Test results indicate poultry at a turkey farm and a chicken farm in B.C.'s Fraser Valley, where thousands of birds have already died, were infected with a high-pathogen, or high-path, strain of H5N2. Previous H5N2 outbreaks in Canada were low path.
Birds at two additional farms that were later placed under quarantine as a precaution have also been infected with H5 avian flu, the agency said, though tests had yet to confirm the subtype and the pathogenicity at those sites.
Dr. Harpreet Kochhar, Canada's chief veterinary officer, said federal and provincial government agencies will be looking for any sign the virus has moved beyond those four farms.
"Our epidemiological investigation, and the symptoms that come up if there are any, will be reflective of whether there is a disease spread or if we've contained it," Kochhar said during a conference call with reporters.
"Our general surveillance has not revealed that there are any other farms with similar symptoms."
Kochhar said it's still not clear how the birds at the first two farms were infected. The agency focused on the additional farms because they had each received birds from the Chilliwack chicken operation.
All of the birds at the four infected farms that are still alive will be euthanized.
The infected barns at the first two farms together housed 18,000 birds, but an additional 17,000 turkeys in adjacent barns at the Abbotsford operation will also be euthanized.
Officials did not have figures for the second pair of farms.
The federal agency has cautioned that the virus does not pose a risk to consumers if poultry meat is properly handled and cooked, though in rare cases it can be transmitted to people who work in close contact with the animals.
Previous H5N2 outbreaks in Canada, including two in B.C. and one in Manitoba, were low path.
Pathogenicity does not indicate the level of danger a virus poses to people. High-path avian flu viruses kill birds, while low-path viruses can reduce egg production.
In 2010, a low-path strain of H5N2 avian flu in Manitoba at a turkey breeder farm led to the destruction of 8,200 birds.
The Fraser Valley has previously seen two outbreaks involving low-path H5N2.
About 74,000 turkeys and chickens were destroyed in 2009 after a low-path strain of H5N2 infected poultry at two Fraser Valley farms, and more than 60,000 ducks and geese were destroyed at two farms in the region in 2005.
The most serious avian influenza outbreak in Canada was in 2004, when a high-path strain of H7N3 spread to 42 commercial farms and 11 backyard coups in the Fraser Valley. In response, the federal government ordered the slaughter of 17 million chickens, turkeys and other domestic birds.
The current outbreak is already having an economic impact on the Canadian poultry industry.
Since this avian flu was reported, Japan has banned all Canadian poultry products, as well as the import of chicks from B.C.; South Korea has banned chicks from Canada; Taiwan has banned all B.C. poultry and poultry products; and Hong Kong has banned poultry products from the Fraser Valley.
The industry group representing B.C. poultry farmers has said consumers likely won't notice signs of the outbreak at the grocery store, as the affected farms still represent a comparatively small proportion of the province's industry.
B.C.'s Ministry of Agriculture said the province's poultry industry produced 160 million kilograms of chicken in 2012, and 21 million kilograms of turkey.
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— With files from Helen Branswell in Toronto
Note to readers: This is a corrected story. A previous version said a 2010 outbreak in Manitoba was high-path H5N2