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

• Published in: PloS one Vol. 10; no. 11; p. e0141475
• Main Authors: Siah, Ahmed, Morrison, Diane B, Fringuelli, Elena, Savage, Paul, Richmond, Zina, Johns, Robert, Purcell, Maureen K, Johnson, Stewart C, Saksida, Sonja M
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04-11-2015; Public Library of Science (PLoS)
• Subjects: Amino Acid Sequence; Animals; Animals, Wild; Base Sequence; Canada - epidemiology; Cladistic analysis; Comparative analysis; Data analysis; DNA sequencing; Fish; Fish Diseases - epidemiology; Fish Diseases - genetics; Fish Diseases - virology; Gangrene; Gene sequencing; Genetic diversity; Genome, Viral; Genomes; Genomics - methods; Geography; Health sciences; High-Throughput Nucleotide Sequencing - methods; Molecular biology; Molecular Sequence Data; Musculoskeletal system; Northwestern United States - epidemiology; Nucleotide sequence; Oncorhynchus mykiss; Phylogenetics; Phylogeny; Plant tissues; Polypeptides; Proteins; Reoviridae; Reoviridae - classification; Reoviridae - genetics; Reoviridae Infections - epidemiology; Reoviridae Infections - genetics; Reoviridae Infections - virology; Ribonucleic acid; RNA; RNA viruses; RNA, Viral - genetics; Salmon; Salmonidae; Salmonidae - genetics; Salmonidae - virology; Salmonids; Segments; Sepsis; Sequence Analysis, DNA - methods; Sequence Homology, Amino Acid; Software packages; Studies; Subgroups; Temporal variations; Trout; Viruses; Northwestern United States; Canada; British Columbia; United Kingdom > UK; United States > US; Norway; British Columbia Canada; Alaska; Chile; North America; Campbell River
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0141475

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.