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s the country battles an especially fierce flu season, experts have struggled to explain why one family of virus — the influenza A virus H3N2 — that has infected a lot of people in recent years is causing so much damage again this winter.

Now, new data from north of the border sheds some light on the question.

Canadian influenza researchers reported Thursday in the online journal Eurosurveillance that the first reckoning of how well the flu vaccine is protecting against H3N2 viruses this year in North America has a dismal answer: not very.

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Their midseason estimate, based on data from the four provinces where roughly 80 percent of Canadians live, suggested that the H3N2 component of the vaccine is 17 percent effective at preventing infection. Last year it was estimated at 37 percent in Canada and 34 percent in the U.S.

Public health authorities have come to expect protection against H3N2 — the weak link of the vaccine — to be in the low-to-mid 30 percent range at best. But this estimate is half that. And the fact that it was so much lower came as a surprise to the Centers for Disease Control and Prevention’s flu experts, who have yet to analyze their midseason flu vaccine effectiveness data.

“It was lower than what the Canadians or we experienced last year,” said Alicia Fry, head of epidemiology for the CDC’s influenza division. Given that there haven’t been major changes in the viruses, “it is a surprising result.”

Fry said the CDC surveillance network will stop collecting data for their interim analysis next week, and the agency will publish their findings mid-month. Both teams will also reanalyze their surveillance data at the end of the season, when more data typically brings a sharper focus to the findings.

The new research also reported that — at least in Canada — a new subgroup of the H3N2 clan has become the dominant H3N2 viruses causing illness this season. It may be that the vaccine isn’t targeting that group of viruses effectively. The U.S. is seeing a similar pattern, said Jacqueline Katz, deputy director of the CDC’s influenza division.

Whatever the reason, the findings confirm the fact that people who’ve been vaccinated are among those contracting flu this season.

“This is low protection. And the overall message is: People who have been vaccinated should not consider themselves invincible against this H3N2 virus that’s circulating,” said Dr. Danuta Skowronski, lead author of the report and an influenza epidemiologist at the British Columbia Center for Disease Control.

“That means getting early medical care, antiviral treatment for those at high risk of influenza complications. That’s the main value of reporting these midseason estimates.”

In working-age adults, the estimated protection is lower still: 10 percent. That is in line with the protection level Australia saw in its harsh winter 2017 flu season.

Because of the small number of people studied — 689 — the confidence intervals around the estimates are wide. You can think of them as the margins of error around a polling number that is said to be accurate within, for example, 3 percentage points up or down.

And in the case of the assessment of the H3N2 component, the confidence intervals cross zero, which means the researchers cannot rule out the possibility there was no benefit from that part of the vaccine. But based on statistical calculations, the 17 percent overall and 10 percent among working-age adults is more likely to be correct, Skowronski said.

That low protection level among working-age adults could explain why the CDC has reported unusually high flu hospitalization rates among people aged 50 to 64 this year.

The Canadian data may provide clues into what is happening in the United States. But flu season activity varies across geographic regions, and it will be important to see U.S. data to see if the Canadian patterns are reflective of what is happening here.

It’s already clear they are not a perfect match. There is considerably more influenza B illness in Canada this year than there has been in the U.S. In fact, where flu B infections make up less than 20 percent of lab-confirmed flu cases here so far this year, the corresponding figure in Canada is about 40 percent. And in this study, flu B infections made up 51 percent of the confirmed flu cases.

The vaccine’s performance against influenza B viruses was substantially better than it was against H3N2. The study estimated the flu shot protected about 55 percent of people who received it against influenza B viruses.

That’s especially interesting given that most of the flu shots given in Canada targeted the wrong flu B viruses.

There are two lineages of influenza B viruses. Some flu shots target both, but older products contain protection against just one. More than two-thirds of the vaccines used in Canada protect against only one B virus, and this year the virus included in those products is not the one causing the most illness.

Even though the two B viruses are quite different genetically, the vaccine appears to be offering cross-protection, Skowronski said.

More than three-quarters of flu vaccines used in the U.S. target both flu B viruses.

The report does not estimate how well this year’s vaccine protects against H1N1 viruses. Skowronski said there has simply been too little H1N1 disease in Canada so far this winter to make that calculation. Fry said the CDC hopes to be able to give an estimate of how well the H1N1 component of the vaccine is working.

Likewise, the Canadian team could not estimate how protective the vaccine has been against H3N2 in children. The end-of-season analysis should be able to answer that question, she said.

This story has been updated with comments from the CDC.

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