{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,2]],"date-time":"2026-11-02T18:43:08Z","timestamp":1793644988166,"version":"4.5.1"},"reference-count":41,"publisher":"Wiley","issue":"6","license":[{"start":{"date-parts":[[2016,8,9]],"date-time":"2016-08-09T00:00:00Z","timestamp":1470700800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006100","name":"Freeman Spogli Institute for International Studies At Stanford University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006100","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Influenza Resp Viruses"],"published-print":{"date-parts":[[2016,11]]},"abstract":"Background<\/jats:title>A diversifying pool of mammalian\u2010adapted influenza A viruses (IAV<\/jats:styled-content>) with largely unknown zoonotic potential is maintained in domestic swine populations worldwide. The most recent human influenza pandemic in 2009 was caused by a virus with genes originating from IAV<\/jats:styled-content> isolated from swine. Swine influenza viruses (SIV<\/jats:styled-content>) are widespread in European domestic pig populations and evolve dynamically. Knowledge regarding occurrence, spread and evolution of potentially zoonotic SIV<\/jats:styled-content> in Europe is poorly understood.<\/jats:p><\/jats:sec>Objectives<\/jats:title>Efficient SIV<\/jats:styled-content> surveillance programmes depend on sensitive and specific diagnostic methods which allow for cost\u2010effective large\u2010scale analysis.<\/jats:p><\/jats:sec>Methods<\/jats:title>New SIV<\/jats:styled-content> haemagglutinin (HA<\/jats:styled-content>) and neuraminidase (NA<\/jats:styled-content>) subtype\u2010 and lineage\u2010specific multiplex real\u2010time RT<\/jats:styled-content>\u2010PCR<\/jats:styled-content>s (RT<\/jats:styled-content>\u2010qPCR<\/jats:styled-content>) have been developed and validated with reference virus isolates and clinical samples.<\/jats:p><\/jats:sec>Results<\/jats:title>A diagnostic algorithm is proposed for the combined detection in clinical samples and subtyping of SIV<\/jats:styled-content> strains currently circulating in Europe that is based on a generic, M\u2010gene\u2010specific influenza A virus RT<\/jats:styled-content>\u2010qPCR<\/jats:styled-content>. In a second step, positive samples are examined by tetraplex HA<\/jats:styled-content>\u2010 and triplex NA<\/jats:styled-content>\u2010specific RT<\/jats:styled-content>\u2010qPCR<\/jats:styled-content>s to differentiate the porcine subtypes H1, H3, N1 and N2. Within the HA<\/jats:styled-content> subtype H1, lineages \u201cav\u201d (European avian\u2010derived), \u201chu\u201d (European human\u2010derived) and \u201cpdm\u201d (human pandemic A\/H1N1, 2009) are distinguished by RT<\/jats:styled-content>\u2010qPCR<\/jats:styled-content>s, and within the NA<\/jats:styled-content> subtype N1, lineage \u201cpdm\u201d is differentiated. An RT<\/jats:styled-content>\u2010PCR<\/jats:styled-content> amplicon Sanger sequencing method of small fragments of the HA<\/jats:styled-content> and NA<\/jats:styled-content> genes is also proposed to safeguard against failure of multiplex RT<\/jats:styled-content>\u2010qPCR<\/jats:styled-content> subtyping.<\/jats:p><\/jats:sec>Conclusions<\/jats:title>These new multiplex RT<\/jats:styled-content>\u2010qPCR<\/jats:styled-content> assays provide adequate tools for sustained SIV<\/jats:styled-content> monitoring programmes in Europe.<\/jats:p><\/jats:sec>","DOI":"10.1111\/irv.12407","type":"journal-article","created":{"date-parts":[[2016,7,11]],"date-time":"2016-07-11T08:20:45Z","timestamp":1468225245000},"page":"504-517","source":"Crossref","is-referenced-by-count":49,"title":["Rapid detection and subtyping of European swine influenza viruses in porcine clinical samples by haemagglutinin\u2010 and neuraminidase\u2010specific tetra\u2010 and triplex real\u2010time RT<\/scp>\u2010PCR<\/scp>s"],"prefix":"10.1111","volume":"10","author":[{"given":"Dinah","family":"Henritzi","sequence":"first","affiliation":[{"name":"Institute of Diagnostic Virology Friedrich\u2010Loeffler\u2010Institute (FLI) Greifswald\u2010Insel Riems Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Na","family":"Zhao","sequence":"additional","affiliation":[{"name":"Institute of Diagnostic Virology Friedrich\u2010Loeffler\u2010Institute (FLI) Greifswald\u2010Insel Riems Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elke","family":"Starick","sequence":"additional","affiliation":[{"name":"Institute of Diagnostic Virology Friedrich\u2010Loeffler\u2010Institute (FLI) Greifswald\u2010Insel Riems Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaelle","family":"Simon","sequence":"additional","affiliation":[{"name":"Anses Ploufragan\u2010Plouzan\u00e9 Laboratory Swine Virology Immunology Unit Ploufragan 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