Skip to main content
ARS Home » Northeast Area » Orono, Maine » National Cold Water Marine Aquaculture Center » Research » Publications at this Location » Publication #405866

Research Project: Genetic Improvement of North American Atlantic Salmon and the Eastern Oyster for Aquaculture Production

Location: National Cold Water Marine Aquaculture Center

Title: Use of Multiplex PCR and Genomic MinION Sequencing to improve our understanding of Genetic Diversity and Relatedness of PRV-1 in Wild and Farmed Salmon in the Northeast Pacific

item JOHNSON, STEWART - Department Of Fisheries And Oceans Canada
item TURCOTTE, LENORA - Department Of Fisheries And Oceans Canada
item SIAH, AHMED - Centre For Agriculture & Biosciences International (CABI)
item BRADSHAW, JULIA - Department Of Fisheries And Oceans Canada
item Polinski, Mark

Submitted to: Western Fish Disease Workshop
Publication Type: Abstract Only
Publication Acceptance Date: 6/15/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary: It is difficult to track pathogen transmission between farmed and wild animals typically due to an inability to correctly identify specific donors and recipients in a real world setting. He we use unique minor genetic variation with a virus genome to track spacial and temporal movement of an aquatic virus (Piscine orthoreovirus) among farmed and wild salmon sampled over the past decade. We identify specific instances where farmed-wild virus transmission likely occurred, and other instances where the virus identified in either wild or farmed fish did not intermingle. These data provide a model for understanding the potential for pathogen spread within coastal ecosystems and specifically how farm and wild-fish interactions could contribute to disease spread.

Technical Abstract: Additional PRV-1 genome sequences are needed to develop a better understanding of phylogeographical patterns and routes of PRV-1 transmission at regional and global scales. Here we used a multiplex PCR and MinION sequencing approach to obtain PRV-1 genome sequences from archived samples of farmed Atlantic salmon, wild Pacific salmon, and seawater. These were collected from 2011 – 2021 from Northeast Pacific locations. Genomes from this study (n = 173) and from GenBank (n = 152) were subjected to Bayesian phylogenetic and Direct PCA analyses. These analyses improved the resolution of phylogenetic relationships of PRV-1 in the Northeast Pacific, and confirmed the relationships of Northeast Pacific genetic variants to those from Chile and the North Atlantic., PRV-1 genomic sequences (whole/partial genome only or S1 phylogenetic as well?) in the Northeast Pacific distributes into 3 well-supported monophyletic groups. Samples from farmed Atlantic Salmon and wild Pacific salmon were found together in two of those monophyletic groups. The third group contained only samples from Pacific salmon. Based on our recovery of partial PRV-1 sequences from samples collected in 1977 we infer that the introduction of PRV-1 into the Northeast Pacific occurred prior to 1977. However, the lack of temporal structure in our Northeast Pacific and Global datasets (poor representation of archived samples) doesn’t support additional analysis of divergence dating. In some of the samples wild salmon carry the same genetic forms of PRV-1 as do farmed salmon. This suggests a transfer between wild and farmed salmon populations or a common source of PRV-1 in coastal waters.