Genetic diversity of influenza A viruses circulating in pigs between winter and summer in a Minnesota live animal market

Jayaveeramuthu Nirmala, Jeff B. Bender, Ruth Lynfield, My Yang, Marie Rene Culhane, Martha Irene Nelson, Srinand Sreevatsan, Montserrat Torremorell

Research output: Contribution to journalArticlepeer-review


There has been little surveillance of influenza A viruses (IAVs) circulating in swine at live animal markets, particularly in the United States. To address this gap, we conducted active surveillance of IAVs in pigs, the air, and the environment during a summer and winter season in a live animal market in St. Paul, Minnesota, that had been epidemiologically associated with swine-origin influenza cases in humans previously. High rates of IAV were detected by PCR in swine lungs and oral fluids during both summer and winter seasons. Rates of IAV detection by PCR in the air were similar during summer and winter, although rates of successful virus isolation in the air were lower during summer than in winter (26% and 67%, respectively). H3N2 was the most prevalent subtype in both seasons, followed by H1N2. Genetically diverse viruses with multiple gene constellations were isolated from both winter and summer, with a total of 19 distinct genotypes identified. Comparative phylogenetic analysis of all eight segments of 40 virus isolates from summer and 122 isolates from winter revealed that the summer and winter isolates were genetically distinct, indicating IAVs are not maintained in the market, but rather are re-introduced, likely from commercial swine. These findings highlight the extent of IAV genetic diversity circulating in swine in live animal markets, even during summer months, and the ongoing risk to humans.

Original languageEnglish (US)
Pages (from-to)243-250
Number of pages8
JournalZoonoses and Public Health
Issue number3
StatePublished - May 1 2020

Bibliographical note

Funding Information:
This work was supported in whole or in part with federal funds from the National Institutes of Health and the U.S. Department of Health and Human Services [HHSN266200700007C] and by the Cooperative Agreement from CDC [U38HM000414]. We thank the public health personnel at Minnesota Department of Health, the Minnesota Public Health Laboratory, the Minnesota Department of Agriculture, the University of Minnesota College of Veterinary Medicine, and the Centers for Disease Control and Prevention (CDC) who assisted in this investigation. We thank the following people: Mary Choi, Sara Chute, the Hmong Healthcare Coalition, Dr. Osman Harare, Ka Thao, Katrina DeVoe, Hannah Fox, Song Her, Wilfredo Dominguez, Fatuma Youb, Nuri Ahmed, Maggie Ayers-Johnson, Stephanie Rothstein, Ted Radintz, Teresa Chirhart, Amy Saupe, Carlota Medus, Franci Livingston, Teresa Chirhart, Heather Fowler, Joni Scheftel, Jennifer Palm, Lyn Finelli, David Wang, Jonathan Ertl and Mike Osterholm. We are especially grateful to the proprietors of the live animal markets for the cooperation and willingness to participate in the study. The authors would like to acknowledge the resources provided by the Minnesota Supercomputing Institute (MSI) at the University of Minnesota. The content of the manuscript is solely the responsibility of the authors and does not represent official views of the National Institutes of Health.

Publisher Copyright:
© 2019 Blackwell Verlag GmbH


  • genetic diversity
  • influenza
  • live animal market
  • swine

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, P.H.S.

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