The complex and unresolved evolutionary origins of the 2009 H1N1 influenza pandemic exposed major gaps in our knowledge of the global spatial ecology and evolution of influenza A viruses in swine (swIAVs). Here we undertake an expansive phylogenetic analysis of swIAV sequence data and demonstrate that the global live swine trade strongly predicts the spatial dissemination of swIAVs, with Europe and North America acting as sources of viruses in Asian countries. In contrast, China has the world's largest swine population but is not a major exporter of live swine, and is not an important source of swIAVs in neighbouring Asian countries or globally. A meta-population simulation model incorporating trade data predicts that the global ecology of swIAVs is more complex than previously thought, and the United States and China's large swine populations are unlikely to be representative of swIAV diversity in their respective geographic regions, requiring independent surveillance efforts throughout Latin America and Asia.
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We thank Drs Sagar Goyal and Devi Patnayak, along with Wendy Wiese, Becca Wheeldon and Lotus Smasal at UMVDL for their virology work, and Rebecca Halpin, Nadia Fedorova, Xudong Lin and Timothy B. Stockwell at the J. Craig Venter Institute for their assistance in viral sequencing. Aaron Schwartzbard was greatly helpful in producing figures using R. This manuscript was prepared while D.E.W. was employed at the J. Craig Venter Institute. Partial support for this work was provided by a grant from the Saskatchewan Ministry of Agriculture contract number C70077. This work was supported in part by the Multinational Influenza Seasonal Mortality Study (MISMS), an on-going international collaborative effort to understand influenza epidemiology and evolution, led by the Fogarty International Center, National Institutes of Health, with funding from Office of Pandemics and Emerging Threats at the U.S. Department of Health and Human Services (A.R., M.I.N., C.V.). This project has also been funded in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under the (contract number HHSN272200900007C). P.L., M.A.S. and A.R. acknowledge the funding from the European Union Seventh Framework Programme (FP7/2007–2013) under Grant Agreement no. 278433-PREDEMICS and ERC Grant agreement no. 260864. E.C.H. is supported by an NHMRC Australia Fellowship (AF30).