A new virus variant and lagging vaccinations may mean the US is in for a severe flu season

Early analysis shows that this season’s flu shots offer some protection against being hospitalized with this variant, especially for kids. The bad news is that many Americans appear to be skipping their flu vaccines this year.

The United States may be heading into its second severe flu season in a row, driven by a mutated strain called subclade K that’s behind early surges in the United Kingdom, Canada and Japan.

Last winter’s season was extreme, too. The US had its highest rates of flu hospitalizations in nearly 15 years. At least 280 children died of influenza, the highest number since pediatric death numbers were required to be shared in 2004.

Now, with a new variant in the mix, experts say we’re on track for a repeat. And with flu vaccinations down and holiday travel on the way, they worry that things may look much worse in the weeks ahead.

The good news: Early analysis shows that this season’s flu shots offer some protection against being hospitalized with this variant, especially for kids. The bad news is that many Americans appear to be skipping their flu vaccines this year. New data from prescription data company IQVIA shows that vaccinations are down compared to where they usually are at this point in the year.

A new player

Flu activity is low but rising quickly in the United States, according to the latest FluView report from the US Centers for Disease Control and Prevention.

Most of the flu viruses identified this season have been an A strain called H3N2, and half of those have come from subclade K, a variant that was responsible for a rougher-than-normal flu season this summer in the Southern Hemisphere.

That variant wasn’t a major player when scientists decided which strains should be in the annual flu shots, so the vaccines cover a related but slightly different group of viruses.

“It’s not like we’re expecting to get complete loss of protection for the vaccine, but perhaps we might expect a little bit of a drop-off if this is the virus that sort of dominates the season, and early indications are that’s probably going to be the case,” said Dr. Richard Webby, director of the World Health Organization Collaborating Center for studies on the ecology of influenza in animals and birds at St. Jude Children’s Research Hospital.

Early analysis by the UK Health Security Agency shows that subclade K has seven gene changes on a key segment of the virus. Those mutations change the shape of this region, making it harder for the body’s defenses to recognize.

“That’s the predominant thing that our immune system targets with antibodies, and that’s also pretty much what’s in the vaccine,” said Dr. Adam Lauring, chief of the Division of Infectious Diseases at the University of Michigan Medical School.

UKHSA scientists found that the current flu vaccines are still providing decent protection against subclade K viruses. Vaccination cut the odds of an emergency department visit or hospitalization for the flu by almost 75% in children. The effectiveness for adults, even those over 65, was lower, about 30% to 40% against needing to visit the hospital or ER.

But the scientists offer a caveat: These results are from early in the season, before the protection from seasonal flu vaccines has had time to wane or wear off. The findings are posted in a recent preprint study, which means it was published ahead of scrutiny from outside experts.

Still, some protection is better than no protection, and while subclade K is expected to dominate the season, it won’t be the only flu strain circulating. No one gets to pick what they’re exposed to. Lauring said his daughter has just recovered from the flu, but it was a B-type strain.

At the same time this new variant has emerged, flu vaccinations appear to be down in the US. According to IQVIA, about 64% of all flu vaccinations were administered at retail pharmacies, which administered roughly 26.5 million flu shots between August and the end of October. That’s more than 2 million fewer shots than the 28.7 million given over the same time frame in 2024.

“I’m not surprised,” said Dr. Jennifer Nuzzo, who directs the Pandemic Center at Brown University’s School of Public Health. Vaccine skepticism expressed by leaders of the US Department of Health and Human Services has “injected chaos into the whole vaccination system,” she said.

“There’s been a lot of attention on really non-issues,” like vaccine ingredients and separating shots, that “I think, at the best, left people confused but possibly at the worst have left people worried about getting vaccinated,” she added.

Flu vaccinations have also fallen in Australia, where subclade K was the predominant virus this year. As a result, flu hit a record, with more than 443,000 cases. Flu season in the Southern Hemisphere typically runs from May to July, so infectious disease experts often look to those countries for a preview of what might be on the way to North America.

“What they saw in Australia is that they had a bad season. And so it’s concerning for you and us, what’s coming,” said Dr. Earl Rubin, director of the infectious disease division at the Montreal Children’s Hospital in Canada.

‘This is the time we start to see the rise’

It’s difficult to say whether subclade K actually makes a person sicker than other flu strains, but if it drives more cases, it will certainly drive hospitalizations too, Rubin said.

“When you look at severity, the more cases you have, if the same percentage get hospitalized, obviously you’re going to have more hospitalization if you have more cases. So it sometimes will look like the severity is also worse,” he said.

Lab testing data has begun to show an uptick in flu cases.

“This is the time we start to see the rise,” said Dr. Allison McMullen, a clinical microbiologist at BioMerieux, which makes the BioFire test, a popular diagnostic tool for respiratory pathogens.

The company anonymously compiles its test results into a syndromic surveillance tool, which can offer a glimpse of what bugs are making people sick at any given time. At the beginning of the month, less than 1% of tests were positive for type A flu. Now it’s 2.4% – still low numbers but going up briskly, which aligns with the CDC trend.

“We’re going to start seeing heavy holiday travel before we know it,” McMullen added. “With the rising cases that we’re seeing the UK and Japan, it can definitely be a bellwether for what we’re going to see in North America.”

Signals are also rising in wastewater, said Dr. Marlene Wolfe, an assistant professor of environmental health at Emory University. In October, 18% of samples in the WastewaterSCAN network – an academically led wastewater monitoring program based at Stanford University, in partnership with Emory – were positive for type A flu, Wolfe said. In November, that number had risen to 40%.

“Flu is something where, when it’s not in season, we don’t detect it very frequently in wastewater,” Wolfe said. Covid, on the other hand, can be detected pretty much all the time, which makes it challenging to know if it’s going up or down, she said.

The scientists can set a threshold for when they can declare that a specific area is in flu season, Wolfe says. So far, just four of the 147 sites they monitor in 40 states have reached that threshold. Those sites are in the Northeast – in Maine and Vermont – in Iowa and in Hawaii.

“I am concerned, I guess, that we could have a big flu season this year based on what we’re seeing in other parts of the world, and particularly Europe and elsewhere,” Michigan’s Lauring said.

“It’s not too late. Go and get your flu shot,” Lauring advised. “And be alert that it’s out there.”

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