The juvenile fish will be placed in pens this fall, more than a year after thousands of fish escaped from a Cooke Aquaculture facility.

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Nearly 1 million more Atlantic salmon are headed to Puget Sound, a year after a catastrophic fish escape caused by the same company that now is stocking more pens.

The Washington State Legislature last session passed and the governor signed into law a phase out of the open net pen Atlantic fish-farming industry in Washington. But the industry is continuing to operate under its existing permits until  valid leases expire, by 2022 at the earliest.

To continue its operations, Cooke Aquaculture Pacific sought and received permission this week from the Washington Department of Fish and Wildlife to restock two of its farms, one at its Orchard Rocks facility in Rich Passage off the south end of Bainbridge Island, and the other at Hope Island near the mouth of the Skagit River. Cooke is stocking the farms with 800,000 young Atlantics to grow to harvest size in about 16 months.

The department in May denied a similar permit for Cooke after testing revealed an exotic strain of piscine orthreovirus (PRV) in the fish.

The department had no basis under which to deny the new permit because testing by both Cooke and the department showed the fish in this batch to be free of PRV, said Ken Warheit, director of fish health for the state Department of Fish and Wildlife.

The department is heightening its attention to the issue of PRV and its potential to affect native salmon.

The fish and wildlife department has initiated its first-ever testing of selected state hatchery facilities in Puget Sound and the Lower Columbia River, to determine if hatchery salmon returning now to the facilities are carrying the exotic strain of PRV.

The department has long been aware of the presence of a version of the virus of eastern Pacific origin in free swimming Pacific salmon, both hatchery and wild.  That strain can be present without necessarily making the fish sick, Warheit said. But the exotic strain is unfamiliar, which is why the department blocked Cooke’s smolts carrying the exotic strain May 2018.

Meanwhile, adding to new concern over the issue, testing last fall of Atlantics on the loose from the Cypress Island escape last August detected a similar exotic strain of PRV. That testing was done by the Wild Fish Conservancy, a nonprofit advocacy group that opposes fish farms.  Unknown, Warheit said, is whether the virus found on the adult Cypress Island fish pose a risk to native Pacific salmon.

The department is doing more research and determining what its management response should be, Warheit said.

Kurt Beardslee, executive director of the Wild Fish Conservancy, said the department should test adult fish in the net pens  of Cooke’s operations and without delay. “Our wild salmon and our killer whales are at the edge of extinction and we can’t afford to take risks with them,” he said. “We know how dangerous non-native viruses can be to native species that have not evolved with them.”

Cooke will plant its new batch of Atlantics this fall, after a mandatory fallow period at the designated pens. Cooke must also repair its Orchard Rocks facility before it can add more fish in the pens, after a Department of Natural Resources (DNR) inspection revealed structural problems, including corrosion, at the facility.

The department initiated inspections at all of Cooke’s farms after the net-pen escape. DNR revoked the company’s license to operate its farm at Port Angeles on the basis of one of those inspections, an action the company is fighting in court. DNR also revoked the company’s license at Cypress Island because of maintenance and lease violations.

State agencies have been working with Cooke to improve the  response in the event of any future escape.  Because of delays last year most fish got away, and the majority of the fish caught were mopped up by the Lummi Nation in an emergency fishery. Adult Atlantics infiltrated rivers all over Puget Sound and while most are believed to have died out, some were turning up months later more than 50 miles up the Skagit River.

A review of the escape by three agencies found Cooke was negligent and to blame for the escape because of inadequate maintenance of nets. Allowing tons of mussels and other sea life to grow on the nets compromised their strength, causing them to give way under normal tidal conditions.  Investigators determined the escape also was much larger than Cooke told the public or state agencies, with as many as 263,000 fish released — not the 160,000 Cooke reported. As many as 206,000 Atlantics are still unaccounted for — more than double what Cooke told the public.

Joel Richardson, vice president of public relations for Cooke, wrote in an email to The Seattle Times Wednesday that the company is glad to be continuing its work in Washington.

“We are pleased that WDFW approved the transport of juvenile Atlantic salmon from our hatchery in Rochester to existing net-pen farming facilities in Puget Sound.” Richardson said. “We worked cooperatively with WDFW through the most rigorous screening ever to ensure the fish met all of the state’s requirements, and have been working with other agencies to document the suitability of those facilities to receive these fish.”

Cooke in May destroyed 800,000 fish after detection of the exotic strain of PRV in the fish by the department.

“In May, our company culled a large batch of juvenile Atlantic salmon that were denied permission by WDFW to be transported from our hatchery near Rochester to net pens at Rich Passage in Kitsap County.”

Richardson said, however, that no example of disease transfer from farmed salmon to wild fish has ever been documented by any regulatory agency in Washington. The Atlantics also do not interbreed with Pacific salmon, making them the most suitable species of salmon to farm, Richardson said.

The Legislature chose to phase out the industry because of concerns about escapes of the fish from the farms, and the possibility of competition with fragile wild stocks and spread of disease. Scientific research has shown the risk to be low. But little research has been done in Washington waters or elsewhere about the effects of escaped Atlantics on native Pacific salmon.