title: Spatial dynamics of human-origin H1 influenza A virus in North American swine.
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 = 1516) 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 US 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.
authors.affiliation: Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America. nelsonma@mail.nih.gov
authors.forename: Martha I
authors.initials: MI
authors.lastname: Nelson
authors.forename: Philippe
authors.initials: P
authors.lastname: Lemey
authors.forename: Yi
authors.initials: Y
authors.lastname: Tan
authors.forename: Amy
authors.initials: A
authors.lastname: Vincent
authors.forename: Tommy Tsan-Yuk
authors.initials: TT
authors.lastname: Lam
authors.forename: Susan
authors.initials: S
authors.lastname: Detmer
authors.forename: Cécile
authors.initials: C
authors.lastname: Viboud
authors.forename: Marc A
authors.initials: MA
authors.lastname: Suchard
authors.forename: Andrew
authors.initials: A
authors.lastname: Rambaut
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.forename: Marie
authors.initials: M
authors.lastname: Gramer
mesh_terms: D000818:Animals; D005075:Biological Evolution; D005843:Geography; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics*; D007251:Influenza, Human / Q000453:epidemiology / Q000821:virology; D009976:Orthomyxoviridae Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D058873:Pandemics; D010802:Phylogeny; D011157:Population Dynamics; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology* / Q000821:virology; D014481:United States / Q000453:epidemiology