Piscine Reovirus: Genomic and Molecular Phylogenetic Analysis from Farmed and Wild Salmonids Collected on the Canada/US Pacific Coast

Abstract

Piscine reovirus (PRV) is a double stranded non-enveloped RNA virus detected in farmed and wild salmonids. This study examined the phylogenetic relationships among different PRV sequence types present in samples from salmonids in Western Canada and the US, including Alaska (US), British Columbia (Canada) and Washington State (US). Tissues testing positive for PRV were partially sequenced for segment S1, producing 71 sequences that grouped into 10 unique sequence types. Sequence analysis revealed no identifiable geographical or temporal variation among the sequence types. Identical sequence types were found in fish sampled in 2001, 2005 and 2014. In addition, PRV positive samples from fish derived from Alaska, British Columbia and Washington State share identical sequence types. Comparative analysis of the phylogenetic tree indicated that Canada/US Pacific Northwest sequences formed a subgroup with some Norwegian sequence types (group II), distinct from other Norwegian and Chilean sequences (groups I, III and IV). Representative PRV positive samples from farmed and wild fish in British Columbia and Washington State were subjected to genome sequencing using next generation sequencing methods. Individual analysis of each of the 10 partial segments indicated that the Canadian and US PRV sequence types clustered separately from available whole genome sequences of some Norwegian and Chilean sequences for all segments except the segment S4. In summary, PRV was genetically homogenous over a large geographic distance (Alaska to Washington State), and the sequence types were relatively stable over a 13 year period.

De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

“…One potential explanation for this disparity may involve genetic variation between PRV isolates. Siah et al [3] recently conducted a phylogenetic analysis of all segments of the PRV obtained from western North America as well as selected Norwegian and Chilean PRV genomes. With the exception of segment S4, samples of North American PRV clustered separately from the Norwegian and Chilean samples indicating that there are genetic differences across the genome between Pacific, Norwegian and Chilean forms of PRV.…”

“…The dsRNA-binding activity of the MRV ơ3 protein inhibits the induction of type-1 IFN and activation of protein kinase R ( PKR ) which through its interaction with translation initiation factor ( eIF2α ) inhibits cellular mRNA translation, thereby, limiting viral protein production. Siah et al [3] compared the predicted structure of the North American PRV ơ3 protein to predicted ơ3 proteins based on Norwegian/Chilean sequences. These authors identified an amino acid difference which results in a predicted change in secondary structure from an “alpha-helix” in Norwegian/Chilean PRV source to a “sheet structure” in North American PRV sequences.…”

“…Subsequent studies have confirmed the presence of PRV in farmed Atlantic salmon in British Columbia [3, 13, 14], and also identified PRV in wild salmonids in both BC and US (Washington and Alaska) waters [3, 14, 15]. Interestingly, although infection with PRV is common in farmed Atlantic salmon in BC, disease manifestations impacting fish performance as observed in Norway has never been reported (reviewed in [16]).…”

“…Its genome consists of 10 nucleic acid segments L1, L2, L3, M1, M2, M3, S1, S2, S3, and S4 that encode for the λ3, λ2/p11, λ1, μ2, μ1, μNS, σ3/p13, σ2/p8, σNS, and σ1 proteins, respectively [1–3]. PRV was first identified by pyrosequencing in 2010 as part of a Norwegian-based study to identify the causative agent of a recently emerged disease of cultured Atlantic salmon ( Salmo salar ) known as Heart and Skeletal Muscle Inflammation (HSMI) [1].…”

Full-Genome Sequencing and Confirmation of the Causative Agent of Erythrocytic Inclusion Body Syndrome in Coho Salmon Identifies a New Type of Piscine Orthoreovirus

“…trutta L.) [18–20] implies that PRV infection not only occurs in Atlantic salmon but also in other salmonid fish species. HSMI-like diseases caused by PRV-related viral infections have also been reported in rainbow trout in Norway [21].…”