Flu vaccine this season may be poorly matched, early CDC data suggests

This season’s influenza vaccine may have been a poor match to a strain of the flu virus that caused many infections this winter, early data released by the Centers for Disease Control and Prevention suggests.

The CDC’s latest data come as much of the U.S. is finally seeing signs of a slowdown in influenza activity after waves of illness this past fall and winter that climbed to the worst rates recorded from hospitals and doctor’s offices since the 2009 swine flu pandemic.

“This is a bad year, no doubt about it,” Dr. Jon LaPook, CBS News chief medical correspondent, told “CBS Mornings” on Tuesday.

Up to 910,000 hospitalizations are estimated to have been caused by the flu since October 2024, which puts the season on track to be the most severe in at least a decade. 

“Depending on the strain, depending on what’s going on, it could really vary. And this year is brutal,” said LaPook.

Every season, the CDC’s scientists test a sample of flu viruses collected from labs around the country against strains that health authorities had picked out for use in the latest update to the annual flu vaccine.

“CDC antigenically characterizes about 2,000 flu viruses during a typical flu season to monitor for changes in circulating viruses and to compare how similar these viruses are to those included in flu vaccines,” Paul Prince, a CDC spokesperson, said in a statement.

Many of the flu viruses that the CDC has tested this season were “well-recognized” by antibodies targeted to the vaccine, which helps the body fight off the infection, the agency reported this month. The testing is done using antibodies from ferrets, which have similar influenza symptoms to humans.

But against the H3N2 strain of influenza, which this season has made up just over half of the influenza A viruses scrutinized by the agency, only around 50.9% of the samples were “well-recognized” by the antibodies. 

That’s far below this time last year, when the CDC reported that all H3N2 viruses they tested were “well-recognized” by the vaccine virus antibodies.

Experts cautioned that many other factors can play a role in changing how effectively vaccines hold up against influenza in the real world. For example, unlike the laboratory ferrets, people’s immune systems build up defenses to parts of the virus encountered in previous years.

“Humans mostly have pre-existing immunity, which can result in different immune responses. These can be broader or narrower or different,” said S. Mark Tompkins, director of the University of Georgia’s Center for Influenza Disease and Emergence Research, in an email.

Tompkins said that it was possible for the vaccines to offer good protection, even in situations where the shots were not a good match.

“Humans, once you get infected and reinfected, your system typically starts to become more focused on the spots on the virus that don’t change as frequently or are more effective at neutralizing it,” Josh Petrie, associate research scientist at the Marshfield Clinic Research Institute, told CBS News.

Petrie said that well-matched vaccines tend to correlate with higher effectiveness. But even with well-matched shots, he said that seasons with more H3N2 viruses often result in lower vaccine effectiveness estimates — and more severe seasons overall — compared to other circulating strains.

“As a rule of thumb, at least in recent years, effectiveness against H3N2 has typically been lower than H1N1. And also as a rule of thumb, H3N2 typically has a higher impact on older adults and you see a lot more hospitalizations,” Petrie said.

More data could come soon. The first estimates from CDC’s influenza vaccine effectiveness studies for this season are expected to be released by the end of this month.

The World Health Organization is also expected to release a report soon from a meeting to decide next season’s influenza vaccine update.

CDC officials are also being allowed to participate in the meeting, a spokesperson said, despite the president’s order that has mostly banned U.S. scientists from talking with the WHO.

Not all early data suggests this season’s vaccines are a poor match. Data published last month from Canada found that vaccines looked to be 54% effective against H3N2 strains there.

“That’s actually pretty good effectiveness for H3. Usually it’s down in the 30 to 40[%] range,” Petrie said.

Scientists in the Canadian report said that a better-matched, updated vaccine strain might explain the higher vaccine effectiveness they found. But they also cautioned that some worrying mutations to H3N2 had also been spotted so far.

“Potential impact on VE [vaccine effectiveness] elsewhere and through the rest of the season requires further monitoring,” they wrote.