The Canadian Food Inspection Agency has cleared the first Nova Scotia aquaculture site to be hit by an outbreak of infectious salmon anemia but say a new strain of the deadly fish virus has been detected.

Last week, federal authorities lifted a quarantine imposed on a Shelburne salmon farm operated by New Brunswick-based Cooke Aquaculture.

The Canadian Food Inspection Agency has confirmed that 450,000 farmed salmon, like those from the undated file photo above, have tested positive for a virus. (CBC)

According to the Canadian Food Inspection Agency, salmon with the virus are safe to consume and the virus and its mutated cousin pose no risk to human health.

The CFIA confirmed the ISA problem was resolved through a mass salmon slaughter, rigorous pen cleanings and a period where the facility was shut down.

A report submitted earlier this week by Dr. Brian Evans, the Canadian delegate to the World Organization for Animal Health and CFIA's former chief veterinary officer, stated a genetic mutation in the deadly salmon virus was detected in the infected Shelburne samples.

Dr. Roland Cusack, Nova Scotia's fish veterinarian, said the effects of mutated virus are the same.

"It's a change in shape but otherwise its the same as any other type of ISA," said Cusack.

"[It's not] more dangerous to the fish."

Despite assurances, some doubt safety

Despite the Canadian Food Inspection Agency's assurances that ISA-infected salmon are safe to eat, some members of the public are not convinced.

"There's no way, even if they said it was fine to eat, I wouldn't eat it," said Lisa Walker.

"The CFIA has completely lost control of this virus on the Atlantic coast," said aquaculture opponent Marike Finlay-de Monchy.

"When you start to get a virus mutating, we all know how dangerous that can be."

According to the Introduction to Modern Virology textbook, viruses have a very high rate of mutation. Combined with their short generation period, that means viral mutations are common and are often benign.

A common example of viral evolution is the common cold and its ability to make people sick many times throughout a single year.

Cusack downplayed the CFIA's decision to allow Cooke Aquaculture to process Nova Scotia raised salmon infected with ISA at its New Brunswick plant. He said this is the first time ISA-infected salmon have been processed on this scale.

"There is no human risk associated with this product," said Cusack.

"They're basically case-by-case deciding what would be taken to market and what wouldn't."

According to the CFIA, up to 90 per cent of infected fish can die of the disease, depending on the strain of the virus. The types of fish that have been confirmed to be susceptible to the virus are: Atlantic herring, Atlantic cod, Atlantic salmon and brown trout.

Fish with the disease may have a loss of appetite or show abnormal swimming patterns and they may have grey gills, a swollen abdomen, according to the federal agency.

The virus can spread in contaminated water or by contaminated equipment.