This year’s flu vaccine may not be as effective against the predominant influenza strain that is circulating this flu season, which tends to cause more severe illness than other strains, U.S. public health officials are warning.

Influenza A (H3N2) has emerged as the dominant virus this flu season in both Canada and the United States, according to the Public Health Agency of Canada (PHAC) and the U.S. Centers for Disease Control (CDC).

However, 52 per cent of the H3N2 virus samples collected from U.S. patients were “antigenically different,” meaning they had “drifted,” from the H3N2 component in this year’s flu vaccine, the CDC says.

This means that while about half of the virus strains circulating in the U.S. are well-matched to this year’s vaccine, about half are not.

“They are different enough that we are concerned that protection from vaccination against the drifted H3N2 viruses may be lower than we usually see,” CDC director Dr. Tom Frieden told reporters during a teleconference Thursday morning.

In past seasons, when the predominant flu viruses have been antigenically different, there tends to be a decrease in the vaccine’s effectiveness, the agency said in an advisory to doctors.

“However, vaccination has been found to provide some protection against drifted viruses. Though reduced, this cross-protection might reduce the likelihood of severe outcomes such as hospitalization and death.”

The flu tends to be more severe during seasons when H3N2 viruses dominate. Rates of hospitalization and death can be “twice as high or more” during these seasons, Frieden said.

Patients with diabetes, asthma, heart or lung disease, and women who are pregnant are also at higher risk of developing severe illness during an H3N2 season, he said.

A spokesperson for PHAC told that he would confirm whether Canadian flu data matches the concerns coming out of the U.S.

According to the latest PHAC FluWatch report, H3N2 is the most common type of influenza that is affecting Canadians. However, there is no mention of whether the strain detected in Canada has drifted.

The vaccine will still offer protection against other influenza strains that have not drifted, such as the H1N1 virus and the influenza B virus, the CDC advised.

However, the agency is recommending that doctors also prescribe antiviral medications such as Tamiflu at the first signs of illness in patients.

The flu season can be unpredictable, Frieden noted, and different virus strains may become more dominant as the season goes on.