{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:27:17Z","timestamp":1760146037245,"version":"build-2065373602"},"reference-count":39,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2024,9,30]],"date-time":"2024-09-30T00:00:00Z","timestamp":1727654400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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 (\u03b1), 1A.2 (\u03b2), 1A.3 (\u03b3), 1B.2.2 (\u03b41) and 1B.2.1 (\u03b42) 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.<\/jats:p>","DOI":"10.3390\/v16101557","type":"journal-article","created":{"date-parts":[[2024,9,30]],"date-time":"2024-09-30T12:06:32Z","timestamp":1727697992000},"page":"1557","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Discriminating North American Swine Influenza Viruses with a Portable, One-Step, Triplex Real-Time RT-PCR Assay, and Portable Sequencing"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0859-9604","authenticated-orcid":false,"given":"Marie K.","family":"Kirby","sequence":"first","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bo","family":"Shu","sequence":"additional","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5850-1698","authenticated-orcid":false,"given":"Matthew W.","family":"Keller","sequence":"additional","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3486-1725","authenticated-orcid":false,"given":"Malania M.","family":"Wilson","sequence":"additional","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benjamin L.","family":"Rambo-Martin","sequence":"additional","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunho","family":"Jang","sequence":"additional","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jimma","family":"Liddell","sequence":"additional","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4490-9289","authenticated-orcid":false,"given":"Eduardo","family":"Salinas Duron","sequence":"additional","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"},{"name":"Chippewa Government Solutions (CGS), Sault Tribe Incorporated (STI), Cherokee Nation Operational Solutions (CNOS), Sault Sainte Marie, MI 49783, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2705-4805","authenticated-orcid":false,"given":"Jacqueline M.","family":"Nolting","sequence":"additional","affiliation":[{"name":"Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0738-8453","authenticated-orcid":false,"given":"Andrew S.","family":"Bowman","sequence":"additional","affiliation":[{"name":"Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C. Todd","family":"Davis","sequence":"additional","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5190-980X","authenticated-orcid":false,"given":"David E.","family":"Wentworth","sequence":"additional","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John R.","family":"Barnes","sequence":"additional","affiliation":[{"name":"Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,9,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"7367","DOI":"10.1128\/JVI.72.9.7367-7373.1998","article-title":"Molecular basis for the generation in pigs of influenza A viruses with pandemic potential","volume":"72","author":"Ito","year":"1998","journal-title":"J. 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