hree-quarters of people who got a flu shot this year were not protected against H3N2 flu, the viruses that have caused the lion’s share of disease in what has been one of the most difficult flu seasons in years in the United States, according to new data from the Centers for Disease Control and Prevention.

While the vaccine was more effective against influenza B viruses (42 percent protection) and H1N1 viruses (67 percent protection), that is cold comfort given that those viruses have been much more minor players this flu season, at least to date. That is especially true of H1N1; only about 8 percent of people who had a positive flu test this season were infected with viruses from that influenza A family.

The estimates, released Thursday, are part of an interim analysis of how well flu vaccine is working this year; data are continuing to be gathered and an end-of-season re-analysis should provide a sharper picture.


But the early indications help to explain why so many people have fallen ill with the flu in a season that has swamped hospitals across the country and appears on track to set records for hospitalization rates.

They are also raising concerns among people in public health about the credibility of flu vaccines.

“We are a bit concerned that the performance of the vaccine right now might reduce interest in getting vaccinated in the future,” Dr. Anne Schuchat, acting CDC director, told STAT in an interview. “But we have the other side that flu was just so bad so far this season, so many people have been sick and see how miserable it is.”

As has been the case for a number of years now, the H3N2 component of the vaccine is its weakest link. A study a few years back looking at H3N2 protection over a number of years found that, on average, its effectiveness hovered around 32 percent or 33 percent.

“We certainly wish we had higher protection against H3N2,” said Dr. Edward Belongia, director of the Center for Clinical Epidemiology and Population Health at Wisconsin’s Marshfield Clinic and the senior author of that earlier study. Belongia’s research group is one of five that make up the U.S. Influenza Vaccine Effectiveness Network, which gathers the data for these vaccine effectiveness analyses CDC compiles ever year.

“It points out that we have an H3N2 vaccine problem more than we have a flu vaccine problem.”

The report was published in the CDC’s online journal, the Morbidity and Mortality Weekly Report.

The report tries to put as positive a spin as possible on sobering figures. For instance, it notes that in young children, the H3N2 component of the vaccine worked better than in other populations; the vaccine effectiveness in children 6 months of age to 8 years old was 51 percent. The text of the report did not point out that in children aged 9 to 17, there appeared to be no protection at all against H3N2 viruses.

So far this season 63 children have died from flu. While tragic, that number is actually low in comparison with other recent seasons. That said, influenza B activity has picked up in the past few weeks and those viruses can be hard on children; the death toll will likely rise before the season is over.

In older adults, the H3N2 vaccine performance was much less impressive. Seniors aged 65 and older saw their risk of needing medical care for flu cut by 17 percent, and in adults 50 to 64 — an age group with an unusually high hospitalization rate this winter — the H3N2 component’s effectiveness was 10 percent.

Those numbers correspond to what was seen last year in those age groups in the U.S. and also to vaccine effectiveness estimates from Canada that were released earlier this month.

The Canadian study, published in the online journal Eurosurveillance, estimated the effectiveness of the H3N2 component of the vaccine at 17 percent.

Dr. Danuta Skowronski, lead author of that paper, said in the real world, there’s not a lot of difference between 17 percent and 25 percent.

“The vaccine is not protecting well against H3N2. And we need to understand why,” said Skowronski, an influenza epidemiologist at the British Columbia Center for Disease Control.


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The CDC paper suggested a variety of factors are likely contributing to the vaccine’s low effectiveness against H3N2 viruses, including the problem of mutations that arise in the vaccine viruses when they are grown in eggs — the method used by most vaccine manufacturers supplying the U.S. market.

“Additional studies are needed to assess whether [vaccine effectiveness] against circulating A(H3N2) viruses varies by vaccine type, including comparisons between egg-based and non–egg-based vaccines,” the CDC report noted.

There is a belief that vaccines that are not produced in eggs may perform better against H3N2, but the studies to test the theory haven’t been conducted.

This story has been updated to include comment from Acting CDC Director Dr. Anne Schuchat and to correct a reference to a figure in the CDC report. It incorrectly stated that the flu shot provided 59 percent protection against H3N2 viruses for young children. The protection estimate is 51 percent.

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