A poorly matched flu shot could mean a bad flu season on top of a Covid surge

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The current flu vaccines appear to be a bad match for the dominant strain so far this influenza season, new research suggests, leading experts to warn that the United States could be in for a bad flu season, on top of what’s already shaping up to be another devastating surge of Covid cases

Before each flu season, scientists must predict which strains will be the most common, and design a flu shot to match these predictions. This year’s flu shot includes four strains. 

But one, a version of the H3N2 strain of influenza, is turning out to be a bad match for the version of H3N2, called 2a2, that’s in wide circulation in the U.S., according to a study from Scott Hensley, a professor of microbiology at the University of Pennsylvania.  Hensley’s study was posted Wednesday to a preprint server, meaning it has not yet been peer-reviewed. 

So far this season, the H3N2 strain makes up for at least 99 percent of all flu cases in the U.S., according to the Centers for Disease Control and Prevention, though the agency does not specify how many of those cases are caused by the 2a2 version of the strain.

The presence of the 2a2 version means the vaccine may not protect as well against infection, because it’s not the version included in the vaccine, Hensley said. 

The flu shot is never a perfect match for the influenza viruses that end up in wide circulation, but even so, the vaccine still reduces a person’s risk of severe illness from the flu. 

Influenza vaccination is the best protection against severe disease and illness,” he said. “Even in these years of mismatch, we see high effectiveness against hospitalizations and severe disease.”

Still, the mismatch Hensley has observed so far is striking. The last time there was a mismatch this significant was during the 2014-15 flu season, he said. Even so, the vaccine prevented nearly 40,000 hospitalizations and almost 4,000 deaths from the flu that season, the CDC estimates. 

Flu experts have warned that the nation could be at risk for a severe flu season this year after flu cases reached an all-time low last year, when large swaths of the country were shut down because of the pandemic. And the mismatch could exacerbate the situation.

“Once this fire gets started, it may spread out of control,” Hensley said.

Health officials are already seeing flu outbreaks. In November, the CDC said it was investigating an outbreak of influenza at the University of Michigan, where at least 528 students have tested positive for the flu since Oct. 6.

Dr. Mark Roberts, director of the Public Health Dynamics Laboratory at the University of Pittsburgh, said the data in the new preprint “is certainly consistent with what I know from the rest of the world right now.”

The potential, he said, for a “really large influenza season this year is real.” 

“So much of the immunity that you get in a population comes from the people who had influenza the year before,” said Roberts, who was not involved with Hensley’s research. “There could be substantially bigger epidemics this year, especially if the strain that appears is different than the strains we’ve seen.”

Still, with the rise of the omicron variant, there’s still a chance the U.S. could have a modest flu season this year, he said. That’s because alarm over the variant could cause more of the public to go back to social distancing and mask wearing.

“That’s all better for the flu, too,” he said.

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