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A Penn scientist says he knows why last year's flu vaccine was so bad

Research showed that changes during the vaccine manufacturing process made the shots less effective against the H3N2 flu strain.

This is an illustration of a flu virus.
This is an illustration of a flu virus.Read moreiStock

New research from the University of Pennsylvania has found that a problem with the way flu vaccine is manufactured explains why many people who got flu shots last year got sick anyway.

Scott Hensley and his team, which included scientists from the University of Chicago and the University of Rochester, concluded that growing flu virus in chicken eggs introduced mutations that reduced vaccine effectiveness. Hensley said this problem is widely known among vaccine experts, but it was particularly bad last year for the H3N2 strain of flu that dominated the season. While experts had accurately predicted which type of virus would be prevalent, he said, the vaccine was only 34 percent effective.

It is possible to grow influenza virus in other mediums, such as insect or canine cell cultures, Hensley said, but only the small percentage of vaccine intended for people with egg allergies is currently grown that way.

"The U.S. in general should evaluate how we make these vaccines," said Hensley, an associate professor of microbiology in the Perelman School of Medicine.

Vaccine companies would have to purchase new equipment to change the production process. Hensley said he did not know what that would cost. "Not only our study but other studies have demonstrated pretty conclusively at this point that it's probably time that these changes are made," he said.

Paul Offit, a vaccine expert at Children's Hospital of Philadelphia, said pharmaceutical companies would have to go through extensive testing before they could change the growing medium. Essentially, they'd be creating a new vaccine. The market is already unusually crowded and companies must make new forms of the vaccine each year. "The cost to make a new vaccine is huge," he said.

He thinks the U.S. Food and Drug Administration should more closely monitor how much viruses change during the manufacturing process, adding that the flu shot is "arguably our least effective vaccine."

Sanofi announced in July that it would acquire Protein Sciences, which makes Flublok, a non egg-based vaccine.

Hensley's study was published Monday in Proceedings of the National Academy of Sciences.

Vaccines against flu are made using proteins purified from the outer layer of killed flu viruses. These prime the immune system to recognize and respond to the virus when someone becomes infected. The problem with H3N2 strains of flu is that they do not grow well in egg cells. They mutate so that they can bind with those cells. That mutation is then incorporated into the vaccine. Last year's mutation was big enough that it created a mismatch between the vaccine and the circulating H3N2 virus.

To some degree, such mutations are present in vaccines for other strains of flu as well, Hensley said, but they are smaller and have not had such a dramatic impact on effectiveness. Last year, for example, the vaccine was 55 percent to 60 percent effective against types of influenza B.

People this year will face a "double whammy" when it comes to flu, he said. H3N2 is again a big force and this year's vaccine includes the same strain — with the same problems — as last year's. Those who got the flu last year should be protected from that strain, but Hensley said a new version of H3N2 started making the rounds after the new shot was already in production. It's too early to know if it will be a major force.

However, Hensley said, the flu season this year in Australia, whose season comes earlier than ours, was "really sort of devastating." That may herald a bad season for the United States as well.

Hensley said people should still get vaccinated. "The last thing we want is for readers to think this is some kind of anti-vaccine story," he said. "Thirty-four percent effectiveness is better than zero."