The early diversification of influenza A/H1N1pdm

Martha Nelson, David Spiro, David Wentworth, Jiang Fan, Eric Beck, Kirsten St. George, Elodie Ghedin, Rebecca Halpin, Jayati Bera, Erin Hine, Katie Proudfoot, Tim Stockwell, Xudong Lin, Sara Griesemer, Michael Bose, Lisa Jurgens, Swati Kumar, Cecile Viboud, Eddie Holmes, Kelly Henrickson

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Article numberecurrents.RRN1126
JournalPLoS Currents
Issue numberNOV
StatePublished - 2009

ASJC Scopus subject areas

  • Medicine (miscellaneous)


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