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Kristi Miller is head of molecular genetics for Fisheries and Oceans Canada.Rafal Gerszak/The Globe and Mail

For years Kristi Miller has been probing the complex and controversial world of fish diseases on the West Coast, where scientists are trying to unravel the mystery of why millions of apparently healthy salmon die annually.

Now Dr. Miller, the groundbreaking head of molecular genetics for Fisheries and Oceans Canada, and Brian Riddell, a former top scientist with DFO who directs the non-profit Pacific Salmon Foundation, are teaming up with Genome B.C. in the most comprehensive study of salmon health ever undertaken in the world.

"This is going to be the first really large-scale effort to look at the health of all salmon," Dr. Riddell said. "It's exciting. It's incredibly exciting."

Dr. Miller, whose cutting-edge genomic research has largely been kept under wraps by the government, testified at the Cohen Commission inquiry into the collapse of Fraser River sockeye stocks in 2011. But she was not allowed to talk to the media at the time.

In her first interview since then, she said the research project will rely on new technologies designed at the Pacific Biological Station in Nanaimo on Vancouver Island.

"There is … technology that I have been developing for the past year … that has the capacity to run about 45 microbes across 96 individual [fish samples] at a time, so one can quite rapidly generate a lot of information from a platform," she said. "And that's our goal at the moment – to assess 45 microbes that are known or suspected to cause disease in salmon worldwide."

Dr. Miller made a startling find a few years ago when she detected a genomic signature in salmon that died in rivers before they had a chance to spawn. Her research caused a big splash in the U.S. journal Science, because it suggested a virus was causing those pre-spawn mortalities. But she was not cleared by DFO to talk about her work. Her silencing was one of the key events that led to complaints against the federal government for "muzzling" scientists.

But Dr. Miller got approval from Ottawa to talk this week about her new research, which she says will build on her earlier work.

"I am speaking now … and I hope that this is a signal [of continued openness]," she said.

Dr. Miller said infectious salmon anemia (ISA), which has wiped out farmed salmon in some areas of the world and is suspected of being loose in B.C., will be one of the key microbes she looks for.

"It is our intention to have ISA as one of the microbes on the chip," she said. "Basically any microbe that you've heard about in the news will be on our chip. It includes viruses, bacteria, parasites and fungal pathogens. So there's quite a wide range."

Juvenile salmon migrate out of coastal rivers in the billions each spring, but 90 per cent die before returning to fresh water. It is thought most die in the first few months at sea. Of those that survive, many die as adults – sometimes millions in a given year – just prior to spawning. Diseases that weaken fish, making them susceptible to environmental stresses, have long been suspected but never proven.

The goal of the new research is to find out exactly what disease microbes salmon carry, where those microbes might have originated, and how they interact to impact the health of salmon.

Dr. Riddell said the research team will be taking thousands of samples from juveniles and adults in three distinct salmon populations: wild fish, those raised in federal hatcheries, and farmed fish which are raised in open-net cages along the B.C. coast.

Some of the microbes being looked for are endemic to B.C., but others aren't supposed to be in Pacific waters and, if found, could raise troubling questions about the role aquaculture may have played in disease transference.

"We'll be able to say, what is the linkage? Is there any relationship between the health of fish in a farm and the risk to fish migrating past a farm?" Dr. Riddell said. "But that will be down the road. Our particular interest right now is to look directly at the health of the different populations of fish."