Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus During a Single Epidemic Season in the United States

PLoS Pathog. 2008 Aug 22;4(8):e1000133. doi: 10.1371/journal.ppat.1000133.

Abstract

To determine the spatial and temporal dynamics of influenza A virus during a single epidemic, we examined whole-genome sequences of 284 A/H1N1 and 69 A/H3N2 viruses collected across the continental United States during the 2006-2007 influenza season, representing the largest study of its kind undertaken to date. A phylogenetic analysis revealed that multiple clades of both A/H1N1 and A/H3N2 entered and co-circulated in the United States during this season, even in localities that are distant from major metropolitan areas, and with no clear pattern of spatial spread. In addition, co-circulating clades of the same subtype exchanged genome segments through reassortment, producing both a minor clade of A/H3N2 viruses that appears to have re-acquired sensitivity to the adamantane class of antiviral drugs, as well as a likely antigenically distinct A/H1N1 clade that became globally dominant following this season. Overall, the co-circulation of multiple viral clades during the 2006-2007 epidemic season revealed patterns of spatial spread that are far more complex than observed previously, and suggests a major role for both migration and reassortment in shaping the epidemiological dynamics of human influenza A virus.

Publication types

  • Historical Article
  • Research Support, N.I.H., Extramural

MeSH terms

  • Genome, Viral*
  • History, 21st Century
  • Humans
  • Influenza A Virus, H1N1 Subtype / genetics*
  • Influenza A Virus, H3N2 Subtype / genetics*
  • Influenza, Human / epidemiology*
  • Influenza, Human / genetics*
  • Molecular Epidemiology
  • Phylogeny*
  • United States / epidemiology