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Title: Spatial dynamics of human-origin H1 influenza A v irus in North American swine

item NELSON, MARTHA - National Institutes Of Health (NIH)
item LEMEY, PHILIPPE - Katholieke University
item TAN, YI - National Institutes Of Health (NIH)
item Baker, Amy
item LAM, TOMMY - Pennsylvania State University
item DETMER, SUSAN - University Of Minnesota
item VIBOUD, CECILE - National Institutes Of Health (NIH)
item SUCHARD, MARC - University Of California
item RAMBAUT, ANDREW - University Of Edinburgh
item HOLMES, EDWARD - Pennsylvania State University
item GRAMER, MARIE - University Of Minnesota

Submitted to: PLoS Pathogens
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/7/2011
Publication Date: 6/1/2011
Citation: Nelson, M.I., Lemey, P., Tan, Y., Vincent, A., Lam, T.T-Y., Detmer, S., Viboud, C., Suchard, M.A., Rambaut, A., Holmes, E.C., Gramer, M. 2011. Spatial dynamics of human-origin H1 influenza A virus in North American swine. PLoS Pathogens. 7(6):e1002077.

Interpretive Summary: This study uses sequence data from the RNA genetic material from swine influenza viruses for understanding the way these viruses are evolving and moving in the swine population in the USA. The study considers the role of the long-distance transport of pigs in the United States in the spread of influenza viruses of the A/H1N1 and A/H1N2 subtypes that were transmitted from humans to swine in 2003. Using the most intensive nationwide sampling of swine influenza viruses to date (n = 1,416 HA1 sequences), a recently developed method of statistical analysis shows that large-scale movements of swine are important in the spread of the influenza virus from the South to the grain-rich Midwestern US, where swine are fattened in the latter stages of life. In sum, this study reveals the effects of large-scale structural changes in the US swine industry on the spread and evolutionary dynamics of an economically important pathogen in the swine industry that also presents a threat to human health. Further understanding of the role of long-distance pig transport in the ecology and evolution of swine influenza viruses in the US may inform targeted surveillance and mitigation strategies in the future.

Technical Abstract: The emergence and rapid global spread of the swine-origin H1N1/09 pandemic influenza A virus in humans underscores the importance of swine populations as reservoirs for genetically diverse influenza viruses with the potential to infect humans. However, despite their significance for animal and human health, relatively little is known about the phylogeography of swine influenza viruses in the United States. This study utilizes an expansive data set of hemagglutinin (HA1) sequences (n = 1520) from swine influenza viruses collected in North America during the period 2003-2010. With these data we investigate the spatial dissemination of a novel influenza virus of the H1 subtype that was introduced into the North American swine population via two separate human-to-swine transmission events around 2003. Bayesian phylogeographic analysis reveals that the spatial dissemination of this influenza virus in the US swine population follows long-distance swine movements from the Southern U.S. to the Midwest, a corn-rich commercial center that imports millions of swine annually. Hence, multiple genetically diverse influenza viruses are introduced and co-circulate in the Midwest, providing the opportunity for genomic reassortment. Overall, the Midwest serves primarily as an ecological sink for swine influenza in the US, with sources of virus genetic diversity instead located in the Southeast (mainly North Carolina) and South-Central (mainly Oklahoma) regions. Understanding the importance of long-distance pig transportation in the evolution and spatial dissemination of the influenza virus in swine may inform future strategies for the surveillance and control of influenza, and perhaps other swine pathogens.