The emergence and evolution of influenza A (H1α) viruses in swine in Canada and the United States

Martha I. Nelson, Marie R Culhane, Nídia S. Trovão, Devi P Patnayak, Rebecca A. Halpin, Xudong Lin, Meghan H. Shilts, Suman R. Das, Susan E. Detmer

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


Swine are a key reservoir host for influenza A viruses (IAVs), with the potential to cause global pandemics in humans. Gaps in surveillance in many of the world’s largest swine populations impede our understanding of how novel viruses emerge and expand their spatial range in pigs. Although US swine are intensively sampled, little is known about IAV diversity in Canada’s population of ~12 million pigs. By sequencing 168 viruses from multiple regions of Canada, our study reveals that IAV diversity has been underestimated in Canadian pigs for many years. Critically, a new H1 clade has emerged in Canada (H1α-3), with a two-amino acid deletion at H1 positions 146-147, that experienced rapid growth in Manitoba’s swine herds during 2014-2015. H1α-3 viruses also exhibit a higher capacity to invade US swine herds, resulting in multiple recent introductions of the virus into the US Heartland following large-scale movements of pigs in this direction. From the Heartland, H1α-3 viruses have disseminated onward to both the east and west coasts of the United States, and may become established in Appalachia. These findings demonstrate how long-distance trading of live pigs facilitates the spread of IAVs, increasing viral genetic diversity and complicating pathogen control. The proliferation of novel H1α-3 viruses also highlights the need for expanded surveillance in a Canadian swine population that has long been overlooked, and may have implications for vaccine design.

Original languageEnglish (US)
Article number000924
Pages (from-to)2663-2675
Number of pages13
JournalJournal of General Virology
Issue number11
StatePublished - Nov 2017

Bibliographical note

Funding Information:
This work was funded with federal funds from the Centers of Excellence for Influenza Research and Surveillance (CEIRS), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) and Department of Health and Human Services (HHS) under contract no. HHSN272201400008C. This work was supported 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, NIH. The sequencing work was supported by the NIAID/NIH Genomic Centers for Infectious Diseases (GCID) programme (U19-AI-110819). Funding for Canadian surveillance was provided by the Saskatchewan Ministry of Agriculture, Saskatchewan Agricultural Development Fund

Publisher Copyright:
© 2017 The Authors.


  • Influenza A virus
  • Phylogeography
  • Reassortment
  • Swine
  • Viral emergence
  • Zoonotic


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