The moment Robert F Kennedy Jr’s name was floated in late 2024 as President Trump’s pick for health secretary serious concerns erupted in the scientific and public health communities about the future of vaccine R&D and policy in the country. This was primarily because of Kennedy’s long history as a very public vaccine critic and a conspiracy theorist, promoting, for example, the discredited claim that vaccines cause autism.
Now at the helm of the US government’s Department for Health and Human Services (HHS), Kennedy oversees agencies like the Food and Drug Administration (FDA), the National Institutes of Health (NIH) and the Centers for Disease Control and Prevention (CDC). After almost a year-and-a-half in position, how has government policy toward vaccines changed?
What has happened at the FDA?
When Peter Marks, the long-time director of the FDA’s centre responsible for assessing vaccines stepped down in April 2025, he complained that ‘truth and transparency are not desired’ by Kennedy and that instead the HHS secretary ‘wishes subservient confirmation of his misinformation and lies’. Marks, a medical doctor with a PhD in cell and molecular biology, became deputy director of the FDA’s Center for Biologics Evaluation and Research (CBER) in 2012 and assumed the role of director a decade ago. Since his departure leadership of the centre, which regulates vaccines and other biological products, has been chaotic.
Epidemiologist Vinay Prasad succeeded Marks as CBER’s director in May of last year. Prasad resigned the post after two months, before being rehired a few weeks later. His tenure was marked by controversial decisions and reported clashes with stakeholders and colleagues. Prasad ultimately left CBER at the end of April 2026, with the role being filled temporarily by a number of people. Most recently, pharmaceutical executive Karim Mikhail was named CBER’s acting director on 15 May.
Have mRNA vaccines been targeted?
HHS cancelled $500 million (£372 million) in funding for messenger RNA (mRNA) vaccine research in August 2025, arguing that the platform fails to protect effectively against upper respiratory infections like Covid-19 and flu. Kennedy expressed a desire to shift toward ‘safer, broader vaccine platforms that remain effective even as viruses mutate’ and have ‘stronger safety records and transparent clinical and manufacturing data practices’, like whole-virus vaccines. The HHS announcement came just months after the NIH began an unexpected review of mRNA vaccine research grants that it funds.
Meanwhile, NIH director Jay Bhattacharya, a physician and health economist who has also served as the acting director of the CDC since February 2026, has said the mRNA vaccine platform is ‘no longer viable’.
What has happened to scientific advisory committees?
Since Trump’s reinauguration, dozens of scientific advisory panels across US science agencies have been overhauled and terminated. In 2025 alone, HHS shuttered 75 advisory committees, representing more than a 25% reduction, according to the consumer rights group Public Citizen.
In particular, Kennedy’s decision in June 2025 to dismiss all members of the CDC’s Advisory Committee on Immunization Practices (ACIP) – which was created more than 60 years ago to develop recommendations on the use of vaccines in the US civilian population – and completely reconstitute it has raised eyebrows. At the time, Kennedy stated that ACIP has been ‘plagued with persistent conflicts of interest and has become little more than a rubber stamp for any vaccine’. This drew public backlash from organisations like the American Medical Association and the Infectious Diseases Society of America. Critics pointed out that among those Kennedy brought in to ACIP were several individuals who lack relevant expertise and have histories of anti-vaccine work.
A US federal judge agreed, and in March he issued a stay on all of Kennedy’s appointments to ACIP, arguing that his newly populated panel violates Congress’s ‘command that advisory committees be fairly balanced’.
The judge’s order also froze an updated vaccine schedule for 2026 that HHS issued following ACIP’s overhaul. The department had announced a major reduction in its childhood immunisation schedule, decreased the number of recommended vaccines from 17 to 11. For now, these changes to the federal childhood vaccine schedule have been blocked.
What are some of the latest developments?
Last month, reporting by The New York Times indicated that the FDA impeded the publication of a study that demonstrated the safety and efficacy of shingles and Covid vaccines. An HHS spokesperson told various media outlets that the studies were withdrawn ‘because the authors drew broad conclusions that were not supported by the underlying data’.
Experts who collaborate with the University of Minnesota’s Center for Infectious Disease Research and Policy have described this as a ‘pattern that signals alarm for us’. When agencies suppress findings showing that vaccines are safe and effective, ‘it slows down the science’ and ‘shapes what people in decision-making roles like policymakers and insurers believe is true’, they added.
Meanwhile, three scientific papers cited by Kennedy and associates to justify the administration’s vaccine policy changes have been removed, retracted or placed under investigation by their publishers since early April, according to reporting by The Guardian earlier this month.
Earlier this year the FDA refused to review Moderna’s application for an mRNA-based influenza vaccine, taking issue with the company’s clinical trial design. The agency then quickly reversed its decision and agreed to the review. A final decision on Moderna’s application is expected in August. If approved, the product would be the first seasonal flu vaccine on the market that uses mRNA technology.
What do senior science advisers make of all this?
A dozen former FDA commissioners collectively warned in December that they are ‘deeply concerned’ about ‘sweeping new FDA assertions about vaccine safety and proposals that would undermine a regulatory model designed to ensure that vaccines are safe, effective, and available when the public needs them most’. Among the signers was Scott Gottlieb, who was the FDA commissioner during Trump’s first term as president, and Brett Giroir, who briefly served as acting commissioner of the agency in 2019 after Gottlieb resigned.
A couple of months before that, six former surgeons general – including Jerome Adams, who was surgeon general during Trump’s first presidency – cautioned that Kennedy’s actions are ‘endangering the health of the nation’.
Adams, who also served on Trump’s Coronavirus Task Force, tells Chemistry World: ‘Under the current administration, we have seen clear and deeply concerning declines in vaccine confidence, uptake and trust in key institutions like HHS and the CDC.’ He notes that polling shows trust in the CDC for reliable vaccine information at historic lows, under 50% overall in early 2026.
‘Actions such as major revisions to the recommended childhood immunisation schedule (reducing targeted diseases), overhaul of advisory committees, shifts in messaging around safety and mandates, and related policy moves have coincided with these trends,’ Adams continues. ‘Leadership means owning outcomes, not just intentions.’
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