Abstract
Piscine orthoreovirus (PRV) infects farmed and wild salmon and trout species in North America, South America, Europe, and East Asia. PRV groups into three distinct genotypes (PRV-1, PRV-2, and PRV-3) that can vary in distribution, host specificity, and/or disease potential. Detection of the virus is currently restricted to genotype specific assays such that surveillance programs require the use of three assays to ensure universal detection of PRV. Consequently, herein, we developed, optimized, and validated a real-time reverse transcription quantitative PCR assay (RT-qPCR) that can detect all known PRV genotypes with high sensitivity and specificity. Targeting a conserved region at the 5′ terminus of the M2 segment, the pan-PRV assay reliably detected all PRV genotypes with as few as five copies of RNA. The assay exclusively amplifies PRV and does not cross-react with other salmonid viruses or salmonid host genomes and can be performed as either a one- or two-step RT-qPCR. The assay is highly reproducible and robust, showing 100% agreement in test results from an inter-laboratory comparison between two laboratories in two countries. Overall, as the assay provides a single test to achieve highly sensitive pan-specific PRV detection, it is suitable for research, diagnostic, and surveillance purposes.
Highlights
Piscine orthoreovirus (PRV) is a segmented double-stranded RNA virus in the family Reoviridae, genus Orthoreovirus, that predominately infects salmonids [1]
In North America, PRV-1 is ubiquitous in farmed salmon populations, while PRV-2 and PRV-3 have not been reported; few surveillance programs have looked for these other genotypes
As the 5 end of the M2 segment between bases 1–131 contained the greatest area of conservation, three primer and probe sets were designed to complement this region (Figure S1) with degenerate bases incorporated into the primer sets in instances where nucleotide heterogeneity occurred across PRV genotypes (Table S1)
Summary
Piscine orthoreovirus (PRV) is a segmented double-stranded RNA virus in the family Reoviridae, genus Orthoreovirus, that predominately infects salmonids [1]. PRV-1, the genotype most well studied, includes strains demonstrated to cause heart and skeletal muscle inflammation (HSMI) in Atlantic salmon (Salmo salar) [6,7]. Surveillance studies reveal widespread distribution with PRV detections recorded in North America, South America, Europe, and Asia [5,9,10,11,12,13,14,15] and are typically observed at higher prevalence in farmed fish. In North America, PRV-1 is ubiquitous in farmed salmon populations, while PRV-2 and PRV-3 have not been reported; few surveillance programs have looked for these other genotypes. Certain PRV strains not associated with disease states [16,17] are not prioritized for genotype-specific screening and may be under-represented in fish populations
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