From Warp Speed to Uncertainty: U.S. Vaccine Policy in Crisis

The United States (U.S.) vaccine policy landscape has been thrown into turmoil, as governance shake-ups, funding cuts, and regulatory shifts collide to create confusion, instability, and mounting public distrust.

Governance upheavals have been especially destabilizing. On August 27, Robert Kennedy, Secretary of the U.S. Department of Health and Human Services (HHS) fired the Centers for Disease Control and Prevention (CDC) Director Susan Monarez after less than a month in office, prompting four senior colleagues—including CDC’s Chief Medical Officer—to resign in protest and leaving the agency with a leadership vacuum.

The departures followed mass layoffs at the CDC in April, when 2,400 employees—about one-fifth of the agency’s workforce—were dismissed, only to have roughly 700 to be rehired soon after.

The turmoil has extended beyond the CDC. In June, Secretary Kennedy abruptly removed the entire Advisory Committee on Immunization Practices (ACIP), severing a key channel for independent expert input on vaccines. And on July 29, the FDA’s Center for Biologics Evaluation and Research (CBER) Director, Vinay Prasad, suddenly resigned but returned to the post only 12 days later at the request of the U.S. Food and Drug Administration (FDA) Commissioner Marty Makary.

Vaccine funding and access have also suffered major setbacks, including the sudden cancellation of $500 million in mRNA vaccine research support and growing uncertainty about COVID-19 vaccine coverage.

Regulatory upheavals have compounded the turbulence. These include a new COVID-19 vaccine framework that raises access concerns for millions, sweeping policy shifts issued with conflicting advice and a lack of transparency, and mounting strain on the regulatory backstop provided by the Vaccine Injury Compensation Program (VICP).

Decoding the Policy Upheaval

On August 21, the Food and Drug Law Institute (FDLI) hosted a webinar, “Essential Vaccine Policy Updates: ACIP, CDC’s COVID-19 Guidance, and What's Next”, to parse what the changes mean in practice and explore how best to move forward.

The panel featured Jesse Goodman, a former FDA Chief Scientist and Deputy Commissioner now at Georgetown University; regulatory attorneys Will Walters (Epstein Becker & Green) and Lance Shea (Foley Hoag); and moderator Eva Temkin, a former FDA official now with Arnold & Porter.

From Universal to Conditional: The FDA’s New COVID Vaccine Framework

The first topic under the spotlight was the rollout of a new COVID-19 vaccine policy that reshapes access for millions of Americans. The policy, unveiled by the FDA on May 20, divided the population into high- and low-risk groups. Under this framework:

• Adults ≥65 are classified as high risk, as are adults <65 with underlying conditions such as asthma or obesity.
• Healthy adults <65 without qualifying conditions are classified as low risk, along with children and pregnant women.

At the time, the FDA also emphasized the need for randomized, placebo-controlled trials (RCTs) to generate evidence on vaccine efficacy in the low-risk tier. Those aged 50–64 were deemed to be in “global equipoise,” meaning the benefit of boosters was uncertain. This cohort was expected to be the primary focus of such trials.

Breaking with Due Process: Governance Upended

The framework’s introduction marked a striking breach of protocol. Normally, revisions to vaccine approvals are vetted by the ACIP. This time, the committee was bypassed entirely.

And in June, Secretary Kennedy went even further, abruptly dismissing all 17 ACIP members, charging that the panel had become “a rubber stamp for industry profit-taking agendas.”

Firing the committee en masse was unprecedented, removing decades of accumulated vaccine expertise in a single stroke and breaking ACIP’s deliberately staggered appointment system designed to preserve continuity and governance. The reconstituted panel, all directly appointed by Secretary Kennedy, now includes several anti-vax appointees.

Adding to the irregularity, the new COVID-19 vaccine framework was not issued through the FDA’s formal guidance process but through a May 20 New England Journal of Medicine editorial authored by Prasad and Makary. The standard procedure requires docketed guidance under the FDA’s Good Guidance Practices (GGPs) regulation (21 CFR 10.115), which mandates transparency, peer review, and public input. In contrast, the NEJM article appeared without peer review or prior public notice.

Timing further compounded the contradictions: only days later, on May 23, the FDA issued a “Gold-Standard Science” pledge aligned with its GGPs, even as the new COVID vaccine framework had sidestepped those requirements.

Experts Highlight Risks to Confidence and Uptake

Panelists at the FDLI session framed the developments as deeply troubling. Goodman pointed to consistent real-world evidence of COVID-19 vaccine benefit, calling the new restriction of access “quite extraordinary and a precedent I most worry about.” He noted the paradox that the May 22 inaugural report of the new Make America Healthy Again (MAHA) Commission urged greater reliance on real-world evidence, even as such evidence was dismissed for COVID-19 vaccine policy.

Vaccination guidance for children and pregnancy was singled out as particularly confusing. By classifying them as low risk, Secretary Kennedy’s HHS dropped its support for routine vaccination. In contrast, the FDA and leading medical groups—including the American Academy of Pediatrics (AAP) and the American College of Obstetricians and Gynecologists (ACOG)—continue to recommend routine vaccination for these groups. This divergence leaves providers and families to navigate the conflicting advice.

The feasibility of the FDA’s proposed RCTs in low-risk groups also came under scrutiny. Panelists argued that such studies would be prohibitively costly, and the now-high background immunity to COVID-19 could make them impractical. Shea suggested that adaptive, Bayesian, or artificial intelligence (AI)-coupled designs may be needed to generate reliable evidence more efficiently.

More broadly, the speakers cautioned that the abrupt policy shift has sown confusion and weakened confidence and warned of destabilizing effects on industry investment and a further decline in vaccine uptake.

Coverage, Access, and Liability Uncertain

Until recently, COVID-19 vaccines carried a “routine” recommendation that ensured universal, no-cost, annual coverage for everyone aged 6 months and older. Under the new framework introduced on May 20, however, the newly defined low-risk groups (healthy adults without qualifying conditions, children, and pregnant women) lost the guarantee of a routine recommendation. This initially created uncertainty over whether they would be able to obtain the vaccine at all.

On August 28, Secretary Kennedy emphasized on X that vaccines would remain available “for all patients who choose them after consulting with their doctors.” This more conditional stance was widely interpreted as requiring a doctor’s consultation and, effectively, a prescription. Major pharmacies in 16 states stopped administering COVID-19 vaccines unless patients had prescriptions, reflecting the uncertainty in the wake of the shifting federal guidance.

Kennedy’s newly appointed ACIP committee held its first session on September 18–19. Addressing the issue, ACIP reclassified vaccine access to “shared clinical decision-making” (SCDM) for all ages ≥6 months.

The SCDM classification makes COVID-19 vaccination an opt-in decision made in consultation with a physician, pharmacist, nurse practitioner, or other qualified clinician. ACIP clarified that a prescription is not required, after a 6–6 vote failed with the chair breaking the tie. Although prescriptions are no longer necessary, the SCDM recommendation still creates a confusing landscape in practice:

Eligibility: For high-risk groups – adults ≥65 and those <65 with underlying conditions – ACIP judged the benefit–risk most favorable, and providers are expected to recommend vaccination when consulted. For adults <65 without qualifying conditions, ACIP stressed that the benefit is lowest. This group may still be vaccinated if a provider is willing, but the weaker endorsement adds friction and may deter uptake. Children and pregnant women remain under SCDM, in direct conflict with guidance from the FDA, the AAP, and the ACOG, which continue to strongly recommend routine vaccination for these groups.

Coverage: Historically, coverage under the Affordable Care Act has depended on ACIP’s “routine” recommendations, which had ensured no-cost access to COVID-19 vaccines. ACIP’s pivot from “routine” to an SCDM recommendation, therefore, raises new uncertainty. In a September 19 press release, HHS said the SCDM vote “allows for immunization coverage through all payment mechanisms.” While this reflects the department’s official position, it stops short of guaranteeing no out-of-pocket costs in every circumstance. Implementation details – including insurer policies, state rules, and provider behavior – could still create gaps. With private-sector doses priced at about $145, even modest copays could reduce uptake, heightening concern that gaps in coverage will further depress vaccination rates.

Access points: SCDM requires consultation with a health care provider – a more onerous pathway than the previous universal recommendation. Vaccination may also depend on whether local pharmacies, clinics, or doctors are willing and able to administer under the new framework. This variability creates further confusion for patients and providers alike, and experience shows that such friction reduces vaccine uptake – especially among groups no longer covered by a routine recommendation.

Beyond questions of access and coverage, panelists also flagged uncertainty around the no-fault VICP. Established in the mid-1980s to stem the tide of manufacturers exiting the market over litigation, the program provides liability protection for vaccine makers while compensating vaccine-related injuries.

Secretary Kennedy has repeatedly promised “big fixes” to the program but has offered no details. Walters warned that poorly designed changes could bankrupt the VICP trust fund, strip liability protections, and once again drive manufacturers out of the vaccine market – with serious consequences for future vaccine access and innovation.

U.S. mRNA Vaccine Push Derailed

The turbulence has extended to mRNA vaccine development. On August 5, HHS announced the abrupt cancelation of $500 million in contracts under the Biomedical Advanced Research and Development Authority (BARDA) mRNA vaccine program. The wind-down targets 22 BARDA-backed projects, predominantly focused on COVID-19 and other respiratory infections.

The decision marks a striking shift given the technology’s proven success during the COVID-19 campaign. It also stands in sharp contrast to the first Trump administration’s Operation Warp Speed, which directed billions into mRNA development and delivered the fastest vaccine rollout in history.

The cancellation was met with broad concern among biopharma leaders and public-health experts. Secretary Kennedy defended the cancellations, arguing that mRNA vaccines “fail to protect effectively against upper respiratory infections like COVID and flu.” But the National Institue of Health (NIH) Director Jay Bhattacharya offered a conflicting explanation, saying the contracts were cut because “the public no longer trusts mRNA.”

At the FDLI meeting, panelists strongly countered those narratives. “mRNA saved millions of lives,” Goodman emphasized, noting also that Phase 3 trial results suggest that RNA-based flu vaccines outperform current seasonal shots.

In Walter’s view, the cancellations represented “politics entering the scientific process.” He highlighted that several GOP-led states are advancing bills that would restrict or even ban mRNA vaccines.

On the federal side, he noted that a Massachusetts district court had found recent NIH contract cancellations “arbitrary and capricious” – an administrative-law term for actions deemed “unreasonable, not supported by evidence, or fail to follow required procedure.” Further suits are expected to follow.

Consequences for mRNA and Pandemic Preparedness

Shutting down mRNA research threatens to destabilize a field that not only proved indispensable in the pandemic but is now showing promise across multiple therapeutic areas, including cancer and genetic disorders.

Goodman warned that the cancellations also undermine government reliability as a research partner. Sudden shifts in support can waste years of scientific effort, pushing companies to stick with “safe bets” instead of pursuing breakthrough innovation. Where the U.S. falters, others will step in. China, in particular, is accelerating mRNA investment and clinical approvals, jeopardizing America’s decades-long lead in biomedical innovation.

The consequences for pandemic preparedness are equally stark. Secretary Kennedy has said HHS will redirect BARDA funding to whole-virus vaccines, which utilize inactivated or weakened pathogens. But Goodman cautioned that these approaches have long struggled with efficacy and adverse-effect concerns, noting “this is a very old technology that has not worked in the past.”

Whole-virus vaccines also take years to develop and manufacture at scale, making them ill-suited to the rapid timelines demanded in a pandemic response. Unlike older modalities, mRNA platform technology allows vaccine candidates to move from genetic sequence to the clinic in a matter of weeks. Removing support for this rapid-response capability severely compromises U.S. preparedness for the next pandemic.

Conclusions

Panelists agreed that uncertainty – regulatory, scientific, and political – has become the new normal in vaccine policy. Goodman warned that such instability threatens to jeopardize “the public health miracle of immunization.”

The central question now is whether the FDA and HHS can steady the framework and restore confidence. Instead, the situation appears to be rapidly unraveling. The September 18–19 proceedings of Kennedy’s newly appointed ACIP committee were marked by confusion, abrupt vote reversals, and unprofessional exchanges, and ultimately failed to resolve the lingering uncertainty over COVID-19 vaccine access, eligibility, and coverage.

The committee also attempted to insert new risk language into CDC’s Vaccine Information Statements – despite the authority resting with CDC, not ACIP. Some members aired unsupported claims about “DNA contamination” in mRNA vaccines, while Robert Malone, a prominent vaccine skeptic, claimed that “there is no established correlate of protection for COVID.”

ACIP also faltered on other vaccines. After considerable debate, it delayed a decision on hepatitis B vaccination for newborns indefinitely, and in the same meeting reversed itself on whether the federal Vaccines for Children program should continue supplying the MMRV vaccine to children under four – first voting in favor and then overturning the decision the next day.

The disarray at the federal level is beginning to feed divergence in the states. Pennsylvania has already broken with ACIP’s recommendations on COVID-19 vaccination, choosing instead to align with guidance from medical groups such as AAP, ACOG, and AAFP. Florida has gone further: on September 3, its Surgeon General announced the state will move to end all vaccine mandates, including those for schools.

What is abundantly clear is that continuing disruption will deepen confusion, restrict access, and further weaken public trust in vaccines – with direct implications for the health of the nation.

Vaccine Policy Upheaval in Focus