Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus

PLoS Pathogens

Bryan T Grenfell¹  Martha I Nelson¹  Igor Volkov¹  Cecile Viboud²  David J Lipman²  Mark A Miller²  Edward C Holmes³  Jeffery K Taubenberger⁴  Lone Simonsen⁵  Naomi A Sengamalay⁶  Elodie Ghedin⁶  David J Spiro⁶  Jill Taylor⁷  Sara B Griesemer⁷  Kirsten St George⁷ 

[1] Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America;Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America;Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America;National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America;National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America;The Institute for Genomic Research, Rockville, Maryland, United States of America;Wadsworth Center, New York State Department of Health, Albany, New York, United States of America

关键词: New York;    Influenza A virus;    Phylogenetic analysis;    Viral evolution;    Influenza viruses;    Evolutionary genetics;    Microbial genetics;    Influenza;   

DOI  :  10.1371/journal.ppat.0020125

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic seasons, the evolutionary processes shaping influenza virus diversity within seasons are less clear. Here we show with a phylogenetic analysis of 413 complete genomes of human H3N2 influenza A viruses collected between 1997 and 2005 from New York State, United States, that genetic diversity is both abundant and largely generated through the seasonal importation of multiple divergent clades of the same subtype. These clades cocirculated within New York State, allowing frequent reassortment and generating genome-wide diversity. However, relatively low levels of positive selection and genetic diversity were observed at amino acid sites considered important in antigenic drift. These results indicate that adaptive evolution occurs only sporadically in influenza A virus; rather, the stochastic processes of viral migration and clade reassortment play a vital role in shaping short-term evolutionary dynamics. Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis.

【 授权许可】

CC BY