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Senior research scientist Dr. Karuna Karunakaran works in the vaccine research lab at the British Columbia Centre for Disease Control on April 30, 2009.DARRYL DYCK

Two provinces and a territory have split ranks with the rest of Canada's health authorities in their fall immunization plans, sowing public confusion and raising questions of whether Canadians are being offered the safest options.

The hodge-podge of vaccination strategies comes after a controversial, unpublished study suggested that people under 50 are twice as likely to contract the H1N1 virus if they have received a seasonal flu shot compared to unvaccinated people.

With no data revealing the optimal way of rolling out vaccines against the looming double threat of seasonal flu and the pandemic swine flu virus, the abrupt changes by provinces and territories could create disarray in inoculation programs, with fewer people turning up for either shot, potentially resulting in more cases of severe illness.

New Brunswick's public health authorities, skeptical about the science behind the Canadian study, have moved up seasonal flu shots for all their residents to October before proceeding to the pandemic vaccine campaign. Meanwhile, Quebec and Nunavut are deferring their seasonal flu campaigns until after their H1N1 mass vaccination clinics.

Other provinces and territories - Ontario, British Columbia, Saskatchewan, Manitoba, Prince Edward Island, Nova Scotia, Newfoundland and Labrador, Northwest Territories and Yukon - have decided on a three-step approach. They will offer seasonal shots next month only to the elderly, who are at low risk of catching H1N1, and residents of long-term care facilities; then they will roll out the swine flu vaccine when it becomes available in November, and resume seasonal flu shots in December or January. Alberta will announce its decision Thursday.

"We'll know who's smarter at the end of the flu season," said Ross Upshur, director of the University of Toronto's Joint Centre for Bioethics and a primary care physician. "What we assuredly have is an outbreak of unpublished research which is causing an epidemic of confusion."

The research in question was led by Danuta Skowronski of the British Columbia Centre for Disease Control and Gaston De Serres of Laval University. The study, currently in the peer-review process for an unnamed scientific journal, found a puzzling association between the seasonal flu vaccination and the risk of acquiring H1N1 infection. Those infected only had mild disease. Authorities in Australia, the United States and Britain say they haven't seen the same link.

Paul Van Buynder, New Brunswick's deputy chief medical officer of health, said even if the association was true, it did not mean the flu shot actually caused people to be infected with H1N1, nor did it result in severe disease among those who contracted the virus.

Further, the risks of seasonal flu are so real - 100 to 150 deaths in the province annually, and as many as 8,000 across Canada - that protecting the public was a priority, he said. The H1N1 virus has killed 78 Canadians since the virus emerged in April.

"Our focus groups were saying that the public couldn't follow who needed what when," Dr. Van Buynder said. "It was decided by planning pro-actively and changing timing, we could protect all target groups against all diseases."

Seasonal flu can peak as early as mid-December. Public health authorities are also bracing for a resurgence of the H1N1 virus, which has disproportionately affected younger people. Doctors believe that while young people have been exposed to other flu strains, they don't respond as well to H1N1 as those born before 1957, who were already exposed to this strain.

Isaac Sobol, Nunavut's chief medical officer of health, said the territory is deferring the seasonal flu campaign because the pandemic virus is the main influenza virus circulating there. There is still some doubt as to whether the territory, or Quebec, which has a similar vaccination program, will even offer seasonal flu shots to their populations.

"We will be closely monitoring the strains of influenza virus circulating in Canada and Nunavut, and if we see that the strains for which the current seasonal influenza vaccine would provide protection are present, we will offer our seasonal influenza vaccine to all Nunavummiut, not just the elderly, as we have done in the past," Dr. Sobol said.

Dr. Upshur of the University of Toronto worries that inconsistency among jurisdictions is not only causing confusion in the short term, but could impact the trust Canadians have in public health authorities and vaccination programs going forward.

As a physician, he is at a loss of what to tell patients about the risks associated with the vaccines.

"It's okay for scientists to be confused and to debate uncertainties. But it's very hard for front-line health-care professionals and providers to instruct their patients," Dr. Upshur said. "And it's very difficult for members of the community to formulate informed decisions about what's best for their health and their families' health."

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