Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses
Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses
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Date
2005
Authors
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.
Advisor
Citation
Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses. E.C. Holmes, E. Ghedin, N. Miller, J. Taylor, Y. Bao, K. St. George, B.T. Grenfell, S.L. Salzberg, C.M. Fraser, D.J. Lipman, and J.K. Taubenberger. PLoS Biology 3:9 (2005), e300
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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.