹  Ryan E Malosh¹  John T McCrone²  Adam S Lauring²  Robert J Woods³ 

[1] Department of Epidemiology, University of Michigan, Ann Arbor, United States;Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States;Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, United States;

关键词: influenza virus;    bottleneck;    transmission;    diversity;    evolution;   

DOI  :  10.7554/eLife.35962

来源: DOAJ

【 摘 要 】

The evolutionary dynamics of influenza virus ultimately derive from processes that take place within and between infected individuals. Here we define influenza virus dynamics in human hosts through sequencing of 249 specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected from individuals in a prospective community-based cohort, they are broadly representative of natural infections with seasonal viruses. Consistent with a neutral model of evolution, sequence data from 49 serially sampled individuals illustrated the dynamic turnover of synonymous and nonsynonymous single nucleotide variants and provided little evidence for positive selection of antigenic variants. We also identified 43 genetically-validated transmission pairs in this cohort. Maximum likelihood optimization of multiple transmission models estimated an effective transmission bottleneck of 1–2 genomes. Our data suggest that positive selection is inefficient at the level of the individual host and that stochastic processes dominate the host-level evolution of influenza viruses.

【 授权许可】

Unknown