Washington state tested smolt in a Cooke Aquaculture incubator and found the Atlantic salmon had a strain of Icelandic virus. The state denied permission for the company to move the 800,000 fish to an open-water net pen.

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After identifying an exotic virus in fish raised by Cooke Aquaculture, Washington state is planning to test at other sites where the pathogen from Atlantic salmon may have been spread.

The state this week blocked restocking of one of Cooke’s net pens after fish at the company’s rearing facility in Thurston County tested positive for the virus.

Ken Warheit, fish-health manager for the Washington Department of Fish & Wildlife (WDFW), will, as soon as possible, test Cooke’s settling ponds at its incubator in Rochester, Thurston County, as well as Scatter Creek and its confluence with the Chehalis River for the presence of the virus found in the Atlantic salmon smolts raised by Cooke.

The pathogen could have contaminated surrounding water, raising a concern for its potential to affect native Pacific salmon, Warheit said.

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Cooke’s request for a permit to transfer the smolts to open-water net pens for growing to harvest size was denied for the same reason, Warheit said.

Cooke also had failed to observe its own biosecurity best practices by seeking to move the fish into pens at its Orchard Rocks farm in Rich Passage near Bainbridge Island without allowing them to lie fallow for at least a month. It also sought to put the fish in pens near older fish. That mixes age classes of fish, another violation of biosecurity protocol. Those were additional reasons the state denied the permit, Warheit said.

It is now up to Cooke to decide what to do with its 800,000 rejected fish, Warheit said. The one thing it can’t do is plant them in state waters. Cooke declined to comment on the situation Friday.

The scientific literature about the virus and its potential effect on native fish has been inconclusive. But out of caution, the state decided to test for the virus in Atlantic salmon ready for transport to open-water net pens

Cooke and the WDFW had been working on a protocol for routine testing for more than a year, and this was the first round. Annual testing of adult fish in the pens also is in the works.

If the state had tested for the virus earlier, it may have found it, Warheit said.

He emphasized that he does not know that the virus is harming fish. Rather, it is the uncertainty as to how the virus could behave that called for caution.

The virus detected in Cooke’s fish is a strain of piscine orthoreovirus (PRV) from the northern Atlantic. Cooke hatched the fish from eggs the company imported from its supplier in Iceland. Those eggs are presumed to be the source of the virus, Warheit said.

The northern Atlantic strain detected in Cooke’s fish is different from the eastern Pacific variety of the virus already known to be present in local waters and in both farmed and free-ranging salmon, including hatchery fish.

“I don’t know if it is more virulent or would affect our native salmon more than the PRV that is already here,” Warheit said. “It created a larger unknown for me.

“We decided we did not want it released here.”

Even the familiar strain of PRV is raising new cause for concern.

A team of researchers from the University of British Columbia and Canada’s federal Department of Fisheries and Oceans (DFO) reported this month that the strain of PRV commonly found in Atlantic salmon in British Columbia pens is associated with health problems in native Pacific chinook salmon, including massive rupture of red blood cells.

“There obviously are things going on with this virus that are associated with disease,” Warheit said. Not all the fish that have PRV get sick, he said. But some — both Atlantic and Pacific salmon — do, and scientists don’t understand why that is, which adds to the concern.

The new Canadian finding called into question the DFO’s long-defended position that PRV is harmless and raised new questions about the effect of salmon farming on critically endangered southern resident killer whales, which feed primarily on chinook salmon from British Columbia and Washington rivers.

Kurt Beardslee of the Wild Fish Conservancy, a nonprofit that opposes Atlantic salmon net-pen farming, said precaution requires an immediate response to the pathogen found in Cooke’s fish.

“I have been asking the state to do this exact thing for years,” he said of the disease testing that WDFW has initiated. The conservancy tested tissues from mature Atlantic salmon that escaped from Cooke’s pens last August and also detected PRV of Icelandic origin.

The fish escape at Cypress Island last summer blew up long-simmering concerns about risks posed by Atlantic salmon farming in open-water net pens in Puget Sound and the Salish Sea. More than 150,000 of the Atlantics were released from Cooke’s Cypress Island net pen, and infiltrated rivers all over the region.

An investigation by the state found Cooke entirely responsible for the escape, because of inadequate maintenance of its nets.

The Washington Legislature last session passed and Gov. Jay Inslee has signed legislation that phases out Atlantic salmon net-pen farming in Puget Sound as soon as 2022.

Beardslee said the pens still in use pose a risk to native salmon in Washington and in British Columbia waters, where the industry is far larger.

“This should be a giant wake-up call, and a coastwide issue,” Beardslee said.