Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States

Martha I. Nelson, Yi Tan, Elodie Ghedin, David E. Wentworth, Kirsten St George, Laurel Edelman, Eric T. Beck, Jiang Fan, Tommy Tsan Yuk Lam, Swati Kumar, David J. Spiro, Lone Simonsen, Cecile Viboud, Edward C. Holmes, Kelly J. Henrickson, James M. Musser

Research output: Contribution to journalArticle

Abstract

Spatial variation in the epidemiological patterns of successive waves of pandemic influenza virus in humans has been documented throughout the 20th century but never understood at a molecular level. However, the unprecedented intensity of sampling and whole-genome sequencing of the H1N1/09 pandemic virus now makes such an approach possible. To determine whether the spring and fall waves of the H1N1/09 influenza pandemic were associated with different epidemiological patterns, we undertook a large-scale phylogeographic analysis of viruses sampled from three localities in the United States. Analysis of genomic and epidemiological data reveals distinct spatial heterogeneities associated with the first pandemic wave, March to July 2009, in Houston, TX, Milwaukee, WI, and New York State. In Houston, no specific H1N1/09 viral lineage dominated during the spring of 2009, a period when little epidemiological activity was observed in Texas. In contrast, major pandemic outbreaks occurred at this time in Milwaukee and New York State, each dominated by a different viral lineage and resulting from strong founder effects. During the second pandemic wave, beginning in August 2009, all three U.S. localities were dominated by a single viral lineage, that which had been dominant in New York during wave 1. Hence, during this second phase of the pandemic, extensive viral migration and mixing diffused the spatially defined population structure that had characterized wave 1, amplifying the one viral lineage that had dominated early on in one of the world's largest international travel centers.

Original languageEnglish (US)
Pages (from-to)828-834
Number of pages7
JournalJournal of Virology
Volume85
Issue number2
DOIs
StatePublished - Jan 2011

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Phylogeography
Pandemics
pandemic
phylogeography
Orthomyxoviridae
Human Influenza
Viruses
Founder Effect
viruses
founder effect
influenza
travel
Disease Outbreaks
spatial variation
population structure
Genome
genomics
genome

ASJC Scopus subject areas

  • Immunology
  • Virology

Cite this

Nelson, M. I., Tan, Y., Ghedin, E., Wentworth, D. E., George, K. S., Edelman, L., ... Musser, J. M. (2011). Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States. Journal of Virology, 85(2), 828-834. https://doi.org/10.1128/JVI.01762-10

Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States. / Nelson, Martha I.; Tan, Yi; Ghedin, Elodie; Wentworth, David E.; George, Kirsten St; Edelman, Laurel; Beck, Eric T.; Fan, Jiang; Lam, Tommy Tsan Yuk; Kumar, Swati; Spiro, David J.; Simonsen, Lone; Viboud, Cecile; Holmes, Edward C.; Henrickson, Kelly J.; Musser, James M.

In: Journal of Virology, Vol. 85, No. 2, 01.2011, p. 828-834.

Research output: Contribution to journalArticle

Nelson, MI, Tan, Y, Ghedin, E, Wentworth, DE, George, KS, Edelman, L, Beck, ET, Fan, J, Lam, TTY, Kumar, S, Spiro, DJ, Simonsen, L, Viboud, C, Holmes, EC, Henrickson, KJ & Musser, JM 2011, 'Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States', Journal of Virology, vol. 85, no. 2, pp. 828-834. https://doi.org/10.1128/JVI.01762-10
Nelson, Martha I. ; Tan, Yi ; Ghedin, Elodie ; Wentworth, David E. ; George, Kirsten St ; Edelman, Laurel ; Beck, Eric T. ; Fan, Jiang ; Lam, Tommy Tsan Yuk ; Kumar, Swati ; Spiro, David J. ; Simonsen, Lone ; Viboud, Cecile ; Holmes, Edward C. ; Henrickson, Kelly J. ; Musser, James M. / Phylogeography of the spring and fall waves of the H1N1/09 pandemic influenza virus in the United States. In: Journal of Virology. 2011 ; Vol. 85, No. 2. pp. 828-834.
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