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

PLoS One. 2015 Nov 4;10(11):e0141475. doi: 10.1371/journal.pone.0141475. eCollection 2015.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Animals, Wild
  • Base Sequence
  • Canada / epidemiology
  • Fish Diseases / epidemiology
  • Fish Diseases / genetics*
  • Fish Diseases / virology
  • Genome, Viral
  • Genomics / methods*
  • Geography
  • High-Throughput Nucleotide Sequencing / methods*
  • Molecular Sequence Data
  • Northwestern United States / epidemiology
  • Phylogeny*
  • RNA, Viral / genetics
  • Reoviridae / classification
  • Reoviridae / genetics*
  • Reoviridae Infections / epidemiology
  • Reoviridae Infections / genetics*
  • Reoviridae Infections / virology
  • Salmonidae / genetics*
  • Salmonidae / virology
  • Sequence Analysis, DNA / methods
  • Sequence Homology, Amino Acid

Substances

  • RNA, Viral

Grants and funding

This study was funded by Marine Harvest Canada. The funder provided support in the form of salaries for authors (DBM), but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of this author are articulated in the ‘author contributions’ section.