Viruses (Sep 2024)

Discriminating North American Swine Influenza Viruses with a Portable, One-Step, Triplex Real-Time RT-PCR Assay, and Portable Sequencing

  • Marie K. Kirby,
  • Bo Shu,
  • Matthew W. Keller,
  • Malania M. Wilson,
  • Benjamin L. Rambo-Martin,
  • Yunho Jang,
  • Jimma Liddell,
  • Eduardo Salinas Duron,
  • Jacqueline M. Nolting,
  • Andrew S. Bowman,
  • C. Todd Davis,
  • David E. Wentworth,
  • John R. Barnes

DOI
https://doi.org/10.3390/v16101557
Journal volume & issue
Vol. 16, no. 10
p. 1557

Abstract

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Swine harbors a genetically diverse population of swine influenza A viruses (IAV-S), with demonstrated potential to transmit to the human population, causing outbreaks and pandemics. Here, we describe the development of a one-step, triplex real-time reverse transcription-polymerase chain reaction (rRT-PCR) assay that detects and distinguishes the majority of the antigenically distinct influenza A virus hemagglutinin (HA) clades currently circulating in North American swine, including the IAV-S H1 1A.1 (α), 1A.2 (β), 1A.3 (γ), 1B.2.2 (δ1) and 1B.2.1 (δ2) clades, and the IAV-S H3 2010.1 clade. We performed an in-field test at an exhibition swine show using in-field viral concentration and RNA extraction methodologies and a portable real-time PCR instrument, and rapidly identified three distinct IAV-S clades circulating within the N.A. swine population. Portable sequencing is used to further confirm the results of the in-field test of the swine triplex assay. The IAV-S triplex rRT-PCR assay can be easily transported and used in-field to characterize circulating IAV-S clades in North America, allowing for surveillance and early detection of North American IAV-S with human outbreak and pandemic potential.

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