title: Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses.
abstract: Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2 influenza A viruses collected between 1999 and 2004 from New York State, United States, and observed multiple co-circulating clades with different population frequencies. Strikingly, phylogenies inferred for individual gene segments revealed that multiple reassortment events had occurred among these clades, such that one clade of H3N2 viruses present at least since 2000 had provided the hemagglutinin gene for all those H3N2 viruses sampled after the 2002-2003 influenza season. This reassortment event was the likely progenitor of the antigenically variant influenza strains that caused the A/Fujian/411/2002-like epidemic of the 2003-2004 influenza season. However, despite sharing the same hemagglutinin, these phylogenetically distinct lineages of viruses continue to co-circulate in the same population. These data, derived from the first large-scale analysis of H3N2 viruses, convincingly demonstrate that multiple lineages can co-circulate, persist, and reassort in epidemiologically significant ways, and underscore the importance of genomic analyses for future influenza surveillance.
authors: Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA.
authors: Edward C
authors: EC
authors: Holmes
authors: Elodie
authors: E
authors: Ghedin
authors: Naomi
authors: N
authors: Miller
authors: Jill
authors: J
authors: Taylor
authors: Yiming
authors: Y
authors: Bao
authors: Kirsten
authors: K
authors: St George
authors: Bryan T
authors: BT
authors: Grenfell
authors: Steven L
authors: SL
authors: Salzberg
authors: Claire M
authors: CM
authors: Fraser
authors: David J
authors: DJ
authors: Lipman
authors: Jeffery K
authors: JK
authors: Taubenberger
mesh_terms: D019143:Evolution, Molecular; D005814:Genes, Viral; D014644:Genetic Variation; D016678:Genome; D006801:Humans; D053122:Influenza A Virus, H3N2 Subtype / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D016865:Reassortant Viruses / Q000235:genetics*; D011995:Recombination, Genetic