Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses

Edward C. Holmes, Elodie Ghedin, Naomi Miller, Jill Taylor, Yiming Bao, Kirsten St. George, Bryan T. Grenfell, Steven L. Salzberg, Claire M. Fraser, David J. Lipman, Jeffery K. Taubenberger

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)1579-1589
Number of pages11
JournalPLoS Biology
Volume3
Issue number9
DOIs
StatePublished - Sep 2005

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H3N2 Subtype Influenza A Virus
human influenza
Influenza A virus
Viruses
Human Influenza
Genes
influenza
Genome
genome
Hemagglutinins
hemagglutinins
monitoring
phylogeny
Phylogeny
Population
Vaccines
genes
vaccines
genomics
viruses

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. / Holmes, Edward C.; Ghedin, Elodie; Miller, Naomi; Taylor, Jill; Bao, Yiming; St. George, Kirsten; Grenfell, Bryan T.; Salzberg, Steven L.; Fraser, Claire M.; Lipman, David J.; Taubenberger, Jeffery K.

In: PLoS Biology, Vol. 3, No. 9, 09.2005, p. 1579-1589.

Research output: Contribution to journalArticle

Holmes, EC, Ghedin, E, Miller, N, Taylor, J, Bao, Y, St. George, K, Grenfell, BT, Salzberg, SL, Fraser, CM, Lipman, DJ & Taubenberger, JK 2005, 'Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses', PLoS Biology, vol. 3, no. 9, pp. 1579-1589. https://doi.org/10.1371/journal.pbio.0030300
Holmes, Edward C. ; Ghedin, Elodie ; Miller, Naomi ; Taylor, Jill ; Bao, Yiming ; St. George, Kirsten ; Grenfell, Bryan T. ; Salzberg, Steven L. ; Fraser, Claire M. ; Lipman, David J. ; Taubenberger, Jeffery K. / Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. In: PLoS Biology. 2005 ; Vol. 3, No. 9. pp. 1579-1589.
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