Doctors still recommend flu shot despite sneaky new strain

Over the holidays, U.S. flu cases skyrocketed. 

Weekly hospitalizations from the virus went from under 7,000 at the start of December to over 33,000 by the last week of 2025, surpassing rates of the past few years. 

The Centers for Disease Control and Prevention estimate that more than 11 million people have gotten the flu so far this season, resulting in over 5,000 deaths.

Why is it so bad? Doctors said that the surge in flu cases is largely related to a new mutation of the influenza A virus called "subclade K" — a strain that is not well covered by this year’s flu vaccine. 

Each year, scientists have to try and predict in the spring what strains to include in the coming season’s flu vaccine. Sometimes they make a good match, but other times, like this year, the virus develops an unexpected mutation that helps it elude the vaccine’s protection. 

Although this year’s flu vaccine doesn’t protect as well against the dominant subclade K strain, doctors still say that getting vaccinated is worthwhile.

It can prevent severe disease and death and protects against other strains of the flu that are circulating. 

How do scientists decide what goes in the flu vaccine? 

There are two major types of influenza that circulate during flu season – influenza A and influenza B. Both can be further broken into subtypes, genetic clades and subclades that describe various different mutations of the virus. A clade is a group of organisms with a common ancestor. 

Every year, the flu virus develops mutations to help it sneak past human immune systems. Each year, scientists try to predict, months in advance, what those mutations might be and which strains will circulate in the coming flu season. 

The vaccine formula has to be decided far ahead of the fall flu season so there is time for manufacturing and distribution.

 "We do all that we can to predict which strains will predominate, but occasionally, strains emerge that are more divergent from what we predicted," said Dr. Buddy Creech, director of the Vanderbilt Vaccine Research Program. "That’s the story of this year."

Why doesn’t the vaccine match? 

This year’s vaccine protected against three different strains — two strains of influenza A (subtypes H1N1 and H3N2) and a strain of influenza B (Victoria lineage). 

But after the Food and Drug Administration had decided on a formulation in March, the influenza A (H3N2) strain began to mutate.

"This happens almost every two years with one or more of the three vaccine strains," said Andrew Pekosz, a molecular microbiology and immunology professor at Johns Hopkins University. "While the vaccine gets ‘locked in,’ the virus still circulates in humans and continues to mutate, resulting in the ‘mismatch.’"

The new subclade K strain only became the dominant strain after the vaccine formulation was decided.

Does the vaccine still offer some protection? 

Yes, and doctors say it is still worth getting if you haven’t yet. 

"Even when the vaccine is not a perfect match to circulating strains, those who are vaccinated have lower rates of hospitalization and death," said Dr. Caitlin Li, a pediatric infectious disease doctor at Lurie Children’s Hospital of Chicago. 

Although there is a mismatch between the H3N2 strain the vaccine was formulated to protect against and the strain that is circulating among the public, that isn’t the case for the other two strains this year's vaccine protects against — influenza A (H1N1) and influenza B, Pekosz told PolitiFact. 

Getting vaccinated offers protection against the other two strains, which are still making people sick this year. "We often see a different influenza strain causing disease late in the influenza season," Pekosz said. Future you might say thanks!

It’s not too late to get vaccinated, Creech said, especially if you’re "at high risk for complications from infection." 

Why are people calling it the ‘super flu?’ 

It’s catchy, but might be misleading. 

"Right now, there is no data suggesting it's either more severe or more contagious," Pekosz said. But because the virus is better than usual at getting around the vaccine’s defenses, more people than usual are susceptible to infection.

Lower than ideal flu vaccination rates, around 40% nationwide, may also be contributing to the intensity of this flu season.