A government email describing a potentially lethal fish virus as a public relations problem has caused a stir at a federal inquiry in Vancouver.

The federally appointed Cohen Commission was called two years ago to examine what caused the 2009 collapse of the Fraser River sockeye.

The suggestion that an influenza-like virus had penetrated B.C. waters came just as the 21-month inquiry was wrapping up, prompting the commissioner to hold three more days of hearings.

On Friday, the federal inquiry heard from an expert in infectious salmon anemia (ISA) who detected the virus in a handful of B.C. fish earlier this year, setting off a chain of alarm bells throughout the government and the West Coast salmon industry.

Fred Kibenge, who runs a prestigious lab on the East Coast, detected the virus in two of 48 sockeye smolts, and the results of his work were widely publicized in October.

The ISA virus has infected and killed millions of fish in Chile, and is believed to have originated in Norway where its own stocks were devastated.

'Turning the PR tide'

The Canadian Food Inspection Agency (CFIA) immediately set about retesting Kibenge's samples, and told the media several weeks later they had found no evidence of the virus.

When news media made that the headline the next day, officials celebrated in a private email that has now been made public.

"It is clear that we are turning the PR tide in our favour, and this is because of the very successful performance of our spokes at the tech briefing," CFIA B.C. manager Joseph Beres wrote.

"One battle is won, now we have to nail the surveillance piece, and we will win the war, also."

Lawyer Don Rosenbloom, who represents two groups of commercial fishermen at the inquiry, isn't buying it.

"One gets the impression they see themselves at war with parties that are pursuing the best interest of the public," he said. "I think it's ridiculous."

While food inspection managers touted the results of their tests, Fisheries and Oceans officials testified the samples they used were so degraded, the results were unreliable.

Discrediting scientists

Kibenge and another Canadian scientist also told the federal inquiry they feared their reputations were being threatened after discovering signs of ISA in B.C. salmon.

The revelation triggered an assessment of Kibenge's independent lab at the University of Prince Edward Island by inspectors from the Canadian Food Inspection Agency. It's one of only two such labs for the virus in the world.

Kibenge told the federal commission in Vancouver on Friday that the way officials behaved led him to believe they were aiming to discredit his work.

"Based on the questioning I got, I sensed that the interest here was to confirm my result was the result of contamination," he said while under cross-examination.

"The second point was that probably I was doing shoddy science."

In the past several weeks, additional research has surfaced that potentially identifies the virus' presence as far back as 2002.

'Most feared threat to aquaculture'

At the inquiry, Kibenge said he felt he was being pressured, even though he considered his science to be "above question."

Sockeye salmon waiting for access to spawning grounds in Scotch Creek, B.C. (Matt Casselman)

"Because aquaculture is a business, of course, the virus or the pathogen ... is a problem," he said. "As far as I know, the spread of diseases is the most feared threat to aquaculture."

But in later testimony, Fisheries official Peter Wright, who manages the national aquatic animal health laboratory system, said the assessment wasn't seeking to discredit Kibenge.

He said its goal was to figure out why Kibenge's test results came up positive when examination of the same fish in the government's own lab did not.

During an earlier hearing, a second scientist who works in a lab based in Nanaimo, B.C., was questioned about her own experiences with federal officials.

Findings investigated

Molecular geneticist Kristi Miller, who runs a research lab for the Fisheries Department in Nanaimo, B.C., told the commission on Thursday she has been "alienated" within the department.

She said that began in late November when she revealed to superiors she, too, had detected the virus in B.C. salmon.

On Thursday, a lawyer for the commission asked a panel of three government officials whether Miller's findings are a "game-changer."

No, it just requires further investigation, was the answer from Stephen Stephen, the director to whom Miller reported her findings.

"Although it may have merit," added his colleague Wright, as he pointed out Miller is using a different testing technique. "It needs to be proven."

Kim Klotins, who was appearing on behalf of the food inspection agency, added the agency has already begun a process of investigating Miller's findings. She said staff have run initial tests, which did not corroborate the results.

The virus found was 95 per cent similar to its European strain, Miller said. A North American strain has previously been detected in Atlantic Canada.

CFIA seizes samples

Miller also noted yet another researcher, Prof. Rick Routledge of Simon Fraser University, came under scrutiny after he made Kibenge's initial results public. Routledge had collected the fish and sent them to the P.E.I. lab for testing.

She said the CFIA removed all samples from Routledge's freezer, meaning his work could not continue.

She said Stephen told her she shouldn't conduct research if she didn't understand its potential "ramifications."

That, along with what happened to Routledge's samples, caused her to feel "some level of intimidation," she told the commission.

Miller's lab is funded by the government to conduct research on fish pathogens. She found the evidence of infectious salmon anaemia in the course of that work.

Evidence of ISA dates back 25 years

Miller has told the inquiry she's not clear whether the virus she discovered causes disease, but she noted there appeared to be some signs of damage in the fish.

But that virus isn't her greatest concern, she said.

She testified she has also found signs of another virus unknown in Canadian fish that causes a condition called heart and skeletal muscle inflammation. She said those results from migrating wild sockeye salmon came back in early testing, and have not yet been shared with officials or been made public.

Kibenge and Miller are among four expert fish scientists who have told the inquiry there is varying evidence the ISA virus may be carried in B.C. salmon, with some findings dating back 25 years.

The scientists say more research is required to know whether it could be a health risk for wild Pacific salmon.

The inquiry's final report is due by the end of June.

With files from The Canadian Press