Tracking salmon viruses

DNA sequencing like that used to track COVID-19 helps scientists trace the origins of salmon pathogens in B.C.

  • May 26, 2021
  • 1,068 words
  • 5 minutes
Juvenile salmon swimming with Darwin’s first known sketch of an evolutionary tree layered on top Expand Image

Confined to working from home this year, I’ve spent hours at my desk, obsessing over what appears to my partner to be a screen full of seemingly indecipherable lines and shapes. To the untrained eye, these cryptic plots don’t give much away, but since each tree depicts a story, their appeal to scientists isn’t so much in the aesthetics, but the biological tale they tell. 

Tree diagrams were first conceived to represent the origins of animal groups in the early 19th century, but were famously immortalised by Darwin when he scrawled ‘I think’ next to a sketch of a branching tree depicting the idea life is not fixed and unchanging, but instead all species change over time and are related through common ancestry. 

The processes Darwin recognised as influencing the evolution of plants and animals apply to all living things, but also to viruses, since their genomes are based on the same genomic code as all of life. Before the global pandemic, few of us were aware of the body of scientists working to track pathogen evolution, but as SARS-CoV-2 diversifies, the tracking of different viral lineages using genome sequencing and viral phylogenetic ‘family’ trees have become useful tools to trace the paths of the ongoing outbreak. 

However, the trees I obsess over tell a different story, of a different virus.

The expansion of Atlantic salmon farming to the west coast of Canada has long been blamed for declines in wild Pacific salmon which have occurred in the region, but since salmon life cycles are so complex, teasing apart the influence of different stressors such as climate change, disease, overfishing and habitat loss is complex. What is clear is that the impact of declining wild salmon populations are severe, with devastating implications for the wildlife and people who depend on them. For example, the reduced availability of Chinook salmon, the preferred prey of the killer whales of the Salish Sea, is thought to be one of the factors linked to the decline of these fish-eating whales.

There is increasing concern around the role that pathogens and parasites play in declines of wild salmon. The occurrence of sea lice on wild Pacific salmon is a stark visual reminder of the role that pathogens might play. However, the dynamics of microbial infections are sometimes more subtle, drifting invisibly between populations, and the most severe infections likely remain unsampled due to mortality or predation. Fortunately, a suite of tools harnessing advancements in genomic technology are now available, which offer a glimpse into this invisible world.

One of the more infamous salmon pathogens, known as Piscine orthoreovirus (PRV) is of particular concern, as it causes an emerging disease in farmed Atlantic salmon in Norway. In British Columbia, the ability of the virus to cause disease has been controversial. However, there is a growing body of evidence associating the virus with disease in Atlantic salmon in B.C. Perhaps more relevant to the health of the ecosystem, we are now beginning to understand the implications of this virus infecting wild Pacific salmon. By using molecular probes that can determine which cells the virus is infecting, PRV has been associated with a disease in Chinook salmon which is different to the disease it causes in Atlantic salmon, highlighting the potential risk PRV and other viruses pose to the health of wild salmon populations.

Molecular tools such as PCR assays (the same technology predominantly used to test for SARS-CoV-2) enable scientists  to carry out testing for viruses such as PRV, but we now routinely go a step further, sequencing the genomes of microbes to identify not just their presence or absence, but their exact identity. It’s a bit like the difference between hearing a knock on the door and knowing someone is there, versus having a security camera that can identify exactly who is standing at your door.

A major question regarding PRV is: where does the virus originate from? This is where the trees come in. By using viral ‘family’ trees comparing viral genome sequences collected in BC with those from around the world, we can build a picture of the transmission history of the virus. Our genomic investigations found that the virus originates from Norway, and was likely introduced to B.C. from the movement of Atlatic salmon for aquaculture. We found that Atlantic salmon aquaculture in B.C. enables continual transmission of the virus between farmed and wild salmon.

These same genomic technologies have also revolutionised our knowledge of the diversity of viruses that infect salmon. By exploiting revolutions in DNA sequencing technology, our work has discovered an assortment of novel salmon viruses, some of which had never before been shown to infect fish. One of the newly discovered viruses is related to mammalian coronaviruses, and although this virus is restricted to infecting fish, and poses little threat to human health, we found that it primarily infects the gill tissue of the salmon, reflecting the respiratory disease caused by related coronaviruses in mammals.

While there is still a lot of work to be done determining if these newly discovered viruses pose a threat to the health of wild salmon, their association with cultured salmon raises concern about how human activity may influence the transmission dynamics of viruses. Ecological degradation increases the risk of viral spillover. For instance. intensification of agriculture and aquaculture has led to increased population sizes and density, which both facilitate disease emergence and transmission. Unlike on land, where there are more barriers to infection between farmed and wild animals, in aquatic environments, wild fish are directly exposed to infectious diseases in cultured fish which share the same water. 

Although at times seemingly abstract, the branching trees on my home office screen offer a view into another world – determining the role of disease in the health of wild salmon populations is an enormous puzzle, but by learning more about the transmission routes of these viruses, we can fit together some of those pieces and help to protect the health of wild salmon and coastal ecosystems

Gideon Mordecai (Twitter: @gidmord) is a Liber Ero Fellow at the University of British Columbia  His research on salmon viruses is in collaboration with Dr. Kristi Miller’s Strategic Salmon Health Initiative and Dr Jeff Joy’s Molecular Epidemiology and Evolutionary Genetics group at the BC Centre for Excellence in HIV/AIDS.


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