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

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

doi:10.3390/v16101557

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

by

Marie K. Kirby

^1,†

,

Bo Shu

^1,†,

Matthew W. Keller

¹

,

Malania M. Wilson

¹

,

Benjamin L. Rambo-Martin

¹,

Yunho Jang

¹,

Jimma Liddell

¹,

Eduardo Salinas Duron

^1,2

,

Jacqueline M. Nolting

³

,

Andrew S. Bowman

³

,

C. Todd Davis

¹,

David E. Wentworth

^1,‡

and

John R. Barnes

^1,*

¹

Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA

²

Chippewa Government Solutions (CGS), Sault Tribe Incorporated (STI), Cherokee Nation Operational Solutions (CNOS), Sault Sainte Marie, MI 49783, USA

³

Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA

^*

Author to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

^‡

Current address: CORVD Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.

Viruses 2024, 16(10), 1557; https://doi.org/10.3390/v16101557

Submission received: 10 September 2024 / Revised: 27 September 2024 / Accepted: 28 September 2024 / Published: 30 September 2024

(This article belongs to the Special Issue Advances in Animal Influenza Virus Research: Third Edition)

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Abstract

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.

Keywords: swine influenza virus; triplex real-time RT-PCR; portable sequencing

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MDPI and ACS Style

Kirby, M.K.; Shu, B.; Keller, M.W.; Wilson, M.M.; Rambo-Martin, B.L.; Jang, Y.; Liddell, J.; Salinas Duron, E.; Nolting, J.M.; Bowman, A.S.; et al. Discriminating North American Swine Influenza Viruses with a Portable, One-Step, Triplex Real-Time RT-PCR Assay, and Portable Sequencing. Viruses 2024, 16, 1557. https://doi.org/10.3390/v16101557

AMA Style

Kirby MK, Shu B, Keller MW, Wilson MM, Rambo-Martin BL, Jang Y, Liddell J, Salinas Duron E, Nolting JM, Bowman AS, et al. Discriminating North American Swine Influenza Viruses with a Portable, One-Step, Triplex Real-Time RT-PCR Assay, and Portable Sequencing. Viruses. 2024; 16(10):1557. https://doi.org/10.3390/v16101557

Chicago/Turabian Style

Kirby, Marie K., 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, and et al. 2024. "Discriminating North American Swine Influenza Viruses with a Portable, One-Step, Triplex Real-Time RT-PCR Assay, and Portable Sequencing" Viruses 16, no. 10: 1557. https://doi.org/10.3390/v16101557

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

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