VANCOUVER - Two Canadian scientists working on opposite coasts say they fear their reputations are being threatened after discovering signs of a potentially lethal fish virus in British Columbia salmon, a federal inquiry has heard.

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

The revelation set off a chain of alarm bells throughout the government and the West Coast salmon industry.

It also triggered an audit 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 the audit was conducted led him to believe officials were attacking his reputation and 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."

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 a 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.

In the past several weeks, additional research has surfaced potentially identifying the virus as far back as 2002.

Earlier this month, officials with the federal Fisheries Department and the Canadian Food Inspection Agency also released findings from their own tests on the fish suspected of carrying the virus. The federal fisheries minister released a statement saying that the in-depth test results showed no signs of infectious salmon anaemia and said there has never been a confirmed case.

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

"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."

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.

Molecular geneticist Kristi Miller, who runs a research lab for the federal Fisheries Department, told the commission on Thursday she has been "alienated" within the department since revealing to superiors in late November she had detected the virus in B.C. salmon.

The virus she found was 95 per cent similar to a European strain of the virus, she said.

She 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.

Miller said the Canadian Food Inspection Agency removed all samples from Routledge's freezer, meaning his work could not continue.

Miller said she was also told by a superior that she wouldn't understand the potential "ramifications" of her research. 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 viruses. She found evidence of infectious salmon anaemia in the course of that work.

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

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

She has also found signs of another virus unknown in Canadian fish that causes a condition called heart and skeletal muscle inflammation. She said the results from migrating wild sockeye salmon came back in early testing that 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 virus may be carried in B.C. salmon, with some findings dating back 25 years.

Infectious salmon anaemia has infected fish in Atlantic Canada and wiped out some stocks in Europe and Chile, but 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.