Whole genome sequencing of porcine reproductive and respiratory syndrome virus 2 (PRRSV) from field clinical samples improves the genomic surveillance of the virus

Article
Version acceptée / Accepted Manuscript

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JCM00097-20R2-Merged_PDF (1).pdf (1.53 MB)

Date de publication

2020-08-12

Autrices et auteurs

Identifiant ORCID de l’auteur

Contributrices et contributeurs

Direction de recherche

Publié dans

Journal of clinical microbiology

Date de la Conférence

Lieu de la Conférence

Éditeur

American society for microbiology

Cycle d'études

Programme

Affiliation

Université de Montréal. Faculté de médecine vétérinaire

Mots-clés

  • Animal viral disease
  • Swine virus
  • Classification
  • Porcine reproductive and respiratory syndrome virus
  • PRRSV
  • Next-generation sequencing
  • NGS
  • Whole-genome sequencing
  • WGS
  • Recombinant
  • Coinfection

Organisme subventionnaire

Résumé

Résumé

Porcine 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 avenues.

Table des matières

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Notes

URI

http://hdl.handle.net/1866/24058

DOI

10.1128/JCM.00097-20

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Faculté de médecine vétérinaire – Travaux et publications

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