President Trump once celebrated the COVID-19 vaccines released at the end of his first term as “one of the greatest achievements of mankind,” echoing the sentiments of mainstream medical officials who praised their rapid development as pivotal in combating the then-raging pandemic.

But as his second administration takes shape, some are sounding the alarm regarding Trump’s picks to lead major public health agencies, concerned that the nominees’ skepticism, if not hostility, toward vaccines could jeopardize the nation’s ability to respond to new or resurgent infectious threats.

There’s Robert F. Kennedy Jr., Trump’s pick to lead the U.S. Department of Health and Human Services, who has called the COVID-19 vaccine the “deadliest vaccine ever made” and said that “there’s no vaccine that is, you know, safe and effective.”

Nominated to lead the U.S. Centers for Disease Control and Prevention is Dr. Dave Weldon, a former congressman from Florida who has expressed skepticism of the safety of vaccines and promoted the discredited idea that a preservative, thimerosal, that has been used in some vaccines, or the measles, mumps and rubella vaccine — which has never used thimerosal — may be linked to autism.

Skepticism and outright conspiracy theories about vaccines are nothing new, and health officials have long warned about the potential pitfalls of such misinformation.

But now, some top doubters could be in the position to shape federal health policy.

While COVID is no longer the grave public health threat it once was, the disease spikes periodically — as it did this summer — and has continued to be responsible for the most hospitalizations and deaths of any respiratory disease nationally, with nearly 60,000 fatalities for the yearlong period that ended Sept. 30. And other infectious threats, be they whooping cough, measles or the latest strain of bird flu, continue to loom.

“We really don’t want to return to the era where these vaccine-preventable diseases were frequent, and children were getting sick or hospitalized or even dying,” said Dr. Anne Schuchat, a former deputy director at the CDC, who served at the agency for more than three decades, starting in the Reagan administration. “We’ve been fortunate in the past couple decades to have high levels of vaccination and low levels of most of the diseases.”

Neither the Trump transition team, a spokesperson for Kennedy, nor Weldon answered requests for comment for this story.

Trump, who had his own brush with the coronavirus near the end of his first term, hailed the rapid development of the COVID vaccines as a “monumental national achievement” and celebrated the production of “a verifiably safe and effective vaccine.”

He continued in 2021 to promote COVID vaccines in interviews and at rallies, though he also said he didn’t support making the shots mandatory. That year alone, the World Health Organization estimates, the vaccines likely saved at least 14.4 million lives worldwide.

But even then, skepticism surrounding the shots was starting to take root — including among Trump’s supporters. A KFF survey found that 60% of Republicans who support his “Make America Great Again” agenda got at least one dose of a COVID-19 vaccine at some point. But by late 2023, another KFF survey found that 70% of self-identified MAGA Republicans were either not too confident or not at all confident in the safety of the COVID-19 vaccine.

That same survey found that only 36% of Republicans were very or somewhat confident the COVID-19 vaccines are safe, compared with 54% of independents and 84% of Democrats.

Kennedy has contended he is not “anti-vaccine,” but his organization, the Children’s Health Defense, has questioned their safety. Kennedy himself has criticized what he sees as deficits in the science on vaccine safety and spread the myth that vaccines commonly injure children.

When asked by a documentary maker whether there were any vaccines in history that were a benefit to mankind, Kennedy replied: “I don’t know the answer to that.”

More recently, he has said he would not “take away anybody’s vaccines.”

But even if a vaccine isn’t taken away entirely, “you can just make it much harder for people to get,” said Dr. Ashish Jha, dean of the Brown University School of Public Health and a former White House COVID-19 Response coordinator under President Biden.

Dr. Ashish Jha, dean of the Brown University School of Public Health, said Robert F. Kennedy Jr. “consistently shows that he doesn’t believe in modern medicine, doesn’t believe in the scientific process that has led to these huge gains that we’ve had” in public health.

(Susan Walsh / Associated Press)

For instance, Jha said, newly appointed officials could demand randomized clinical trials for every annual update to the COVID vaccine — “even though we don’t do that for the flu vaccines.”

“If that is a new standard that they create, it probably will make it impossible for [updated] COVID vaccines to be available in time for the holiday season,” Jha said. “If they follow through on their own previous critiques, they may box themselves in and make it very, very hard for Americans to even get COVID vaccines.”

Kennedy has also advanced the baseless claim that thimerosal in vaccines can cause autism, which has been thoroughly discredited by scientists. Thimerosal has been removed from childhood vaccines since 2001, according to the CDC, and “research does not show any link between thimerosal and autism.” While it is still used in some flu vaccines, parents can request a formulation without the preservative for their children.

Organizations like the American Academy of Pediatrics also say the MMR vaccine — which protects against measles, mumps and rubella and is a major target of the anti-vax movement — is safe.

Critics have also accused Kennedy of spreading misinformation regarding the safety of the measles vaccine in Samoa. The Associated Press reported that Kennedy traveled to the island nation in June 2019 and met with anti-vaccine activists before a severe outbreak that killed 83, mostly infants and children.

At the time, public health officials said anti-vaccine misinformation had made the nation vulnerable. Kennedy has denied playing a role in the outbreak, which he has characterized as “mild.” “I had nothing to do with people not vaccinating in Samoa. I never told anybody not to vaccinate,” Kennedy told an interviewer in the 2023 documentary “Shot in the Arm.”

In a video published by the New York Post in 2023, Kennedy floated the conspiracy theory that COVID-19 may have been engineered to avoid harming Jews and Chinese people. Critics called his comments antisemitic and anti-Asian.

In a social media post, Kennedy said “the insinuation” that “I am somehow antisemitic, is a disgusting fabrication.” In another post, Kennedy said he has “never, ever suggested that the COVID-19 virus was targeted to spare Jews” and asserted “that the U.S. and other governments are developing ethnically targeted bioweapons and that a 2021 study of the COVID-19 virus shows that COVID-19 appears to disproportionately affect certain races.”

Some scientists have dismissed some of Kennedy’s assertions as absurd and not based in science.

“One of my biggest concerns about about him is the misinformation that he spreads around vaccination,” said Dr. Richard Besser, who served as acting CDC director during the initial response to the 2009 H1N1 “swine flu” pandemic and is now president and chief executive of the Robert Wood Johnson Foundation.

The Health and Human Services secretary plays a major role in setting health priorities for the nation — suggesting how much money various agencies should get, helping determine what is covered for people on Medicare or Medicaid, and having a say in what kind of public recommendations the agency issues, Besser said.

Kennedy “consistently shows that he doesn’t believe in modern medicine, doesn’t believe in the scientific process that has led to these huge gains that we’ve had” in public health, Jha said.

Dr. Scott Gottlieb, whom Trump appointed as commissioner of the U.S. Food and Drug Administration during his first term, said on CNBC that if Kennedy follows through on his rhetoric, “You’re going to see measles, mumps and rubella vaccination rates go down,” which he expects would result in large outbreaks. “For every 1,000 cases of measles that occur in children, there will be one death,” he added.

Trump’s apparent skepticism toward some vaccine requirements — during the campaign he pledged to “not give one penny to any school that has a vaccine mandate” — is also raising alarm bells in some corners.

Making moves that would erode the share of schoolchildren receiving vaccines they have been getting for generations would “create health risks” for the community at large, said Dr. Mark Ghaly, former secretary of California’s Health and Human Services Agency.

“I can imagine that some states may be pushed into a corner” if federal funding for public health work is reduced, said Dr. Mark Ghaly, former secretary of California’s Health and Human Services Agency.

(Rich Pedroncelli / Associated Press)

If a policy scrapping federal funding at schools that enforce vaccination requirements for schoolchildren were enacted, some districts or states may have to make tough decisions. While most public schools largely rely on state and local funding, federal dollars flow to support certain programs, such as school lunches.

California is a little less reliant on federal funding for public health work, but “I can imagine that some states may be pushed into a corner,” Ghaly said.

State and local health officials should also speak up if they see messaging from the federal government that amounts to misinformation, Jha said. “It is, I think, really critical for state and local public health officials to speak up and not cede the floor to federal officials, especially if those federal officials are not sort of sticking to where the scientific evidence is,” Jha said.

Different leadership at national health agencies could also affect the availability or cost of vaccines.

“Could they become harder to get? Could it become more expensive to get in some places? Maybe not in the first year or two, but down the road, absolutely,” Ghaly said.

The federal government’s childhood vaccination program, run out of the CDC with oversight from Health and Human Services, plays a major role in getting half the kids in America their childhood vaccines essentially for free, Jha said. If federal officials decide to gut the program, “a lot of poor kids are not going to have easy access to vaccines, which, of course, would be tragic and would put everybody at risk.”

Other questions include whether future federal health officials would seek next fall to water down the CDC’s current recommendation that everyone age 6 months and up get vaccinated against COVID — and whether that would affect whether insurers cover the costs of vaccines.

One glimpse into a sharply different way of managing COVID vaccination recommendations is in Florida.

In a move at direct odds with the CDC and the Food and Drug Administration, Florida’s surgeon general, Dr. Joseph Ladapo, advised against getting mRNA COVID vaccinations this fall and suggested that healthcare providers look into a non-mRNA shot for the elderly and immunocompromised. The Pfizer and Moderna vaccines both use mRNA technology, while a different vaccine from Novavax does not.

Ladapo, a former professor at UCLA, is viewed favorably by some highly ranked Republicans, including Ron DeSantis, the Florida governor who appointed him. Just after the election, DeSantis urged Trump to appoint Ladapo as the next secretary of Health and Human Services.

The CDC and FDA have rebuked earlier claims by Ladapo, saying his suggestion that there was an increased risk of harmful, life-threatening side effects caused by the COVID-19 vaccines was “incorrect, misleading and could be harmful to the American public.” The letter said the FDA-approved COVID vaccines have met rigorous standards for safety and effectiveness.

Jha said he thought some of Trump’s other administration picks were reasonable, including the nomination of Dr. Marty Makary, a surgical oncologist at Johns Hopkins University, to run the FDA.

Makary drew attention for a February 2021 op-ed in which he wrote he expected COVID-19 to be “mostly gone” by that April, a prediction that failed to materialize. Later that year, he criticized federal recommendations to have 16- and 17-year-olds receive a COVID-19 vaccine booster, citing a lack of supporting clinical data. In early 2022, he criticized experts who he said discounted infection-derived immunity to COVID.

Jha said he disagrees with Makary on a number of topics — such as, in his view, discounting the value of COVID vaccinations in kids. The difference between Kennedy and Makary, Jha said, is that Makary’s views “are within the range of medical professionals who believe in modern medicine, who can disagree honestly.”

Among Trump’s other picks Jha said he considered reasonable was Dr. Jay Bhattacharya, a Stanford University health policy professor and economist who was critical of pandemic lockdowns, and offered pandemic policy advice to Florida. Nominated to run the National Institutes of Health, Bhattacharya supported a pandemic response called “focused protection” — protecting those at highest risk of death while allowing others to “live their lives normally to build up immunity to the virus through natural infection.”

“I think some of his ideas and recommendations during the pandemic were really problematic and caused a lot of suffering,” Jha said of Bhattacharya, adding that no state was able to implement “focused protection” and that “lots of Floridians died.”

But, Jha added, “If the question is — is he qualified? This is a guy who has an MD, PhD at Stanford … he’s got a very broad body of work, mostly in health economics … He’s very smart, very experienced.”