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Researchers have found three new-to-science viruses in chinook and sockeye salmon in British Columbia. The discovery, led by Gideon Mordecai, a University of British Columbia molecular biologist who studies the ecology of viruses, is part of a larger investigation into whether viruses are contributing to the steep declines in wild British Columbia salmon populations over the past 30 years. The researchers now aim to find out if these infectious agents are being transmitted from farmed to wild fish. Whether farmed fish sicken wild fish is a key concern of fishers; local First Nations, for whom salmon is a critical part of their livelihoods and cultures; and people who worry about the fate of the struggling, chinook-eating southern resident killer whales.
Of the three new viruses, one, an arenavirus, was found in farmed, hatchery, and wild chinook and sockeye salmon. A nidovirus was found in farmed, hatchery, and wild chinook. And a reovirus was found only in farmed salmon.
Arenaviruses are known to primarily infect mammals, so the researchers were surprised to find one in salmon. Farmed fish with the arenavirus had anemia and damage to their gills, kidneys, spleens, swim bladders, and livers. The nidovirus is from a group that includes the viruses behind severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), which affect mammals’ lungs. This nidovirus was mostly found in the salmon’s gills. The reovirus is related to viruses that cause hemorrhagic diseases that have killed many fish in Chinese aquaculture.
The discoveries contribute to a growing understanding of the threats facing British Columbia’s wild salmon.
A decade ago, people thought the main causes of salmon population declines were development of land around rivers, which makes streams warmer and pushes sediment into rivers, and climate change, which warms the ocean and causes currents and prey species to move. But in 2011, Kristi Miller, head of molecular genetics at the Pacific Biological Station in Nanaimo, British Columbia, showed that infectious diseases may be contributing as well.
In 2013, Miller became the head of genomic research for the Strategic Salmon Health Initiative, a collaboration among Fisheries and Oceans Canada, and the nonprofits Pacific Salmon Foundation and Genome BC.* This new study is one of more than 30 the initiative has done to investigate the population declines.
In the project, Mordecai, Miller, and their colleagues first studied dead and dying farmed chinook and used DNA analyses to identify the previously unknown viruses.
They looked at the farmed fish first because it is difficult to find diseased fish in the wild. On fish farms, diseases are much more obvious because fish are routinely found dead or dying with abnormalities on their bodies. As with any type of factory farming, the unnatural, crowded conditions of fish farms foster disease. “Sick wild fish don’t usually die from their diseases,” says Miller. “As soon as their swim performance or visual acuity is affected, they’re eaten.” This is a big part of why salmon viruses are understudied, says Mordecai.
But thanks to new tools, Mordecai’s team was able to find the viruses in wild salmon, which they had collected and tested in the lab. Although the wild fish were not yet showing evidence of disease, the researchers used molecular analyses to see if their immune responses were triggered by a virus. If researchers could not detect a known virus, they looked for new viruses using next-generation DNA sequencing that allowed them to map genomes quickly, searching much more broadly than earlier methods. “This is so incredibly powerful; it essentially allows fish to talk to us,” says scientist turned activist Alexandra Morton, who was not involved with this study.
Although the scientists found that the viruses were infecting the salmon’s cells, they have not proved that they cause diseases, says Mordecai. Although it might seem obvious to assume that dead farmed salmon died from disease, their deaths could be caused by something other than the viruses in question. Linking the new viruses to diseases is the next research step.
The scientists are also unsure if the viruses are being passed between farmed and wild fish. They tested chinook and sockeye salmon from different locations as a first step to understanding possible transmission. Then they will use genomic sequencing to see whether viruses found in different populations are the same. Tracking transmission “is relatively easy to do with viruses … because they mutate rapidly … so you can follow the transmission pathway,” says Miller.
As Mordecai puts it: “If you infected me with a cold virus, we could look at the sequence of the virus in me and the virus in you and see they’re closely related. Whereas a virus someone picked up a six-hour drive away or in the UK might be different.”
First Nations activists who are fighting fish farms in their territories feel certain that farmed fish are spreading disease to wild fish. Chief Ernest Alfred of the ‘Namgis First Nation in Alert Bay occupied the Swanson Bay fish farm in protest for 280 days. He and other occupiers took daily photos of sick fish, including some that were deformed or yellowing, a sign of jaundice. “There were also all sorts of skin disorders, there was blindness.” He’s also seen wild salmon in British Columbia’s rivers and streams with similar symptoms, many of which die before spawning.
Despite recent studies highlighting the likelihood of transmission of another virus—Piscine orthoreovirus—from farmed to wild salmon, neither government nor industry has taken preventative action, such as testing farmed fish prior to moving them to ocean pens. In the current federal election campaign, the Liberal and Green parties announced a commitment to phase out ocean fish farms by 2025. But Alfred and Morton, who are following political developments closely, say they remain skeptical that government will get tough on industry to protect wild salmon.
Miller also questions whether election promises will translate into real change, but she is encouraged that public pressure is having an effect. As for whether that results in shifts in policies and regulations, “we have to wait and see,” she says.
Correction: Genome BC is a nonprofit, not a private company.