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Unusual flu virus is hitting children hard, and this season’s vaccine is a poor match

Ethan Getman, 15, gets a flu shot last week at a clinic in Memphis. (Jim Weber/Daily Memphian/AP)

An unusual viral strain is dominating flu activity across the United States and may be one reason for the severe infections in children so far, according to a new report from the Centers for Disease Control and Prevention, and this season’s influenza vaccine is not a close match for the virus.

There are different types of flu viruses, and the strain causing illnesses in most parts of the country is an influenza B virus. In most years, the A strain of influenza dominates during the early months, and the B strain shows up toward the end.

Flu activity also started early this season, with some cases showing up by July. In more typical seasons, flu activity starts around October and lasts through March or April.

Flu hit hard in the South with influenza B before spreading to much of the rest of the country. It’s the first time in nearly three decades that an influenza B strain has been the dominant circulating flu virus in the United States.

Generally, that type of virus isn’t as dangerous to people 65 and older, who make up the majority of flu hospitalizations and deaths. But the B virus is more likely to cause complications in children and younger adults than in the elderly. In the latest available weekly flu data released Friday, five pediatric deaths were reported for the week ending Jan. 4, for a total of 32 such deaths since the season began.

Flu viruses change constantly, which is why health officials must choose the influenza strains that vaccine makers should target for an upcoming season months in advance, when it is hard to know what strains might be circulating. Seasonal flu vaccines are generally formulated to protect against two influenza A strains and two influenza B strains. When flu vaccines are well matched to circulating viruses, effectiveness is, at best, around 60 percent. (Measles vaccine, by comparison, is about 97 percent effective with two doses.) In a year when the circulating flu strains closely match the vaccine, that effectiveness rate means that about three out of five people who get shots are protected from getting so sick that they require a visit to a doctor.

The beginning of the flu season in Louisiana was unusually early and intense. One pediatric hospital in New Orleans reported more than 1,200 laboratory-confirmed influenza B virus infections, including 23 hospitalizations, between July 31 and Nov. 21, 2019, “a time when influenza activity is typically low,” according to the CDC report.

CDC scientists sent teams to rapidly sequence the virus sickening patients. In a sample of 198 pediatric patients, none of whom had yet been vaccinated, largely because it was so early in the season, the CDC found that virtually all had been infected by a subgroup of one of the influenza B viruses that is not included in the current vaccine.

The vaccine should still be useful, however. Although the circulating virus is genetically different from the influenza B virus in the vaccine, CDC officials said the two are similar.

“They are close enough so the vaccine offers some protection,” said Lynnette Brammer, who heads the CDC’s domestic influenza surveillance team.

But the mismatch is one of many hypotheses scientists are working with to explain this season’s severe impact on children, said Melissa Rolfes, an epidemiologist in CDC’s influenza division and author of the report. CDC officials will know more about the vaccine’s effectiveness in February.

In general, “if you look at the data, among kids who die, B is more frequent among those kids who die than among kids who got flu,” Rolfes said.

Of the 32 pediatric deaths this season, 21 were the result of influenza B infection, and 11 were sickened by influenza A. More children have died from flu at this point in the season than at any other time since the CDC began collecting pediatric death data in 2004, except for the 2009-2010 swine flu pandemic.

But CDC officials cautioned against such comparisons because different viruses dominate each season, and each flu season differs in duration. During the extremely severe 2017-2018 flu season, when a particularly virulent strain caused one of the worst outbreaks in decades, most of the infections early in the season affected adults. But by the end of that season, flu killed 187 children, the most since federal health authorities began tracking pediatric deaths 16 years ago. About 80 percent of those children were unvaccinated.

The most recent weekly data shows flu is widespread in virtually every state. The CDC reported a slight drop in one of its key measures, the percentage of people with flu symptoms seeking treatment from clinicians. But officials said that decline may reflect the holiday in the first week of the year, when most people don’t schedule doctor visits.

“It could go back up again once the holidays are over and the children are back to school,” Brammer said. “We really won’t know for the next two weeks or more whether we have hit the peak. There is still the other half of the season to go, and weeks and weeks more of flu.”

The CDC recommends a flu vaccine for everyone 6 months or older as soon as possible. The body takes about two weeks to produce a full immune response.

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