This post has been updated.
Still, experts said the current vaccine offers some protection against H3N2. Its 25 percent effectiveness rate means that one in four people who get the shot reduce their risk of becoming sick enough to need to see a doctor. In Australia, interim estimates showed the vaccine to be only 10 percent effective against H3N2, and researchers recently reported that early data show that the vaccine is about 17 percent effective in Canada against that strain. The vaccine's effectiveness may have changed as it is measured at the end of the season.
Seasons when this flu bug is dominant are associated with more severe complications, especially for people older than 65, young children and others with certain chronic conditions. The number of people going to doctors’ offices and emergency rooms has surged to levels not reported since the peak of the 2009 swine flu pandemic. Hospitalizations are also at record levels.
Each year, health officials must choose the three or four influenza strains that vaccine makers should target for an upcoming season. The decision is made months in advance, when it is hard to know what strains will be circulating.
Even in a good year, the flu vaccine is never as effective as most other vaccines. When well matched to circulating viruses, its effectiveness is about 60 percent. (The measles vaccine, by comparison, is about 97 percent effective with two doses.)
Flu vaccines generally provide greater protection against the other influenza A strain and influenza B strains now circulating. The CDC report found that the current vaccine is 67 percent effective against the other influenza A strain, H1N1, and 42 percent effective against influenza B viruses.
But there is a piece of surprising good news: In children younger than 9, it offers much greater protection, reducing by more than half the risk of becoming so sick that they need to see a doctor.
“That’s higher than we typically see for H3N2,” said Ed Belongia, an infectious-disease epidemiologist at the Marshfield Clinic Research Institute in Wisconsin. Marshfield is one of five U.S. sites measuring flu vaccine effectiveness.
Children’s vulnerability is of special concern this season. At least 63 child flu deaths have been reported since Oct. 1. As in past winter flu seasons, about three-quarters of children who have died were not fully vaccinated, officials said.
Based on current trends, the number of child deaths could exceed the 148 reported for the especially severe 2014-2015 season, when the same strain was dominant and the vaccine's poor match resulted in overall effectiveness of 19 percent. States are not required to report adult flu deaths.
Still, even with lower effectiveness against H3N2, “I would still take 25 percent over nothing any day of the week,” Belongia said.
A new analysis of seasonal flu deaths in U.S. children in the six seasons since the 2009 pandemic found that children ages 2 and younger are most at risk. Of the children who died during those years, less than a third had been vaccinated.
Officials and clinicians are still recommending that people get a flu shot because they expect several more weeks of flu activity, and the shot can reduce the severity of illness and prevent hospitalizations and deaths. Studies have shown that flu is associated with an increased risk of heart attacks and stroke.
At a briefing for reporters, Health and Human Services Secretary Alex Azar likened getting a flu shot to wearing a seat belt, “a sensible precaution” that Americans should take. He said he, his wife and two children have all been vaccinated. So, too, has President Trump, according to Azar, who said he spoke to the president Wednesday about the continuing flu threat.
In terrible flu seasons like this one, the CDC estimates that as many as 56,000 Americans will die.
Many details about how the immune system fends off the virus and protects the human body remain unknown. Immune responses differ by age, and previous infection or vaccination history can affect vaccine protection.
“We know that whatever that first flu infection you had as a child causes your immune system to respond in a certain way for the rest of your life,” Belongia said. That “may make you better able to respond to that type of virus decades later,” yet less able to fight off other strains.
Recent research suggests that the traditional production process may make flu vaccines less effective, especially for H3N2. Flu vaccines are killed or highly weakened viruses that trigger the body’s immune system to produce antibodies to protect against the real virus. Most U.S. flu vaccines are grown in chicken eggs, a process that takes six to eight months.
When the H3N2 virus is inserted into eggs, tiny changes take place that make the egg-grown virus look less similar to the circulating viruses, affecting the vaccine’s ability to target the circulating strain.
“No one is saying that is the whole story, but that seems to be a contributing factor,” Belongia noted. “Fairly minor differences in genetic changes can lead to really meaningful differences in how much protection the vaccine is providing.”
Two other flu vaccines on the U.S. market are made without eggs. One is grown in dog kidney cells, and the other is a synthetic virus grown in insect cells. CDC data show that fewer changes take place in the non-egg-based viruses, making for a closer match to the circulating virus.
Scott Gottlieb, the commissioner of the Food and Drug Administration, said in a statement Thursday that a preliminary analysis of CDC data and information from patient databases indicate the cell-based vaccines offer better protection against H3N2 this year than the egg-based vaccine. Gottlieb said scientists at the FDA, CDC and National Institutes of Health are trying to understand why.
Ultimately, scientists say the only real solution is a “universal” influenza vaccine that would not only protect against seasonal flu but also guard against a future pandemic. Researchers have made progress in understanding how to thwart the virus’s ability to constantly mutate. But experts say the effort is likely to take many more years.