title: 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.
authors.affiliation: British Columbia Centre for Aquatic Health Sciences, Campbell River, British Columbia, Canada.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Siah
authors.affiliation: Marine Harvest Canada, Campbell River, British Columbia, Canada.
authors.forename: Diane B
authors.initials: DB
authors.lastname: Morrison
authors.affiliation: Veterinary Sciences Division, AFBI Stormont, Stoney Road, Belfast, United Kingdom.
authors.forename: Elena
authors.initials: E
authors.lastname: Fringuelli
authors.affiliation: Veterinary Sciences Division, AFBI Stormont, Stoney Road, Belfast, United Kingdom.
authors.forename: Paul
authors.initials: P
authors.lastname: Savage
authors.affiliation: British Columbia Centre for Aquatic Health Sciences, Campbell River, British Columbia, Canada.
authors.forename: Zina
authors.initials: Z
authors.lastname: Richmond
authors.affiliation: British Columbia Centre for Aquatic Health Sciences, Campbell River, British Columbia, Canada.
authors.forename: Robert
authors.initials: R
authors.lastname: Johns
authors.affiliation: US Geological Survey, Western Fisheries Research Center, Seattle, WA, United States of America.
authors.forename: Maureen K
authors.initials: MK
authors.lastname: Purcell
authors.affiliation: Pacific Biological Station, Nanaimo, British Columbia, Canada.
authors.forename: Stewart C
authors.initials: SC
authors.lastname: Johnson
authors.affiliation: British Columbia Centre for Aquatic Health Sciences, Campbell River, British Columbia, Canada.
authors.forename: Sonja M
authors.initials: SM
authors.lastname: Saksida
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000835:Animals, Wild; D001483:Base Sequence; D002170:Canada / Q000453:epidemiology; D005393:Fish Diseases / Q000453:epidemiology / Q000235:genetics* / Q000821:virology; D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D005843:Geography; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008969:Molecular Sequence Data; D015205:Northwestern United States / Q000453:epidemiology; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D012087:Reoviridae / Q000145:classification / Q000235:genetics*; D012088:Reoviridae Infections / Q000453:epidemiology / Q000235:genetics* / Q000821:virology; D012487:Salmonidae / Q000235:genetics* / Q000821:virology; D017422:Sequence Analysis, DNA / Q000379:methods; D017386:Sequence Homology, Amino Acid
chemical_list: D012367:RNA, Viral