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Researchers Find Deadly Salmon Virus on the Pacific Coast

Posted by Richard Conniff on January 11, 2016

Fish farm in British Columbia (A salmon jumps out of the water while feeding at the mouth of Capilano River in West Vancouver, British Columbia. (Photo: Andy Clark/Reuters)

A salmon feeding at the mouth of Capilano River in West Vancouver, British Columbia. (Photo: Andy Clark/Reuters)

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A pathogen that is “arguably the most feared viral disease of the marine farmed salmon industry” has now turned up for the first time in farmed and wild fish in British Columbia, according to a new study in Virology Journal. The co-authors warn that the presence of the virus, called infectious salmon anemia virus (ISAV), could greatly increases the risk of devastating outbreaks for salmon fisheries from Alaska down to the Pacific Northwest.

“This is first of all a salmon virus, and a member of the influenza family and it mutates easily and rapidly,” said co-author Alexandra Morton, an independent marine biologist. “There is no place in the world where this virus has existed quietly. It has always caused a problem. It was detected in Chile in 1999, and nothing was done to contain it. They allowed it to reproduce and mutate, and in 2007 a form appeared that swept the coast and caused $2 billion in damage.”

The B.C. Salmon Farmers Association promptly responded to the new study with a fierce attack on its science. “We have great concerns about the methodology, and the ethics of the researchers involved, given their history of reporting false positives with respect to ISA,” said Jeremy Dunn, executive director. “None of the results reported in this paper have been confirmed by an outside laboratory.”

Morton called the response unhelpful. “This is a dangerous virus to the industry and to the wild salmon, and we need to deal with this in a scientific way,” she said, adding that the fish farmers had denied her group access to farmed salmon for testing. “They deny everybody access. It really inhibits the work. You have to go and get the dying fish out of these farms and test them.”

Instead, Morton and her co-authors tested more than 1,000 farmed and wild salmon from British Columbia supermarkets and found evidence of ISAV in 78. The virus also turned up in sea lice from the Discovery Islands, a region known for salmon farms, raising concern that the pathogen was introduced from open net fish farming.

The new study used PCR (polymerase chain reaction) technology, the standard technique for amplifying segments of DNA and identifying them to a particular species. But in a comment forwarded by the BC Salmon Farmers Association, Gary Marty, British Columbia’s chief fish pathologist, argued that the paper did not “provide a balanced review” of the thousands of past PCR studies on BC salmon that were negative for the virus. He also raised the “possibility of sample contamination” in the “cramped, untidy conditions” of the laboratory where the new PCR studies took place.

If there had been contamination, Morton replied, the ISAV found by the new study would have been an exact match for ISAV found elsewhere. Instead, the researchers found a mutation at a critical area sampled in PCR testing. This is a difficult strain of ISAV to detect,” she said, “and it is easy to see how it was missed,” in past studies. Different laboratories also use different methods and they interpret the results using different standards.

But Morton said the new study had “cracked the code” for ISAV, with a methodology that passed peer review in one of the top virology journals. “We not only got detection of the virus, we got pieces of the virus, and ran them through GenBank,” the National Institutes of Health genetic database, “which is like running a fingerprint.”

Morton conjectured that resistance to the new study was based mainly on the economic value of the wild and farmed salmon industry, worth perhaps $1 billion a year in British Columbia. ISAV is a “notifiable” disease, meaning that, if the finding is confirmed, Canada would be obliged to report it to the International Organization for Animal Health in Paris. That notification would permit other countries to block imports without fear of incurring trade penalties.   “If B.C. is positive for ISAV,” said Morton, “the United States and other governments will in all likelihood close theirs borders to the export of farmed salmon,” and salmon eggs.

“What needs to happen now,” she said, “is that all laboratories need to do the same test—so we don’t compare apples to oranges—and we need access to the farmed fish. So far no one has stepped up to accomplish that. It is critical that we learn from what happened to Chile. In my view, this work gives B.C. the opportunity to avoid tragic consequences.


One Response to “Researchers Find Deadly Salmon Virus on the Pacific Coast”

  1. Here’s a comment by email from fish pathologist Gary Marty:

    The story on the “discovery” of the ISA virus in BC has been published. It contains some information from Alexandra Morton that is not consistent with our understanding of this virus:

    1) The ISA virus is a member of the Family Orthomyxoviridae (virologists do not recognize an Influenza Family; I can see that falsely stating that the ISA virus is an influenza virus tends to make it sound scarier to the general public)

    2) The abstract of the scientific paper makes it clear that “ISA outbreaks have only been reported in farmed Atlantic salmon”. Indeed, despite over 20 years of looking, the disease (ISA) has never been detected in wild Atlantic salmon or in any Pacific salmonids (e.g., coho salmon and steelhead). Even in Chile, were every year they produce more coho salmon than BC produces all salmon, the “$2 billion in damage” did not involve a single coho salmon—even though coho salmon were sometimes grown on the same farms as infected Atlantic salmon during an ISA outbreak.

    3) A quote from Ms. Morton related to farm access states, “They deny everybody access.” This statement is not true. The BC government (and now DFO) have had access to the farms for testing since the early 2000s. From 2003 – 2015, samples from 7,910 recently dead farm salmon have been tested for the ISA virus by the independently accredited BC Animal Health Centre, and all results have been negative—no virus. As I mentioned in the critique that you have, the single mutation noted in the new paper would not prevent our tests from finding the virus. Our veterinary virologist, Dr. Tomy Joseph, earned his Ph.D. working on the ISA virus in Dr. Kibenge’s laboratory; it makes no sense that he would be jeopardize his professional standing by hiding results to protect trade.

    4) The article states that “the researchers found a mutation at a critical area sampled in PCR testing.” My virology colleagues did a GenBank search for the mutation sequence and found that it was entered by Dr. Kibenge’s laboratory in 2004 (accession # AF315466). So, yes, Dr. Kibenge’s laboratory seems to have found the mutated sequence, but in 2004, not 2016. This match is not reported in the 2016 paper.

    5) To summarize, the evidence best supports the conclusion that the ISA virus is not a threat to wild Pacific salmon.

    Best regards,


    Gary D. Marty, D.V.M., Ph.D., Diplomate, A.C.V.P.

    Senior Fish Pathologist
    Animal Health Centre
    Ministry of Agriculture

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