A B.C.-based biologist stunned U.S. scientists last year with trace findings of a virus usually linked to farmed fish in wild salmon.

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BROUGHTON ARCHIPELAGO, B.C. — She’s perched in her boat near a fish farm, talking about diseases, the kind that might escape and kill wild salmon. Then she spies a worker peeling toward her in a boat.

Alexandra Morton, bane of North America’s salmon farms, runs a hand over tired eyes and awaits a confrontation.

It’s no surprise this eco-provocateur is again in someone’s sights.

The biologist has spent countless days just like this — zipping through a pristine jumble of uninhabited bays and islands to check on Canada’s remote fish farms. Few activists try harder to convince the globe that salmon farming threatens the marine world. Few are taken as seriously — much to the chagrin of her many enemies.

It was Morton who stunned U.S. scientists last fall with trace evidence found in wild salmon of a virus that killed millions of farmed fish in Chile.

Researchers from Washington state to Washington, D.C., scrambled to grasp the risks of so-called infectious salmon anemia (ISA), a virus typically linked to fish farms. Congress demanded federal agencies test American fish. Wild-salmon lovers seethed. Leaders of British Columbia’s $500 million-a-year salmon-farming industry scoffed — in part because they so distrust Morton.

Then, just last week, another virus raced through salmon farms at Vancouver Island and Bainbridge Island, forcing operators to kill hundreds of thousands of farmed fish on both sides of the border. Unlike ISA, this virus, infectious hematopoietic necrosis (IHN), is native to wild Northwest salmon, but experts worry that the clustering of nonnative Atlantic salmon in farm-fish net pens could amplify the pathogen and make it more virulent or cause it to mutate into something far more deadly for wild stocks.

Now, as researchers in both countries struggle to determine if a wild fish-killing pathogen is here or coming, Morton — a Connecticut native and former killer-whale biologist — is everywhere. She’s testifying in Canadian court, blogging about viruses, shuttling about in her sea dory. She gathers farmed-fish heads at ethnic groceries and travels the province teaching groups to sample fish. She hunts for clues to support her belief that Atlantic-salmon farms are big trouble.

Her single-mindedness, bombast and memorable white mane make her a target for an industry sensitive to criticism. (One company sued an activist friend of hers for creating cartoon cigarette packs with the slogan “Salmon Farming Kills Like Smoking.”)

Morton has heard rumors fish-farm workers keep pictures of her boat thumb-tacked to their bulletin boards. The B.C. Salmon Farmers Association dedicates a Web page to correcting Morton’s statements. The B.C. government is considering making it a crime for anyone to release — or a journalist to publish — information about disease outbreaks, including on salmon farms. Fines could reach $75,000.

“Alex hides nothing about the fact that she doesn’t believe in salmon aquaculture,” says Ian Roberts, with Marine Harvest, a seafood company that raises half of B.C.’s farmed salmon. “She’ll go to any length to prove her feelings are justified.”

Already on this windy mid-May morning, Morton has trained her field glasses on a farmed-salmon pen only to find a worker staring back through binoculars. When another farmer warily pulls alongside her boat, Morton turns to her most potent weapon: charm.

“Can I help you guys at all?” he asks.

“We’re just looking,” Morton says cheerily and pumps him for information. “How old are these fish? How long have they been in the water?”

Morton extracts a few nuggets before the man jets away, a victim of Morton’s disarming agreeableness. She shrugs. “It’s not the workers I have a beef with,” she says.

Her home waters

If there’s a front line in the battle over farmed fish, it is in the Broughton Archipelago, a tremendously wild clutter of fjords and islands 300 miles north of the border.

Roughly two dozen of B.C.’s salmon-farm sites are here, though only about half operate at one time. It is also Morton’s home.

Morton, 54, settled among the porpoises and humpbacks in the 1980s as she and her husband studied orcas. He later died in a diving accident, but Morton stayed and has spent 26 years in and around Echo Bay, in cottages and boathouses and a lab she helped build. From here, she watched the number of salmon farms explode.

At first Morton applauded their presence. But fishermen complained that farms blocked hot spots, where wild fish migrated. When farmworkers used guns and noisemakers to drive off marine mammals, Morton feared for her whales.

She tried parlaying relationships with government biologists into influence to get farms moved. She got back letters demanding more proof. Morton found her activist soul and became B.C.’s leading salmon-farm opponent.

“I knew nothing about salmon,” she says from her purple home on nearby Malcolm Island. “I didn’t even know how to catch them. But then I noticed the juvenile migrations. It’s like looking at the wildebeest migrating across the plain, it’s that huge. And I’d never noticed because I only saw the whales.”

At any one time, 80 to 90 working salmon farms dot B.C.’s marine waters, most rearing tens or hundreds of thousands of Atlantic salmon in swimming-pool-sized net pens. Most of the fish are sold in the U.S.

Over the years, the industry has faced many battles — over black fish waste that piled up below pens; over the massive volume of wild fish needed to feed farmed fish; over antibiotics and pesticides used to keep out disease; over parasites and pathogens that spread to wild fish.

The Monterey Bay Aquarium’s popular “Seafood Watch” wallet cards still urge fish-eaters to avoid farmed Atlantic salmon, citing these concerns. The industry says the cards are outdated.

But it was Morton’s work with sea lice and bacteria that brought her attention and cost the industry prestige. In the 1990s, she saw disease outbreaks associated with fish farms turning up in local wild salmon. Then she noticed baby wild chum and pink salmon that swam past farms contracted sea lice.

Morton, who doesn’t have a doctorate, howled. She said farms would drive Broughton’s pink salmon to extinction. She was ignored, her fears dismissed as ludicrous.

Morton, undaunted, opened her Echo Bay laboratory to university researchers, who partially confirmed her findings. Today it’s accepted that farmed fish can pass sea lice to wild juveniles and that those juveniles often die. But the impact that has on wild populations is a controversial question. (Pink salmon are plentiful in the North Pacific.)

“My take is that she was on to something early, and people pooh-poohed it, and there was a little bit of sarcasm about her being a nonscientist,” said University of Washington fisheries professor Thomas Quinn. “The Canadian government just didn’t want to hear it. They were really pushing aquaculture, and she wasn’t a card-carrying Ph.D. But, then again, neither was Darwin.”

Says UW fish scientist Ray Hilborn: “Alexandra clearly has an agenda and is an activist, and I’m always suspicious of people like that. They’re not looking for the answer; they’re looking for the data to support what they think. But what separates her from a lot of activists is she works with really good scientists.”

Salmon farmers are far less generous.

Roberts, at Marine Harvest, says Morton doesn’t talk about research — her own — that shows lice problems drop off when farms apply pesticides, which they do.

“She’s selective with information,” says Mary Ellen Walling, director of the salmon-farming association. “She’s clearly passionate about her work, but that passion has moved her discussion into a realm built around fear and misinformation. She’ll repeat mistruths over and over, and nobody holds her accountable.”

Morton’s response: “For sure I’m not saying anything good about them, because I’m very, very worried.”

Virus controversy

It’s against this backdrop that Morton last year stumbled onto the ISA virus.

A Simon Fraser University professor was searching for clues to the decline of wild fish in Rivers Inlet north of Vancouver Island. Morton suggested he test for ISA.

While not harmful to humans, the virus has killed millions of farmed fish in Europe. It traveled from Norway to Chile on imported fish eggs and killed millions more salmon there.

Morton knew a scientist had been looking into the role fish diseases might play in plummeting runs of Fraser River sockeye. She knew B.C. fish farms years earlier had received eggs from Europe. Scientists feared that if ISA got into West Coast farms, it could mutate, escape and kill off wild fish.

So the professor sampled 48 wild fish. He sent them to a lab run by a world expert on ISA. The lab found trace genetic evidence of the virus in two fish. “I thought, ‘Oh my god,’ ” Morton says.

Was the virus here, and if so, where were the dead fish? Had this pathogen just not yet mutated into a virulent form? Or was this an unrecognized harmless strain?

Canadian officials reacted sharply: No fish were sick. The virus couldn’t be isolated, replicated or confirmed with other tests. It had to be a mistake — a false positive.

But the U.S. took the findings seriously and started preparing its own fish-testing plans. (Those plans will be submitted to Congress in coming weeks.)

In the wake of Morton’s find, U.S. scientist were dismayed by a new revelation: Another Canadian in 2002 had found ISA evidence in 100 wild fish, but the Canadian government had told no one. Morton had sparked an international scandal.

Presuming the government was hiding something, she decided to do more work herself. “I kept thinking, ‘I can’t do viruses, I can’t do viruses,’ ” Morton says. “I kept waiting for the government to do its own testing. When they didn’t, I did.”

This winter and spring she visited other rivers. She bought farmed-fish heads at stores and took samples in parking lots. They showed more trace findings of ISA.

Canadians suspected lab contamination, but not U.S. scientists. With one facility run by a world ISA expert, “I find it hard to imagine he doesn’t keep his lab spotless,” says Jim Winton, fish virologist with the U.S. Geological Survey.

There are enough positive hits that Winton believes something’s out there. It may be harmless — or something that could mutate.

“At this point, I have to tell you, I’m really confused,” he says. “This may end up being nothing but a huge diversion. Or it may be the real thing. I don’t know.”

B.C.’s fish farmers are certain they aren’t the culprits. They’ve run 7,000 tests, Roberts says — all negative. He suspects false positives, or a virus brought over with Atlantic salmon introduced earlier for sport fishing. He even points a finger at hatcheries.

Walling agrees. “Disease management in hatcheries is an issue that needs to be more fully explored,” she says.

Morton, as always, points right back to salmon farms.

“That’s how it happens,” she says. “These viruses arrive, they simmer, and then ‘Whammo!’ “

Craig Welch: 206-464-2093 or cwelch@seattletimes.com. On Twitter @craigawelch.