🔗 Permalink : https://doi.org/1866/24058
Whole genome sequencing of porcine reproductive and respiratory syndrome virus 2 (PRRSV) from field clinical samples improves the genomic surveillance of the virus
Article [Accepted Manuscript]
Is part of
Journal of clinical microbiologyPublisher(s)
American society for microbiologyAbstract(s)
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.
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