A Surprise Flu Variant Threw Off the Vaccine. Get Ready for a Brutal Winter

Scientists are sounding the alarm: The upcoming flu season this winter in North America could be a real nightmare, thanks to the rapid arrival of a variant that doesn’t match well with the seasonal flu vaccine.

Health officials in Canada issued the warning in a paper late last month. They noted that an unexpected type of H3N2 influenza, called subtype K, emerged quickly during the end of the Southern Hemisphere flu season this year. Subclade K is now expected to become one of the most dominant strains of the flu season in the United States and Canada, and our vaccines will likely be less effective overall against influenza this winter than experts expected.

“While mismatched vaccines are still able to provide protection against circulating variants, enhanced surveillance is warranted,” the researchers wrote in their paper published in the journal. Journal of the Society of Medical Microbiology and Infectious Diseases of Canada.

Drift mismatch

During the peak of flu season, multiple types of influenza A and B viruses circulate between people. Because it takes about nine months to ramp up vaccinations to everyone in a hemisphere, scientists and health authorities meet twice a year (once for the northern hemisphere, once for the southern hemisphere) to predict which variants are most likely to spread through the population and, therefore, which variants the seasonal flu vaccine should cover. Part of this educated guess comes from tracking which flu strains were moving around the world at the time.

Typically, the outlook is not that far off, and vaccines will provide at least moderate protection from the disease. But influenza viruses are always evolving, and variants can gradually develop mutations (a process called drift) that make them significantly different from what scientists expected. That appears to be what happened here with the latest versions of the H3N2 virus, a type of influenza A.

According to the researchers, an increasing amount of H3N2 virus variants with worrisome mutations emerged during last winter’s flu season in the Northern Hemisphere. These variants may be one of the main reasons the United States had such severe influenza last winter.

More recently, another drifting, poorly matched strain of H3N2 virus — subtype K — emerged at the end of the Southern Hemisphere winter. This strain is now expected to dominate among A(H3N2) viruses for the 2025-2026 New Hampshire season, the researchers wrote.

The possibility remains that subtype K will not spread widely in North America, as there will be other types of influenza circulating at the same time. But the odds of that don’t look very good. In the United Kingdom, health officials have already announced an early start to the flu season, with the majority of these cases caused by subtype K. Hospitals in the region are now bracing for a major flu wave.

It is also worth asking whether the deteriorating state of public health in the United States will further hamper efforts to contain influenza. president Donald Trump and Health Secretary Robert Kennedy Jr. oversaw major funding cuts and layoffs across the Centers for Disease Control and Prevention and other health agencies this year, while Robert Kennedy Jr. fired or pressured top health officials to leave the Centers for Disease Control and Prevention.

Why are vaccines still important?

Despite the bleak outlook, vaccines remain one of the most important tools against influenza this season. There are other strains of influenza that the vaccine will cover, and a mismatched vaccine can still provide some protection against the worst outcomes of influenza, which can include death. Fortunately, there is good news on this front.

The UK’s Health Security Agency this week announced the latest data from its influenza surveillance programme. Even with a mismatched variant in the picture, estimates are that the vaccine is currently 70% to 75% effective at preventing flu hospitalizations in children and 30% to 40% effective in adults.

“These results provide reassuring evidence that this season’s influenza vaccines currently provide important protection for children and adults, despite concerns about the new subclass,” Jamie Lopez Bernal, a consultant immunization epidemiologist at UKHSA, said in a statement from the agency.

So it’s still beneficial to get a flu shot as soon as possible. But given the mismatch this winter, it’s even more important to practice good hygiene, stay home if you’re sick, and potentially wear a mask in higher-risk situations for added protection (well-fitting, high-quality masks like KN95 or N95 are the most effective).