Influenza evolution: the importance of chance processes
Extensive within-season genetic diversity in influenza A H3N2 viruses in New York State appears to arise from successive introduction of new variants from elsewhere; most viruses circulating in a given season are introduced from elsewhere.
Author(s): Martha I. Nelson, 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
Title: Stochastic processes are key determinants of short-term evolution in influenza A virus
Journal: PLoS Pathogens 2(11): e125
Transmission electron micrograph of an influenza virion. Image courtesy of the Public Health Image Library (no. 8430)
Had your 'flu shot this year? If it's been a while since you were vaccinated or naturally infected, you may well be susceptible. Influenza virus is well known to demonstrate immune escape: genetic changes lead to changes in surface antigens, so your immune system is less likely to recognize the virus on re-encounter.
What's less clear is the extent of evolution during a single season's influenza epidemic, how the genetic diversity in one place in one year is reflected in the virus population there the following year, and how much of within-season genetic change is adaptive (in that it contributes to antigenic change, hence immune escape).
Now a team led by CIDD researchers have tackled these questions by analyzing 413 complete genomes of influenza A subtype H3N2 from New York State in the USA, the largest such study yet conducted.
They discovered that:
- There is extensive within-season genetic diversity in the viruses circulating in New York State. However, this variation appears to arise from successive introductions of variants from elsewhere, rather than from in situ evolution. Within any one season, several different genetic variants co-circulate, sometimes exchanging material by reassortment.
- Viral lineages observed during one season do not seed those seen in later seasons; instead, most viruses circulating in a given season are introduced from elsewhere in the world.
- Adaptive evolution in the haemagglutinin (HA) antigen is rarely seen within seasons. This suggests that antigenic drift may happen more sporadically than previously thought.
The authors detail these findings, and their implications, in a December 2006 issue of PLoS Pathogens. In particular, they highlight how influenza virus diversity and evolution is strongly affected by chance events, such as reassortment between strains coinfecting a host or introduction of a particular variant from elsewhere.