Dissecting wild Pacific salmon tissues for molecular analysis and viral genomic sequencing.

PRV spreads from salmon farms to wild Chinook, study says

“Our findings show that salmon farms are, indeed, a source of infection for wild fish. Viruses leave a genetic fingerprint. The genetic fingerprint shows that the same viruses that are on the farms are in the wild fish. All the evidence suggests that the virus is being transmitted from the farm to wild fish. I haven’t seen any evidence that says that’s not happening,” said Dr Gideon Mordecai, a viral ecologist at the University of British Columbia and the lead author of a paper published in Science Advances last month.

Dr Gideon Mordecai = photo by Amy Romer

The interview

Cortes Currents was not able to connect with him until late last week, at which point I also had a list of responses from the BC Salmon Farmer’s Association.

Mordecai pointed out that most of the resulting interview questions arose from industry responses to his research: “Which is fine and I am happy to speak to anyone who has questions and I’ll answer them to the best of my ability … (but) I didn’t put much weight to the industry response to my paper and that is because I do not think they come from a place of scientific integrity, free of bias. It is a bit like approaching an oil company to comment on the latest climate change research – you maybe wouldn’t trust the answer.” 

The unidentified industry correspondent(s) wrote that this study comes out of the Strategic Salmon Health Initiative (SSHI) – “and highlights yet again the long-standing concerns of the BC salmon farming industry regarding the credibility of its research.”

“Their publications have largely focused on viral discovery; they have failed to publish any scientific studies that investigate whether the viruses they discovered are actually threatening wild or farmedstocks.” 


Pacific salmon are a foundation species which are consumed by many animals and provide nutrients for the ecosystem.  

Farmed Atlantic salmon were introduced to BC in the early 1980s.  

The Federal Government released more than 8 million Atlantic salmon into West Coast waters between 1905 and 1935, but they do not appear to have survived. 

Since then, Mordecai explained, “There are growing concerns that there may be a spillover of pathogens from farmed Atlantic salmon to wild salmon and that maybe these spillovers contribute to the widespread decline of Pacific Salmon that we are observing.”   

PRV spreads from salmon farms to wild Chinook,
Dr Emiliano Di Cicco and Dr Andrew Bateman (co-authors of the study) sampling wild Pacific salmon – Amy Romer photo

PRV arrives in BC

The paper ‘Aquaculture mediates global transmission of a viral pathogen to wild salmon’ studies a virus known as Piscine Orthoreovirus-1 (PRV-1).

“PRV is common in salmon farming operations and it is known to cause heart disease in Atlantic Salmon. Our study used genome sequencing. A little like how during the SARS‑CoV‑2 (COVID 19) pandemic, we’ve used viral genome sequencing to track transmission of viral variants around the world. We applied the same thing to salmon viruses,” said Mordecai.

“The Piscine Orthoreovirus which is in BC, originates in the North Atlantic. We tried to estimate the timing of this arrival in all the genome sequences we collected suggested the arrival happened about thirty years ago. What’s interesting about that is this matches the timing of salmon egg imports from Europe to British Columbia, which helped take off salmon farming in the province.”  

BC Salmon Farmers response 

The industry correspondent(s) disputes this date, “the authors dismiss the fact that a wild-source steelhead trout sampled in 1977 tested positive for PRV by PCR analysis. The authors defend their dismissal of the 1977 positive test by stating that it has not been verified by genetic sequencing. However, in May 2020, researchers at Fisheries and Oceans Canada repeated the positive PRV test in the 1977 sample through sequencing.”

They demand that Mordecai et al submit a correction to Science Advances

Regarding the 1977 sample

As regards the 1977 PRV sample, Mordecai said the original results were “at a low level” and originally seemed “not repeatable.’”  

He looks forward to seeing the recent sequencing being published and peered reviewed, “with all the checks and measures that you’d expect in a peer reviewed publication.” 

“From what I’ve seen in the online database, the sequence from that sample is 100% similar to more modern day sample sequences. Which is a little bit of a surprise, and that is why I say am looking forward to seeing how the data is analyzed,” said Mordecai

“If that 1977 is real and prior to the introduction of aquaculture, there has definitely been introductions since and the exact date of the introduction actually does not inform to the risk posed by PRV.”

PRV spreads with the arrival of salmon farms
Global transmission map of Piscine orthoreovirus – Courtesy Dr Gideon Mordecai

More than one Introduction

Mordecai agreed that, “A positive PRV sample from 1977 suggests that the virus was here at that time,” but “the idea that there has only been one introduction is a little bit simplistic.” 

His study found there has actually been several introductions of PRV. In the podcast above, he talks about a strain that can be traced back to Atlantic Salmon that escaped from a fish farm in Washington state

“On our phylogenetic tree, it is pretty clear that sits outside of one of the main clade, or branch, in the region. This introduction seemed to have happened more recently. What our tree showed is that there was a lineage that moved from Norway to Iceland in about 2009,” said Mordecai.

“ … That sequence came from Atlantic salmon from a farm which collapsed in Washington state. These were Washington salmon that escaped, were sampled and some people sequenced their (PRV) virus. What’s really interesting is the genomic evidence said this looks like the Icelandic PRV and the paper that found the escapees noted that the net pen was stocked with brood stock from Iceland.”

From Salmon farms to wild Chinook

The paper that Mordecai et al worked on was concerned about the spread of PRV from farmed to wild salmon. 

“What we found was that wild Chinook salmon were more likely to be infected with PRV when they were close to farms” he said. “ … And then when we look at the sequencing, we see they share the same viral variants.” 

Fish farm smolt are ‘PRV free’

The BC Salmon Farmers email replied, “the authors did not take account of other factors that might influence PRV-1 prevalence (e.g. different environmental conditions or differences in host condition between regions).”

Industry also insisted that salmon are verified as PRV free before they enter the pens, which means they must have picked the virus up in the ocean.

Mordecai replied, “What we do know, for sure, is that Atlantic salmon farms in BC have very, very high rates of PRV infection. What our study found is that over the production cycle of net pens, more and more fish get infected until by the end of their production cycle the probability of a fish infected in that net pen is almost 100%.”

Detection does not equal disease

The industry correspondent(s) emailed, “Pathogen detection alone is insufficient to allow inferences of the overall health status of wild fish populations and requires the context of host susceptibility, virulence of pathogen strains, and environmental conditions. Therefore, it is inaccurate to assume that the detection of pathogens or their DNA in proximity to a salmon farm is an indicator they are causing disease issues for wild salmon swimming near a farm…”

“There is, however, a weight of evidence that indicates that the PRV isolate found in BC does not cause disease in wild or farmed salmon in the Pacific  (Garver et al., 2016Polinski et al., 2019Zhang et al., 2019Purcell et al., 2018) – and Heart and Skeletal Muscle Inflammation (HSMI) (associated with PRV elsewhere) has not been diagnosed by licensed veterinarians caring for fish in British Columbia. Moreover, infection with high loads of PRV does not impede the physiological capacity, biological performance, or the migratory lifecycle of wild Pacific salmon.”  (Purcell et al., 2018Zhang et al., 2019).

How do farmed fish get infected?

“Where that infection comes from is a different question. There are a few possibilities,” said Mordecai. 

“One of them is that we know PRV has been present, in the past at least, in the hatcheries. There is a study from which Andrew Bateman is the lead author of, which detected PRV in freshwater hatcheries. So that is one possibility, that the Atlantic salmon in the hatchery is infected and that gets moved into the ocean.” 

Dr Bateman subsequently emailed Cortes Currents that, “Bear in mind that the data comes from 2013/2014, and practices have changed since then, from what I understand.  I’ve been told that salmon aquaculture hatcheries now ‘double disinfect’ their eggs, and apparently the incidence of PRV in hatchery fish is much, much lower.  I have not seen the data.”

Mordecai added, “I haven’t seen any data. What’s published is that PRV is in the hatcheries … If they are all put into the ocean clean, then there is the possibility that they are picking up the infection from the environment, but the end result is the same … You have net pen full of infected fish and that poses a risk it will spill over to the wild fish.” 

He added that he was pleased to hear that industry is screening fish before putting them into pens, because they should not be allowed to put infected fish into the ocean.

Wild Sockeye Salmon are not in the vicinity long enough to be infected

The BC Salmon Farming Association cited a study that found “ … sockeye salmon migrating through the main migration routes of the Discovery Islands only remain within ~200-800 metres of a farm for approximately 4-11 minutes.” 

Mordecai pointed out that his study focused on Chinook salmon, “a totally different species, with a totally different life history.” 

Sockeye “swim out the rivers, they swim out the ocean and it all happens fairly quickly.” 

As for their not lingering near salmon farms long enough to be infected: “That’s not my area of expertise. What I would say is that the virus is likely to be able to last a long time in the water and is highly infectious …”

Young Chinook head out into the ocean and winter in the same area as the farms.  

“For this species, the time they are around the salmon farms is likely to be much much longer than the sockeye, which spend most of their adult life out in the ocean.” 

PRV spreads from salmon farms to wild Chinook,
Sampling wild Pacific salmon on the West Coast of Vancouver Island. Dr Andrew Bateman (right), is a co-author on the study. – Amy Romer photo

DFO’s Minimal Risk Assessment

Mordecai said, “There are lots of pieces of evidence that all add up to the same thing, that these farms do pose a risk. Whether that’s sea lice, or other types of pathogens and bacteria, or in Europe with the escapes and genetic changes to wild Atlantic Salmon. This is just another piece of evidence and they are not unique in that they find there is a risk.”

He added, “ I should be clear our paper is not about Fraser River sockeye salmon, it is mainly about Chinook. We are just looking at one virus, our role wasn’t to be looking at all the things that pose a risk. That should be the role of the Department.”  

One of the problems with the recent  Department of Fisheries and Oceans Review, which found that aquaculture poses a minimal risk to sockeye salmon migrating through the Discovery Islands, “is that it missed whole questions.”

“An important one, which it is too bad Andrew isn’t here to speak to you about … is the role that sea lice play. The risk that farms pose isn’t just about one virus, but a whole host of things.” 

Links of Interest:

Top photo credit: Dissecting wild Pacific salmon tissues for molecular analysis and viral genomic sequencing – Amy Romer photo

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