Stochastic processes are key determinants of short-term evolution in influenza A virus

Martha I. Nelson, Lone Simonsen, Cecile Viboud, Mark A. Miller, Jill Taylor, Kirsten St. George, Sara B. Griesemer, Elodie Ghedi, Naomi A. Sengamalay, David J. Spiro, Igor Volkov, Bryan T. Grenfell, David J. Lipman, Jeffery K. Taubenberger, Edward C. Holmes

Research output: Contribution to journalArticle

142 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1144-1151
Number of pages8
JournalPLoS pathogens
Volume2
Issue number12
DOIs
StatePublished - Dec 2006

All Science Journal Classification (ASJC) codes

  • Parasitology
  • Microbiology
  • Immunology
  • Molecular Biology
  • Genetics
  • Virology

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