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Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States

By MI Nelson, L Edelman, DJ Spiro, AR Boyne, J Bera, R Halpin, E Ghedin, MA Miller, L Simonsen, C Viboud and EC Holmes

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

Year: 2008
DOI identifier: 10.1371/journal.ppat.1000133
OAI identifier: oai:d-scholarship.pitt.edu:12984
Provided by: D-Scholarship@Pitt

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