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. 2006 Dec;2(12):e125.
doi: 10.1371/journal.ppat.0020125.

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

Martha I Nelson  1 , Lone Simonsen, Cecile Viboud, Mark A Miller, Jill Taylor, Kirsten St George, Sara B Griesemer, Elodie Ghedin, Naomi A Sengamalay, David J Spiro, Igor Volkov, Bryan T Grenfell, David J Lipman, Jeffery K Taubenberger, Edward C Holmes
Affiliations

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

Martha I Nelson et al. PLoS Pathog. 2006 Dec.

Erratum in

  • PLoS Pathog. 2006 Dec;2(12):e138. Ghedi, Elodie [corrected to Ghedin, Elodie]

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.

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Conflict of interest statement

Competing interests. The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Phylogenetic Relationships of the NA Gene of Influenza Viruses Sampled from New York State and Globally during 1997–2005, Estimated Using an ML Method
Rectangles represent clusters of related New York State isolates, with the size of the rectangle reflecting the number of isolates in the clade. Roman numerals indicate separate clades, with the numbers assigned on an arbitrary basis. Rectangles are color-coded according to season: 1997–1998, orange; 1998–1999, yellow; 1999–2000, light green; 2001–2002, dark green; 2002–2003, light blue; 2003–2004, dark blue; and 2004–2005, purple; globally sampled background isolates are in red. The 2003–2004 clade V corresponds to the reassortant “clade B” defined previously [13]. Bootstrap values (>70%) are shown for key nodes. The tree is midpoint rooted for purposes of clarity, and all horizontal branch lengths are drawn to scale.
Figure 2
Figure 2. Phylogenetic Relationships of the HA Gene of Influenza Viruses Sampled from New York State and Globally during 1997–2005, Estimated Using an ML Method
Rectangles represent clusters of related New York State isolates, with the size of the rectangle reflecting the number of isolates in the clade. Roman numerals indicate separate clades, with seasons colored as in Figure 1. Note that Roman numerals only denote the number of separate entries and do not correspond to the clade numbers given in Figure 1. Bootstrap values (>70%) are shown for key nodes. The tree is midpoint rooted for purposes of clarity, and all horizontal branch lengths are drawn to scale.
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