Flu vaccines saved an estimated 40,000 American lives between 2005 and 2014, but they are not good enough.The vaccine used during the 2016–17 flu season, for example, was only 43 percent effective against the predominant influenza A H3N2 strain, and protection has been almost as low in other years. Two studies now suggest a new reason for the problem: The vaccine strain mutates during the manufacturing process in ways that cause mismatches with real circulating flu strains.

Researchers already knew the flu shot had a flaw. Because the virus evolves very quickly, an inoculation devised months before flu season often differs from what ends up infecting the public. Now it appears other important mismatches are triggered because vaccines are grown inside chicken eggs. “We’ve got to get out of chicken eggs,” says Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota, who was not involved in the research. He concedes, though, “that’s not easy to do, and that’s expensive—very expensive.”

Last year’s flu vaccine should have worked well. The strain that the U.S. Food and Drug Administration chose for the seasonal vaccine did indeed closely match the viruses that sickened people. So when its effectiveness proved disappointing, Scott Hensley, a microbiologist at the University of Pennsylvania Perelman School of Medicine, and his colleagues began to investigate. Flu vaccines are killed or highly weakened viruses that, when injected into the body, alert the immune system to fight the real thing. For 70 years most flu vaccine strains have been grown in fertilized chicken eggs because egg growth incites excellent yield. But it has long been known that the viruses also evolve in these egg hosts. They adopt genetic changes that help them grow in the egg environment. What Hensley and his colleagues found was such changes can cause problems for the end product.

In a paper published online today in Proceedings of the National Academy of Sciences, Hensley’s team zeroed in on a new molecule that the H3N2 virus started wearing on one of its surface proteins in 2014. This molecule, a type of sugar, has become chemically glued to a location on the virus’s surface near where human antibodies—immune system watchdogs—attach to mark the virus as a dangerous invader. The sugar made it hard for antibodies to stick, so it helped the virus avoid immune destruction. When flu researchers learned about this new sugar-adorned H3N2 virus in 2014, they made sure to include that strain in the 2016–17 seasonal flu vaccine so that immunized individuals would mount an immune response against it.

But when Hensley and his colleagues studied the strain that ended up in the U.S. vaccine, they saw that, mysteriously, the sugar molecule had disappeared. The loss was bad for the vaccine: In a series of experiments Hensley and his colleagues showed antibodies from humans and ferrets (a good animal model for influenza A studies) that had been exposed to the egg-grown vaccine did not effectively kill the circulating sugar-adorned viruses. Antibodies incited by a similar vaccine that was not grown in eggs, on the other hand, worked quite well. (Two U.S. influenza vaccines do not use egg-adapted strains. One, FLUCELVAX, is grown in canine kidney cells, and the second, Flublok, is grown in insect cells.)

The new sugar molecule hinders the virus’s ability to grow in eggs—so once the vaccine strains are put into eggs, they ditch it. “The viruses, originally isolated in humans, are simply adapting to the new cells in their environment,” says Sarah Cobey, an ecologist and evolutionary biologist at the University of Chicago and one of the paper’s co-authors. But by eliminating the sugar molecule, the new mutation also affects “a key region in the virus that is targeted by the immune system,” Hensley adds, making the vaccine less effective.

Egg-based production changes the flu virus in other important ways, too. In a separate study published on October 23 in PLOS Pathogens, a team of researchers—including Hensley—showed vaccine virus strains grown in chicken eggs also acquire a mutation that alters the structure of the same region important for human antibody binding. Basically, “in acquiring that mutation, the vaccine looks like a triangle, but the viruses that are circulating look like a circle,” Hensley says. “So if you mount responses against the triangle, they’re not going to bind very well to the circle.” Hensley and his team reported this egg-induced mutation, which was present in the 2016–17 U.S. seasonal flu vaccine, decreases the ability of certain antibodies to attach to and destroy the flu virus—by a whopping three orders of magnitude.

These egg-based changes bode ill for the real world. A 2014 study used epidemiological data to show egg-based mutations are associated with low vaccine effectiveness in human populations. The vaccine used during the 2012–13 flu season in Canada did not work very well, despite the fact that the circulating flu viruses had not seemingly changed much after the vaccine strains had been chosen. Upon investigating further, Danuta Skowronski, the lead epidemiologist for flu and emerging pathogens at the British Columbia Centers for Disease Control, and her colleagues reported in PLOS One that the egg-production process had induced three mutations at immunologically important sites in the vaccine virus strain and that these mutations were linked with low vaccine protection.

Recent data from the U.S. Centers for Disease Control and Prevention suggest this season’s vaccine may suffer from similar problems. Since May 21, 2017, the agency has analyzed H3N2 viruses that have circulated in the U.S. and internationally. Only 33 percent of these viruses were neutralized by antibodies from ferrets vaccinated with egg-grown strains, whereas 97 percent of viruses were inhibited by antibodies from ferrets inoculated with a non–egg-grown vaccine. A recent study from Australia, which is just finishing its flu season and used the vaccine strains that the U.S. is now using, suggests the H3N2 component of this season’s vaccine is only 10 percent effective. This futility is not surprising since this egg-grown vaccine still contains the two mutations described in the new papers.

But although abandoning egg-based vaccines is the obvious fix, that move is not going to be easy, Hensley says. “There’s a great amount of infrastructure that exists in producing these vaccines in eggs because that’s how it’s always been done,” he points out. It may take years, if not decades, to shift the majority of flu vaccine production out of chicken eggs and into other bio-factories like cells. In the meantime the CDC is working to improve the process. It is using next-generation genetic sequencing to study egg-induced mutations in the hopes of identifying some that improve rather than reduce vaccine effectiveness. Then the agency will select for these viral strains and use them for future vaccines.

Hensley emphasizes that even though the current vaccine does have limitations, people should still get annual flu shots. The vaccine lowers infection risk--it works very well against influenza B--and may also minimize the risk of severe infection. And vaccinated individuals also protect vulnerable people such as those with immune conditions and severe allergies who cannot get vaccinated. The goal of these new studies is not to pooh-pooh the flu vaccine; they are “just trying to make things better,” Hensley says. Scientists have to acknowledge there’s room for improvement in order to make progress.

Editor's note: The first paragraph has been clarified on Nov. 6, 2017 to compare low protection rates to a 43 percent figure.