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Cases of winter viruses in the U.S. have exploded in recent months—and soon kids may be less protected from them, thanks to new vaccine guidelines.

Amid a worsening respiratory illness season, the Centers for Disease Control and Prevention recently rolled back its universal childhood vaccine recommendations from addressing 17 diseases to just 11. The CDC no longer recommends that all children be vaccinated against influenza and rotavirus—instead, it recommends these vaccines based on individual discussions with doctors only. And the agency recommends that vaccines that protect against meningococcal bacteria and hepatitis A and B be given to children in high-risk groups only.

All of these vaccines remain available to parents who want their kids to receive them, and they are fully covered by both private and public insurance. Nevertheless, public health experts warn that the changes will reduce vaccination rates and increase disease rates.

Concerningly, the changes prominently affect seasonal diseases that spike during the winter and are notorious for causing high rates of pediatric hospitalizations and even deaths—most notably, influenza. The timing couldn’t be worse: nationwide health care visits for flu-like symptoms recently hit a record high in nearly 30 years of tracking.

“The speed at which the flu season is ramping up in terms of total cases is quite impressive,” says Andrew Pekosz, a virologist at the Johns Hopkins Bloomberg School of Public Health. And he anticipates the numbers will only grow. “We’re closer to the beginning than the end of the flu season,” Pekosz says.

It’s still too early to understand whether certain age groups are being hit worse this year than others, he adds, although the CDC has already reported 17 pediatric deaths this season. But the 2024–2025 flu season was remarkably deadly for kids—289 children were reported to have died of the virus, the highest number of pediatric deaths from flu since the CDC started tracking pediatric flu deaths in 2004. Of those who died that had a known vaccination status, only one in 10 was fully vaccinated—a testament to the flu shot’s protection.

Children are more likely than those in any other age group to catch the flu. Yet only slightly more than half of two-year-old children in the U.S. were fully vaccinated against the flu in 2023, the latest year for which full data are available. Until this month the CDC recommended annual shots beginning at six months of age. “Uptake for the flu vaccine has been relatively low and dropping,” says Flor Muñoz, a pediatric infectious diseases specialist at Baylor College of Medicine. So far this flu season, childhood vaccination is at less than 43 percent. More children may still get vaccinated, but for comparison, the pediatric uptake rate at this point in the 2019–2020 season, before COVID truly hit, was 54 percent.

The CDC’s new policy entirely removes the formal recommendation for the influenza vaccine for kids, leaving discussions of the vaccine entirely in the hands of parents and care providers. “To me, it doesn’t really make much sense to take away that recommendation when you know, scientifically, that there’s a benefit,” Pekosz says.

Instead, decisions about flu vaccination will be made through shared clinical decision-making—having health care providers discuss the risks and benefits of a medical intervention with the patient or their family.

But providers already routinely have these discussions with parents, says Kathryn Edwards, a pediatric infectious disease specialist and vaccinologist, now emerita at Vanderbilt University School of Medicine. “Parents are always part of the decision for vaccines to be administered.”

Shared clinical decision-making now applies to vaccines for three key infections; the COVID vaccine received the designation this summer, and the new guidelines extended it to the rotavirus vaccine, as well as influenza. Rotavirus causes a diarrheal infection that spreads year-round but is most common in the winter and spring. The disease has largely flown under the radar because vaccines introduced in 2006 starkly reduced hospitalization rates from the virus. This vaccine is administered orally and has had a relatively high uptake—vaccination rates have hovered between about 70 percent and 75 percent since the 2010s. Muñoz fears that the move away from a universal recommendation to shared clinical decision-making could result in increasing cases of and hospitalizations from rotavirus as soon as this year.

Experts worry the CDC’s new approach to vaccines will erode other recent victories for children’s health as well. Respiratory syncytial virus, or RSV, is another “big hitter” winter infection, alongside flu, Edwards says. Traditionally, nine in 10 children have caught the virus within their first two years, and it sends more than 58,000 kids younger than five years old to the hospital every year in the U.S. The disease is the leading cause of hospitalization in babies.

An RSV vaccine for pregnant people and a protective antibody shot for babies were both approved for general use in 2023. In the 2024–2025 season, the prevention efforts caused “a remarkable reduction in the burden of RSV,” Edwards says. The new guidelines don’t change RSV vaccinations for either pregnant people or babies, but Secretary of Health and Human Services Robert F. Kennedy, Jr., has questioned the antibody shots’ safety despite evidence from clinical trials.

Other standard childhood vaccines—including against polio, measles, whooping cough, and chickenpox—remain fully recommended for all children, but experts still worry that the broad hits to the vaccine schedule will ultimately reduce those vaccines’ usage as well.

In addition, reducing pediatric vaccine coverage for very contagious infections will increase overall cases for everyone as children spread illness among their peers and older family members. And for seasonal illnesses, the risk runs highest during the winter. “We are really surrounded by a sea of viral infections,” Edwards says.

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