Three Previously Unknown Viruses Discovered In Endangered Pacific Salmon Species

Chinook salmon found dead at British Columbia spawning grounds. Kristi Miller-Saunders, Fisheries and Oceans Canada

Genetic analysis of endangered Pacific salmon populations has identified three previously unknown viruses, one of which belongs to a group of viruses that's never been known to infect fish.

Chinook and sockeye salmon in the cool waters of America and Canada’s Pacific Northwest are considered keystone species, playing a pivotal role in supporting the ecosystems that they live in. Both anadromous fish, the two spend their lives in both fresh and saltwater habitats, transporting vital nutrients between the two and providing a primary food source for apex predators like orcas and sea lions.

Researchers say they aren’t sure how the salmon will be impacted, but closely related viruses have been known to cause serious disease in other species.

“We were surprised to find viruses which had never before been shown to infect fish,” researcher and study author Gideon Mordecai said in a statement. “Although there’s no risk to humans, one of the viruses is evolutionarily related to respiratory coronaviruses, and is localized to the gills. That suggests it has a similar infection strategy to its distant relatives that infect mammals.”

DNA was first sequenced from more than 6,000 dead and dying salmon from along Canada’s British Columbia coastline – including wild, hatchery, and farm-raised fish – after which point scientists used specific tests unique to each virus to screen for infection. They found evidence of a novel arenavirus, reovirus, and nidovirus, two of which were present in all three sources whereas the third was only seen in farmed fish.

A Pacific Salmon Foundation researcher dissects tissue samples from overwintering Chinook to detect for the presence of infectious agents, Quatsino Sound, BC, March 2019. Amy Romer

“We found the new viruses widely distributed in dead and dying farmed salmon and in wild salmon,” said virologist Curtis Suttle. “It emphasizes the potential role that viral disease may play in the population dynamics of wild fish stocks and the threat that these viruses may pose to aquaculture.”

One virus in particular infected more than 15 percent of all hatchery-born Chinook, or “king”, salmon. A second was found in 20 percent of all Chinook salmon from adults and sub-adults raised in fish farms. Overall, fish viruses were found more in captive-bred fish than those born in the wild.

In the last three decades, there have been declines in Chinook and sockeye salmon populations, which are important to commercial and recreational anglers, as well as indigenous communities and the general public who rely on salmon. It is unclear why salmon populations are decreasing but the study authors note infectious diseases may play a role.

“Being able to screen so many fish for these viruses was an exciting breakthrough, and meant we were able to identify hotspots of infection,” said Mordecai. “One of the viruses was relatively common in juvenile migratory salmon as they enter the ocean – a period thought to be critical to their survival into adulthood.”

The authors say that their work will help to inform conservation efforts and may help pave the way in determining how such viruses could infect people. The study is published in eLife.

Pacific Salmon Foundation researchers sample overwintering Chinook to be screened for infectious agents, Quatsino Sound, BC, March 2019. Amy Romer
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