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Risk Assessment Detects Two Viral Pathogens in Farmed Atlantic Salmon

Final report and summary for Atlantic salmon virus testing project.

ATSalm HeadFollowing detections of Infectious Salmon Anemia virus (ISAV) and Infectious Hematopoietic Necrosis virus (IHNV) in farmed Atlantic salmon (Salmo salar) in British Columbia in 2011-12, as well as detections of IHNV in Washington state (Puget Sound), we became concerned about the potential for shipments of farmed salmon to introduce these highly pathogenic viruses into watersheds of the Pacific Northwest. Detections of a third virus, Piscine Reovirus (PRV), an “emerging pathogen” in Norwegian salmon aquaculture, were reported in 2012 from B.C. and confirmed in the scientific literature. These were the first reports of PRV in the Pacific Northwest, and fueled environmental controversy in B.C. As a result, our growing concern over the spread of this virus to U.S. waters led us to include testing for the presence of this virus in the samples collected as part of this project.

Overall, samples from 115 Atlantic salmon originating in “B.C.” or “Canada” were collected from markets in WA, OR, and CA and submitted to the lab for testing. However, due to poor handling and preservation at distributors and/or the fish markets where the samples were purchased, many of these samples’ RNA had degraded to the point where they could no longer be tested. Eventually, 56 samples were analyzed for ISAV and IHNV (8 of these viable samples came from near Davis, CA, 11 from the Portland area, and 37 from the Seattle area). None of the samples tested positive for Infectious Salmon Anemia virus (ISAV) -- good news for native salmon populations in the Pacific Northwest. Slightly more than 14% of these samples were positive for ATSalm qPCRInfectious Hematopoietic Necrosis virus (IHNV) (14.29%; 8/56 positive). Only 23 of the original 115 samples had enough RNA remaining at this point to allow for testing by RT-PCR; all of these were from Washington state. More than half of the samples (56.52%; 13/23 positive) were positive for PRV. Three fish, all from the Seattle area markets, were positive for both IHNV and PRV.

To demonstrate that viral pathogens from net pens may pose a threat to wild salmon and trout populations in the Pacific Northwest, we must show that: (1) the pathogen has been detected in the host’s tissues (here, in net-pen Atlantic salmon via PCR assays), (2) demonstrate that the pathogen remains infectious, and (3) determine that the pathogen is likely to infect and harm other nearby populations (of the same species or other species). Our work has demonstrated that RNA from both IHNV and PRV are present in the gill and/or muscle tissue of Atlantic salmon from B.C. (or, in some cases, simply “Canada”) imported to U.S. markets, and thus there is potential for the import of these products to spread these diseases. However, the second requirement - demonstrating that the pathogen detected remains infectious - has yet to be fulfilled. While the PCR assays are extremely sensitive and specific, they may detect RNA or DNA that is no longer viable (for example, a virus that is no longer infectious because it has been partly degraded, either by the immune system or by environmental conditions). For this reason, an “official” detection requires that a pathogen be cultured in the laboratory to demonstrate that it is still viable (infectious). To fulfill this requirement was beyond the scope of the present study -- extremely fresh samples of infected tissue are needed to culture viruses; samples taken post-international shipment will not suffice. To do so, a full microbiology laboratory would be needed to culture cells to host the virus under sterile conditions. Note also that ISAV occurs in several strains, and some the less pathogenic forms (for example, strain HPRO) cannot be reliably cultured; the culture of PRV is also not yet fully established.

Our primary concern for the introduction of the viruses detected is fish-processing plants, which have been shown to release infectious organisms back into the environment and may have minimal pathogen oversight. Circumstantial reports suggest that it is also possible that individual consumers who purchase Atlantic salmon carcasses may dispose of them in a manner that may place local watersheds at risk (some people fillet salmon and “return” the carcass to local streams in an attempt to input nutrients into the system; this practice should be discouraged).

None of these viruses is a direct threat to humans, either by close contact or consumption of infected salmon. Financial support for this project came from a consortium of private foundations, including Patagonia’s World Trout initiative.

Final Report: Risk Assessment Detects Two Viral Pathogens in Farmed Atlantic Salmon: Implications for Native Salmon in the Pacific Northwest; September, 2014

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