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dc.contributor.authorLalonde, Christian
dc.contributor.authorProvost, Chantale
dc.contributor.authorGagnon, Carl A.
dc.publisherAmerican society for microbiologyfr
dc.subjectAnimal viral diseasefr
dc.subjectSwine virusfr
dc.subjectPorcine reproductive and respiratory syndrome virusfr
dc.subjectNext-generation sequencingfr
dc.subjectWhole-genome sequencingfr
dc.titleWhole genome sequencing of porcine reproductive and respiratory syndrome virus 2 (PRRSV) from field clinical samples improves the genomic surveillance of the virusfr
dc.contributor.affiliationUniversité de Montréal. Faculté de médecine vétérinairefr
dcterms.abstractPorcine reproductive and respiratory syndrome virus (PRRSV) is a major economic concern worldwide. There are currently large data sets available about the ORF5 gene of the virus, with thousands of sequences available, but little data are currently available on the full-length genome of PRRSV. We hypothesized that whole-genome sequencing (WGS) of the PRRSV genome would allow better epidemiological monitoring than ORF5 gene sequencing. PRRSV PCR-positive serum, oral fluid, and tissue clinical samples submitted to the diagnostic laboratory for routine surveillance or diagnosis of PRRSV infection in Québec, Canada, swine herds were used. The PRRSV reverse transcription-quantitative PCR Cq values of the processed samples varied between 11.5 and 34.34. PRRSV strain genomes were isolated using a poly (A)-tail method and were sequenced with a MiSeq Illumina sequencer. Ninetytwo full-length PRRSV genomes were obtained from 88 clinical samples out of 132 tested samples, resulting in a PRRSV WGS success rate of 66.67%. Three important deletions in ORF1a were found in most wild-type (i.e., not vaccine-like) strains. The importance of these deletions remains undetermined. Two different full-length PRRSV genomes were found in four different samples (three serum samples and one pool of tissues), suggesting a 4.55% PRRSV strain coinfection prevalence in swine. Moreover, six PRRSV whole genomes (6.52% of PRRSV strains) were found to cluster differently than they did under the ORF5 classification method. Overall, WGS of PRRSV enables better strain classification and/or interpretation of results in 9.10% of clinical samples than ORF5 sequencing, as well as allowing interesting research
UdeM.ReferenceFournieParDeposantLalonde C, Provost C, Gagnon CA. Whole-Genome Sequencing of Porcine Reproductive and Respiratory Syndrome Virus from Field Clinical Samples Improves the Genomic Surveillance of the Virus. J Clin Microbiol. 2020 Oct 21;58(11):e00097-20. doi: 10.1128/JCM.00097-20. PMID:
UdeM.VersionRioxxVersion acceptée / Accepted Manuscriptfr
oaire.citationTitleJournal of clinical microbiologyfr

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