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Danuta Skowronski, a physician epidemiologist with the British Columbia Centre for Disease Control, says flu viruses are always changing and that there is rarely a perfect vaccine match.Daniel Kozin/The Associated Press

Hospitals across Canada are bracing for an intense influenza season, driven by worries of lower vaccine uptake and concerns that this year’s shot is a mismatch for circulating strains.

Canada’s flu season has officially begun, according to new data released on Friday from the Public Health Agency of Canada. It shows that the percentage of positive tests for the virus surpassed the 5-per-cent seasonal threshold in the week ending Nov. 15.

Nearly 1,300 flu cases were detected from roughly 23,400 tests, representing a positivity rate of 5.5 per cent. The dominant subtype that has been detected is H3N2, which hasn’t had a significant presence in the past number of years.

I’ve heard the flu shot isn’t a good match for the virus this year. Should I still get it?

Danuta Skowronski, a physician epidemiologist with the British Columbia Centre for Disease Control, said flu viruses are constantly changing and that there is rarely, if ever, a perfect vaccine match.

“That’s nobody’s fault. Influenza viruses are inherently changeable, especially H3N2 viruses and this particular Subclade K,” Dr. Skowronski said. “But the question is, how much protection might we still get from the vaccine?”

That’s a question that cannot yet be answered, but there will be some protection. It is also too soon to say whether this strain will continue to dominate throughout the season. Either way, Dr. Skowronski said vaccination is encouraged, especially among those who at higher risk of severe complications from the flu.

“It’s not that this virus is a more severe variant – that’s not the case – but because it has this immune-evasion potential, we could see higher incidence of influenza overall,” she said.

This is one of the reasons that children’s hospitals and health care workers are preparing for an expected increase in flu cases, in addition to COVID-19 and respiratory syncytial virus that circulate simultaneously. PHAC data show RSV is stable currently with COVID-19 on the decline after a spike in September.

Sidd Thakore, a pediatrician at the Alberta Children’s Hospital in Calgary, said the respiratory-virus season in his province is still in its early stages but cases are increasing. He said the recent teachers’ strike, which closed classrooms for three weeks, could have stifled earlier spread.

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Last season, his hospital came under intense strain, relying on staff to pick up extra shifts and adding dozens of extra beds to care for an influx of sick children. Dr. Thakore, at that time, said patients who would normally be admitted in intensive care were placed in other units because of capacity issues.

To avoid a repeat of last year, ACH has pro-actively added extra health care staff, including residents and respiratory therapists, into rotation and rooms have been prepped for double bunking.

Dr. Thakore said the bigger problem, however, is infection prevention in Alberta more generally. “You wear a seat belt to prevent yourself from getting injured when you get in an accident,” he said. “We don’t have a seat belt here.”

Alberta, unlike other provinces, does not offer a universal RSV immunization program for infants. There are also broader concerns about vaccine uptake in the province, said Dr. Thakore, with the COVID shot no longer being publicly covered for all and limited public-health messaging on vaccines, including flu.

“Hospitals have to deal with the ramifications of that, which we know last year was quite substantial, and we worry about that again this year,” he said.

In Ottawa, the Children’s Hospital of Eastern Ontario has reinstated public-health measures to protect against viral spread. People attending the site must wear a mask and only one caregiver is allowed to attend appointments. No visitors are allowed.

Nisha Thampi, medical director for CHEO’s infection prevention and control program, said the hospital is already seeing increased RSV admissions and influenza cases are gaining ground.

Dr. Thampi noted that most patients admitted to the hospital are those who have not been protected against the circulating viruses. She’s concerned that people may be questioning flu vaccination because of the potential mismatch.

“These different variants have not changed my own decision and my recommendation to colleagues and families and loved ones,” she said.

“I still very much support getting the flu vaccine.”