Dr. Rana Alissa hears it daily in the clinic.

“It’s better for my kid to get the virus than get the vaccine.”

“The more you [doctors] vaccinate, the more money you get.”

“I did not vaccinate any of my kids, and I’m not going to vaccinate this one. So, please, don’t waste your time.”

The Jacksonville, Florida, pediatrician said on average, she’d hear vaccine skepticism from a couple of parents a month, at most, before the COVID-19 pandemic. “Now, it’s every day,” said Alissa, who is also president of the Florida Chapter of the American Academy of Pediatrics.

Medical experts say hesitancy is likely to increase further as a result of misinformation pouring from the Trump administration — and turmoil at the federal agency largely responsible for setting vaccine policy.

On Thursday, three top officials were escorted out of the Atlanta headquarters of the federal Centers for Disease Control and Prevention.

All three officials resigned to protest the effort by Secretary of Health and Human Services Robert F. Kennedy Jr. to dismiss CDC Director Susan Monarez for pushing back against Kennedy’s vaccine policies.

One of the officials, Dr. Demetre Daskalakis, director of the CDC’s National Center for Immunization and Respiratory Diseases, posted on X that he’s resigning because “the intentional eroding of trust in low-risk vaccines” will cause the nation to suffer.

Earlier this week, the U.S. Food and Drug Administration restricted access to updated COVID-19 shots. The new rules include limitations for young children that the American Academy of Pediatrics called“deeply troubling.” The FDA only approved COVID-19 vaccines for people who are 65 and older and those who are known to be at risk for a severe case. Consultation with a medical provider will be required before the shot is given to healthy children under 18, meaning parents can’t simply take their kids to a vaccination clinic or pharmacy.

In June, Kennedy ousted all 17 members of the vaccine advisory committee at the CDC, replacing them with some members who are vaccine skeptics. Many states use the committee’s recommendations to develop their vaccine requirements. And in May, Kennedy rescinded recommendations for kids to get vaccinated against COVID-19.

In his books, experts say, Kennedy appears to promote his own version of miasma theory, an obsolete belief dating back to ancient times that diseases are caused by vapors from rotting organic matter. Scientists have since proven that microbes, not bad air, cause infectious diseases.

Experts say Kennedy’s actions are likely to make vaccination rates worse, paving the way for more outbreaks.

“Every vaccine that we give prevents a serious and life-threatening disease,” New York pediatrician Dr. Jesse Hackell, chair of the Committee on Pediatric Workforce at the American Academy of Pediatrics, told Stateline. “I don’t want to force anybody, but I do want to make sure that the information they’re getting is quality information — and that’s not what is coming from HHS.”

Nonmedical exemptions

Every state requires kids to get certain shots to attend school. All states exempt children who can’t be immunized for medical reasons, but nonmedical exemptions for religious or personal reasons vary from state to state.

Vaccination rates among kids are declining. Flu vaccinations, for example, hit their lowest rate since 2019. And since the beginning of the pandemic, exemption requests have increased across the country.

Among kindergarteners, nonmedical exemptions have increased each year since 2020, from 1.9% in the first year of the pandemic to 3.4% in the 2024-25 school year, according to the latest data from the federal Centers for Disease Control and Prevention. Exemptions increased in 36 states and Washington, D.C. Seventeen states reported exemption rates over 5%.

The changes may seem small. But experts say even slight increases in exemptions and decreases in vaccinations make a big difference.

“With a disease that’s as infectious as measles … small increases in vaccination rates could really go a long way,” epidemiologist Sophia Newcomer, a University of Montana associate professor, said in a recent panel discussion hosted by Montana Families for Vaccines.

Alissa and other experts say rampant confusion around the shots, including federal officials casting doubt, is exacerbating the problem. Often, parents aren’t sure whom they can trust, finding conflicting information and unreliable sources, she said.

“[Parents] come to our clinic and the hospitals and they say, ‘We looked it up, and we just don’t want it,’” she said. “There’s different kinds of reasoning: the ingredients of the vaccine, the side effects of the vaccine, ‘vaccines don’t work.’”

But research consistently shows vaccines protect children from serious illness. Shots also protect the most vulnerable who can’t get vaccinated, such as babies who are too young, or children and adults who are immunocompromised. Babies up to age 2 are more likely to get very sick from COVID-19, making up the most hospitalizations among kids.

Ultimately, Alissa said, “We are endangering each other.”

In Florida, where Alissa practices, religious exemptions have increased monthly, according to a state report that tracked the numbers through April. Some counties have higher rates of children with religious exemptions than others, ranging from about 1.5% to 15%, the state department of health reported. Among kindergarteners in the state, the rate of nonmedical exemptions rose from 2.7% in the 2020-21 school year to 4.8% in the 2024-25 school year, CDC data shows.

Five states — California, Connecticut, Maine, New York and West Virginia — don’t allow nonmedical exemptions, according to the National Conference of State Legislatures. Two West Virginia families with immunocompromised kids brought lawsuits over Republican Gov. Patrick Morrisey’s January executive order mandating religious exemptions despite state law.

Kennedy defended religious exemptions and endorsed the governor’s order in a post on X. His agency also sent letters to West Virginia health departments warning of civil rights violations if they don’t allow such exemptions.

“There’s a ton of variability across states in how easy it is to not get vaccinated,” Newcomer, of the University of Montana, said. Some states require parental vaccine education as part of the exemption request while others don’t.

“Increased exemptions needs to be fought at every level — working to make sure there’s access, to make sure that there’s good information, and to make sure that there’s strong policy at the state level, so that people aren’t exploiting exemption loopholes,” Northe Saunders, American Families for Vaccines president, said during the panel discussion.

Other vaccines

Doctors are worried that other vaccines will be targeted by the Trump administration, such as those for whooping cough. By April, preliminary CDC data showed more than 9,000 cases this year, about twice as many compared with the same time last year and more than there were right before the pandemic. Whooping cough, or pertussis, can be deadly for babies. Vaccines help prevent severe whooping cough illness.

Hackell said that when he was training in the 1970s, there were no pneumococcal and haemophilus vaccines. Babies would come in with 104-degree fevers and they were immediately tested for the infections, he recalled. For babies under age 2, those bacterial infections can show up as only a high fever, but the infection can rapidly turn fatal without treatment, he told Stateline.

“When I trained, we didn’t have these vaccines, and these kids kept us up at night,” Hackell said. “I never want to practice in those days. I never want to go back to that. … To me, that is unacceptable to submit my patients to those risks that we’ve been able to reduce.”

This week the FDA removed one of the available COVID-19 vaccines for young children, limiting the Spikevax vaccine to only kids with at least one serious health issue. Moderna’s shot is still available for children 6 months and older. Pfizer’s shot is no longer available for kids under 5, as the FDA is ending its emergency use authorization for the age group.

But the American Academy of Pediatrics recommends COVID-19 shots for children 6 months to 2 years. It also recommends them for older children with underlying health issues. Healthy children whose parents want them to get the shot should also be offered them, the AAP says.

Hackell is concerned by the FDA’s new limitations on the shot.

“As a parent, as a grandparent and as a physician who takes care of vulnerable kids, it disgusts me,” Hackell said.

He’s also concerned about vulnerable kids who get their shots through the federal Vaccines for Children (VFC) Program, which covers shots if parents can’t afford them and follows federal vaccine advisory recommendations.

“If you’re covered by VFC, which is basically kids on Medicaid and a few other populations, then you’re out of luck,” Hackell said. “To me, that’s a huge inequity in access to care, which is indefensible.”

He added that the move breaks with the administration’s emphasis on individual decision-making, saying the new restrictions limit parental decisions.

‘Normalization’ of outbreaks

During the Montana panel discussion, Dr. Paul Offit, director of the Vaccine Education Center at Children’s Hospital of Philadelphia, pointed to CDC data showing that over the past year alone, about 1 in 5 children and adolescents hospitalized with COVID-19 were put in the ICU. And between September 2023 and last August, 152 children died of COVID-19 and 213 children died of the flu.

While Texas officially declared its measles outbreak over — which means the state hasn’t reported a new case in six weeks — neighboring New Mexico continues to see new cases.

“What we’re going to see is, you know, sadly, a normalization of these outbreaks,” said Rekha Lakshmanan, chief strategy officer at The Immunization Partnership, a Texas-based vaccine education organization. “We need to make sure that kids are protected against the diseases that they can be protected against, because we truly are in a vulnerable state right now.”

Newcomer, the Montana epidemiologist, said that under-vaccination trends are usually due to disparities in access, such as challenges in reaching vaccine providers in rural communities. At rural health care centers lacking staff and technology, it’s harder to automate vaccination reminders for patients — which can increase the likelihood patients show up for appointments but require technical infrastructure, she explained.

Adding misinformation to the mix only makes matters worse, experts say.

“Parents are confused and understandably concerned,” Offit told Stateline. “It’s the most vulnerable among us that will suffer, and that will be our children.”

He added that he’s also wary about the federal administration’s removal of data, concerned that vaccination figures will be next.

“It’s nightmarish,” he said. “What worries me the most is we’re not going to know the degree that we’re suffering. We’re not, because the CDC is losing its capacity to do adequate surveillance across the country.”

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Stateline reporter Nada Hassanein can be reached at nhassanein@stateline.org.

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