title: The early diversification of influenza A/H1N1pdm.
abstract: Background Since its initial detection in April 2009, the A/H1N1pdm influenza virus has spread rapidly in humans, with over 5,700 human deaths. However, little is known about the evolutionary dynamics of H1N1pdm and its geographic and temporal diversification.Methods Phylogenetic analysis was conducted upon the concatenated coding regions of whole-genome sequences from 290 H1N1pdm isolates sampled globally between April 1 - July 9, 2009, including relatively large samples from the US states of Wisconsin and New York. Results At least 7 phylogenetically distinct viral clades have disseminated globally and co-circulated in localities that experienced multiple introductions of H1N1pdm. The epidemics in New York and Wisconsin were dominated by two different clades, both phylogenetically distinct from the viruses first identified in California and Mexico, suggesting an important role for founder effects in determining local viral population structures. Conclusions Determining the global diversity of H1N1pdm is central to understanding the evolution and spatial spread of the current pandemic, and to predict its future impact on human populations. Our results indicate that H1N1pdm has already diversified into distinct viral lineages with defined spatial patterns.
authors.affiliation: Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Martha
authors.initials: M
authors.lastname: Nelson
authors.forename: David
authors.initials: D
authors.lastname: Spiro
authors.forename: David
authors.initials: D
authors.lastname: Wentworth
authors.forename: Eric
authors.initials: E
authors.lastname: Beck
authors.forename: Jiang
authors.initials: J
authors.lastname: Fan
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
authors.forename: Rebecca
authors.initials: R
authors.lastname: Halpin
authors.forename: Jayati
authors.initials: J
authors.lastname: Bera
authors.forename: Erin
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authors.lastname: Hine
authors.forename: Kathleen
authors.initials: K
authors.lastname: Proudfoot
authors.forename: Tim
authors.initials: T
authors.lastname: Stockwell
authors.forename: Xudong
authors.initials: X
authors.lastname: Lin
authors.forename: Sara
authors.initials: S
authors.lastname: Griesemer
authors.forename: Swati
authors.initials: S
authors.lastname: Kumar
authors.forename: Michael
authors.initials: M
authors.lastname: Bose
authors.forename: Cecile
authors.initials: C
authors.lastname: Viboud
authors.forename: Edward
authors.initials: E
authors.lastname: Holmes
authors.forename: Kelly
authors.initials: K
authors.lastname: Henrickson