Flu shot may be a 'bad match' for dominant strain

The dominant strain of influenza that's circulating this season has picked up a troublesome mutation, making this year's flu vaccine a "bad match," a new study suggests. 

"From our lab-based studies it looks like a major mismatch," study coauthor Scott Hensley, a professor of microbiology at the Perelman School of Medicine at the University of Pennsylvania, told CNN. Hensley and his colleagues have been monitoring the H3N2 subtype of the influenza virus, looking out for any genetic mutations that crop up in the virus as it spreads. Through their surveillance, they recently identified a new H3N2 "clade," or a split in the virus's family tree. 

They named the clade "3C.2a1b.2a2," or 2a2 for short, and posted their finding on Thursday (Dec. 16) to the preprint database medRxiv. The study has not yet been peer-reviewed or published in a scientific journal, and it only measured antibody responses in 40 individuals who were mostly young and healthy. But the research hints that mutations carried by the new clade may make this year's flu vaccine less effective against H3N2, Hensley told CNN. 

Related: Why is the flu shot less effective than other vaccines?

That doesn't mean the flu shot you got was useless, however.

"Studies have clearly shown that seasonal influenza vaccines consistently prevent hospitalizations and deaths even in years where there are large antigenic mismatches," the authors wrote in the preprint. So even if this year's flu shot doesn't match the dominant strain, the vaccines will reduce the odds of severe disease and death. 

So why is the newly-identified 2a2 clade such a problem? Viruses within the clade carry mutations in genes that code for hemagglutinin (HA), a protein on the surface of the virus, the researchers found. 

Flu vaccines train the immune system to recognize the HA protein, which juts off influenza viruses like a lollipop on a stick, Live Science previously reported. The problem is that the HA protein mutates so rapidly that its structure can change in the time between when the flu vaccine is developed and when flu season reaches its peak, typically between December and February. And of the four influenza subtypes covered by the annual flu shot — two influenza A viruses, H1N1 and H3N2, and two influenza B viruses from the Victoria and Yamagata lineages — H3N2 mutates the fastest.

For this reason, the flu shot tends to be least protective against H3N2, and this has seriously undermined the vaccine's efficacy in the past. The changes in the H3N2 virus this year are reminiscent of the mutations that rendered the vaccine so weak in the 2014-2015 flu season, when it offered only 6% protection against H3N2, Hensley told CNN. 

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"Importantly, we found that antibodies elicited by the 2021-2022 Northern Hemisphere influenza vaccine poorly neutralize the new 2a2 H3N2 clade," Hensley tweeted on Dec. 16. "55% of vaccinees had undetectable levels of neutralizing antibodies against 2a2 H3N2 after vaccination." 

This may partially explain a recent outbreak of influenza cases on the University of Michigan's Ann Arbor campus, which was primarily driven by H3N2, Live Science previously reported. The surge affected more than 700 people, of which around a quarter were vaccinated against the flu, CNN reported.  

But not all is lost. "While cases of 2a2 H3N2 infections are quickly rising in the United States and other parts of the world, it is possible that other clades of H3N2 will become predominant in the future," the researchers wrote. "It is also possible that H1N1 or influenza B viruses might dominate later in the 2021-2022 season."

You can read more about the new research at CNN.

Originally published on Live Science.