Trump Administration's Anti-Vaccine Policies Trigger Measles Resurgence, FDA Rejection of Moderna Flu Shot, and Retreat from Vaccine Innovation

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The Trump administration—under Health and Human Services Secretary Robert F. Kennedy Jr., and, at the Pentagon, Defense Secretary Pete Hegseth—has pursued a series of vaccine policy changes that public health experts, medical associations, and vaccine manufacturers warn are undermining decades of progress against preventable disease and threatening American leadership in vaccine innovation.

COVID-19 Vaccines Saved Millions of Lives

The mRNA vaccine platform now under attack by the administration was itself a product of the first Trump administration's Operation Warp Speed, which funded Moderna's COVID-19 vaccine development with billions in taxpayer support.

Peer-reviewed research has consistently demonstrated the vaccines' enormous impact. An NBER study by economists at USC and Brown University found that the global COVID-19 vaccination campaign averted approximately 2.4 million excess deaths across 141 countries in just the first eight months, with the value of lives saved estimated at $6.5 trillion. The United States was the largest beneficiary, with roughly 429,000 deaths averted. A separate NBER analysis estimated that vaccines saved 748,600 American lives through June 2023—meaning that without vaccines, U.S. COVID-19 deaths would have approached 1.91 million rather than the 1.13 million recorded.

A peer-reviewed study published in the American Economic Journal: Applied Economics in January 2026 found that COVID-19 vaccination reduced individual cases by 80%, and that this protection spilled over to close contacts, producing household-level indirect effects about three-fourths as large as the direct effect.

Despite this evidence, RFK Jr. has long spread misinformation about mRNA vaccines, including testifying to the Louisiana legislature in 2021 that COVID vaccines were the "deadliest vaccine ever made" and formally petitioning the FDA to revoke authorization for mRNA COVID vaccines during the mass vaccination campaign.

Childhood Vaccine Schedule Overhaul

On January 5, 2026, the CDC announced an unprecedented overhaul of the childhood vaccine schedule, reducing universally recommended vaccines from 17 to 11. Vaccines against rotavirus, influenza, hepatitis A, hepatitis B, and meningococcal disease were moved from routine recommendations to "shared clinical decision-making" or recommended only for high-risk children.

Kennedy justified the changes by citing a 33-page assessment comparing the U.S. schedule to Denmark's—a country with 6 million people, universal healthcare, and a national patient registry, compared to 330 million Americans with 27 million uninsured.

The changes bypassed the established scientific review process. Kennedy had fired all 17 members of the CDC's Advisory Committee on Immunization Practices (ACIP) in June 2025 and replaced them with members who largely shared his skepticism of vaccines. The American Medical Association stated that the changes emerged from "a vastly less vigorous and science-based review" and warned that altering longstanding recommendations "without a robust, evidence-based process" would "undermine public trust and put children at unnecessary risk."

The American Academy of Pediatrics filed a lawsuit in federal court challenging the legality of the schedule changes and the reconstituted ACIP panel.

Kennedy's actions contradicted pledges made during his Senate confirmation, where he told lawmakers "Senator, I support vaccines. I support the childhood schedule. I will do that." Senator Bill Cassidy (R-LA), who voted to confirm Kennedy based on these assurances, declared on the Senate floor that Kennedy had pledged to maintain ACIP recommendations without changes.

Measles Resurgence

The consequences of declining vaccination rates are already visible. The United States experienced its worst year for measles in over three decades in 2025, with 2,280 confirmed cases across 45 states—compared to just 285 cases in all of 2024. As of February 12, 2026, 910 additional cases have already been reported in 24 states, with case counts increasing roughly 25% week over week.

At least four people have died—two unvaccinated children in Texas, an unvaccinated adult in New Mexico, and a child in Los Angeles County—the first U.S. measles deaths since 2015. Approximately 94% of cases occurred in people who were unvaccinated or had unknown vaccination status.

In November 2025, the Pan American Health Organization announced that the Americas—including the United States—had lost measles elimination status after endemic transmission persisted for more than 12 months. The U.S. had held elimination status since 2000.

The MMR vaccine is 97% effective with two doses. Nationally, kindergarten MMR vaccination rates fell from 95.2% in 2019-2020 to 92.7% in 2023-2024—below the 95% threshold needed for herd immunity. In the community at the center of the Texas outbreak, the vaccination rate was 82%.

Beyond immediate illness, a 2019 Harvard Medical School study found that measles infection can wipe out up to three-quarters of a person's existing antibodies against other diseases, leaving survivors vulnerable to infections they were previously immune to.

Flu Outbreak at Lackland Air Force Base After Hegseth Makes Military Flu Shot Optional

The anti-vaccine agenda extended to the Pentagon in April 2026—and produced a measurable outbreak within two months. On April 21, 2026, a policy announced by Defense Secretary Pete Hegseth took effect ending the longstanding requirement that U.S. troops be vaccinated against influenza. Hegseth called the requirement an "absurd, overreaching" mandate that had served to "weaken our warfighting capabilities," casting the change as a matter of religious freedom and medical autonomy: "We will not force you because your body, your faith and your convictions are not negotiable." Even some prominent Republicans objected at the time. Senator Roger Wicker of Mississippi, chairman of the Armed Services Committee and an Air Force veteran, said: "The reason it was mandatory was to enhance readiness... You know, you do give up certain rights when you take the oath."

The New York Times reported on June 18 that a major flu outbreak had sickened nearly 160 troops at Lackland Air Force Base in San Antonio, Texas—the Air Force's basic-training hub—racing through a Basic Military Training wing where new recruits sleep on bunk beds in open bays and share meals at communal tables. In the weeks after Hegseth's policy took effect, only about 40 percent of Air Force trainees had opted to take the vaccine, according to an Air Force official. A trainee in his sixth week of basic training, Keon McDaniel, died after falling ill and being taken to Brooke Army Medical Center; the Air Force said it was not immediately clear whether his death was related to the flu outbreak, and a comprehensive medical review is underway.

The outbreak continued to grow: cases rose to 222 by around June 21 and to 275 within about a week of the initial report, according to The Hill. The Air Force initially issued an exception to the voluntary policy requiring all recruits at Lackland to get flu shots, and MSNBC's Maddowblog noted that the military was carving out exceptions to Hegseth's vaccine policy as the outbreak grew. Then, on about June 24, the military services quietly reinstated the flu-shot requirement for all recruits in basic training—a rapid reversal of Hegseth's two-month-old policy. CNN reported that the Air Force had formally requested permission to bring back mandatory flu shots weeks before the outbreak, signaling internal alarm at the policy among military leaders.

The Pentagon defended the policy even as the outbreak spread. Chief spokesman Sean Parnell said the changes were "based upon thorough risk assessments" designed to maximize the readiness and lethality of the force, and Air Force officials described the outbreak as "localized" to the basic training wing, with medical personnel offering antiviral medication to trainees in contact with the ill. A White House spokeswoman referred the Times' questions to the Pentagon.

The episode fits the broader pattern the Times identified: crowded basic-training environments are precisely why the military's flu mandate was instituted decades ago, and the outbreak highlighted the risks of the administration's overall approach to vaccines. Hegseth has also fought to reinstate—with back pay, benefits, and former rank—the roughly 8,700 troops who left the military after refusing the COVID vaccine before that mandate was rescinded in 2023, extending the application deadline to April 1, 2027. Kennedy, for his part, had rescinded federal recommendations for flu vaccines containing thimerosal in summer 2025, based on a debunked link to autism promoted by the anti-vaccine movement. Military personnel remain required to receive vaccines against measles, mumps, and polio.

FDA Rejects Moderna's mRNA Flu Vaccine

On February 10, 2026, Moderna announced that the FDA had refused to even review its application for the first mRNA-based flu vaccine—a rare "refuse to file" action that the agency takes in roughly 4% of applications, typically only when critical information is missing.

Dr. Vinay Prasad, the FDA's top vaccine regulator appointed under Kennedy, personally handled the rejection and overrode staff recommendations to proceed with review. The director of the FDA's Office of Vaccines Research and Review, Dr. David Kaslow, wrote a memo recommending that the application be reviewed.

Prasad's stated rationale was that Moderna's Phase 3 trial—which enrolled 41,000 participants and found the mRNA vaccine was 27% more effective than a standard flu vaccine at preventing symptomatic flu and 49% more effective against hospitalization—had used a standard FDA-approved flu vaccine rather than a high-dose vaccine as its comparison product for older adults. The FDA cited no safety or efficacy concerns.

Moderna said the FDA had agreed to the trial design in April 2024 and as recently as August 2025 indicated it would review the application and address comparator issues during that process. The company also provided separate data comparing its vaccine head-to-head against a high-dose flu vaccine in adults 65 and older, showing superiority—but the application was still refused.

Economist Alex Tabarrok of George Mason University noted the contradiction at the heart of the administration's vaccine stance: the FDA rejected the trial for not using a high-dose vaccine as comparator (implying participants deserved the most effective product), while Kennedy has separately ordered that all new vaccines be tested against inert placebos (implying participants need not receive any active vaccine at all).

Drug regulators in Canada, Europe, and Australia all accepted Moderna's application for review.

On February 11, FDA Commissioner Dr. Marty Makary suggested on Fox News that the agency might eventually approve the vaccine, characterizing the rejection as "part of a conversation that occurs with all drug makers."

On February 18, following intense backlash from the biotech industry, the FDA reversed course and agreed to review Moderna's application. Under the deal, the FDA will review the vaccine for adults 50 to 64 through its regular approval pathway, and for adults 65 and older via accelerated approval with a requirement that Moderna run a post-marketing confirmatory study using a high-dose flu vaccine as comparator. The review deadline is August 5, 2026. While the reversal was welcomed, the episode underscored the regulatory unpredictability that had already prompted Moderna to halt new vaccine investment. As NPR reported, the company agreed to the additional study requirements to salvage the application.

The Wall Street Journal editorial board condemned Prasad's decision, writing that it was "arbitrary government at its worst" and asking whether the White House understood the harm being done to public health. The editorial noted that Prasad had also rejected a gene therapy for the fatal rare disease Hunter syndrome despite the company following FDA guidance precisely—the third rare disease drug he had blocked in as many months.

Moderna Halts Vaccine Investment

On January 22, 2026, Moderna CEO Stéphane Bancel told Bloomberg TV at the World Economic Forum in Davos that the company would no longer invest in new late-stage vaccine trials for infectious diseases. Asked if the anti-vaccine climate would affect Moderna's business, Bancel replied: "100%."

"You cannot make a return on investment if you don't have access to the U.S. market, or because of delays—regulatory-wise—or because your market is much smaller, because you don't have a recommendation by the government," Bancel said.

Vaccines for Epstein-Barr virus, herpes simplex, and shingles have been shelved. The company has discontinued four clinical mRNA programs, cut its workforce by 10%, and is pivoting its focus to oncology.

Pfizer CEO Albert Bourla, also at Davos, said the administration's vaccine policies were "almost like a religion" and "anti-science."

Broader Pattern of Anti-Vaccine Actions

The administration's vaccine policy changes extend beyond the schedule overhaul and Moderna rejection:

• mRNA research defunded: In August 2025, HHS canceled approximately $500 million in BARDA contracts for mRNA vaccine development, claiming that mRNA vaccines "fail to protect effectively against upper respiratory infections"—a claim contradicted by extensive peer-reviewed evidence.
• Bird flu vaccine terminated: HHS canceled a contract worth nearly $600 million with Moderna to develop a vaccine against avian influenza in humans, amid an ongoing outbreak in U.S. poultry and cattle.
• COVID vaccine access narrowed: The FDA tightened eligibility criteria for COVID-19 vaccines, and Kennedy's reconstituted ACIP recommended making COVID shots less routine.
• Military flu mandate lifted: Defense Secretary Hegseth made the flu vaccine optional for all troops effective April 21, 2026—a policy reversed for recruits in June after the Lackland outbreak described above.
• Thimerosal recommendations rescinded: In summer 2025, Kennedy rescinded federal recommendations for all flu vaccines containing thimerosal, a mercury-based preservative the anti-vaccine movement has falsely linked to autism.
• Vaccination funding clawed back: The CDC pulled back $11 billion in COVID-era grants that local health departments were using to fund vaccination programs. A federal judge later ordered HHS to distribute the money. The NIH also yanked dozens of research grants supporting studies of vaccine hesitancy.
• CDC website altered: Kennedy directed the CDC to walk back its decades-old statement that vaccines do not cause autism, changing the webpage to say health authorities have ignored evidence of a link—a claim that has been extensively and repeatedly debunked by large-scale studies.
• FDA staffing disrupted: Prasad's management has caused morale at the FDA to fall and triggered an exodus of veteran staffers, according to the Wall Street Journal.

Blocking Publication of Research Showing Vaccines Are Safe

The administration has also moved to suppress its own scientists' findings when those findings support vaccine safety. A New York Times investigation published May 5, 2026, found that FDA officials had blocked publication of several studies supporting the safety of widely used COVID-19 and shingles vaccines—research that cost millions in public funds and analyzed millions of patient records. An HHS spokesman, Andrew Nixon, confirmed the withdrawals, saying the studies "drew broad conclusions that were not supported by the underlying data" and that the FDA had acted "to protect the integrity of its scientific process."

In October 2025, FDA scientists were directed to withdraw two COVID-19 vaccine safety studies that had already been accepted for publication in peer-reviewed journals. One, posted earlier on a preprint server, reviewed the records of about 7.5 million Medicare beneficiaries over 65 and examined 14 potential adverse outcomes—including heart attacks, strokes, and Guillain-Barré syndrome—in the days after vaccination; it found a statistically significant elevated risk for only one, anaphylaxis (about 1 in a million) from the Pfizer vaccine. It was withdrawn after acceptance by the journal Drug Safety. The second study examined 4.2 million recipients aged 6 months to 64 years across 17 conditions, found only the rare adverse effects already known to be associated with the vaccines, and concluded that "the benefits of vaccination outweigh the risks." It was withdrawn from the journal Vaccine; its withdrawal was first reported by STAT News.

In February 2026, top FDA officials declined to sign off in time for staff to submit two abstracts on the Shingrix shingles vaccine to a major drug-safety conference. One study found the vaccine's efficacy consistent with pre-approval clinical trials; the safety study found an elevated but low risk of Guillain-Barré syndrome already noted on the vaccine's label. Separately, Dr. Jay Bhattacharya, while serving as interim CDC leader, canceled publication of a report concluding that the COVID vaccine sharply reduced the odds of hospitalization and emergency-room visits, citing study limitations and writing that "we cannot afford to lower our standards."

The study Bhattacharya blocked did not stay buried. On June 23, 2026, it was published in JAMA Network Open, a peer-reviewed journal of the American Medical Association, after originally being scheduled for release in March in the CDC's flagship Morbidity and Mortality Weekly Report (MMWR). Examining adults who visited a hospital or urgent care with Covid-like symptoms across seven states from September to December 2025, the study found that the 2025–26 Covid vaccine lowered the odds of a Covid-related emergency-room or urgent-care visit by 50% and of hospitalization by 55%. Bhattacharya had raised his methodological objections only after the paper had cleared scientific review and MMWR editors had approved it. His concern centered on the study's "test-negative design"—which compares the vaccination status of people who test positive for Covid with those who test negative—arguing in a Washington Post op-ed that the method disregards data on people who were never hospitalized and that its effectiveness estimates "could be an overestimate or an underestimate; it's impossible to tell." He said he preferred longitudinal cohort studies, which follow vaccinated and unvaccinated people over time—an approach outside experts note is more expensive and slower. Natalie Dean, an Emory University biostatistician who peer-reviewed the JAMA study and wrote an accompanying editorial calling the test-negative design "an important and practical approach," said its quality was unchanged from the CDC's own scientific review and that researchers have long agreed the method's known limitations do not undermine its conclusions: "It just feels funny that this has become the difference between whether or not something makes it out in MMWR." She added that she worried the tool would "get caught up in some culture war."

Outside experts who reviewed the withdrawn studies at the Times' request found no basis for suppressing them. Dr. Caleb Alexander of Johns Hopkins said there was "nothing inherently problematic regarding these reports," and University of Pennsylvania biostatistics director Jeffrey Morris said they were "generally well done." Dr. Aaron Kesselheim, a Harvard professor who studies FDA regulation, called the request to pull the papers an act of "censorship" that "at any other time in history" would have prompted "congressional hearings and resignations." Dr. Jeanne Marrazzo, the former NIAID director fired by Kennedy, called the withdrawals "a pretty active act of sabotage," warning that "this black box of decision making around data suppression should be having people very alarmed." The Times noted the contrast with the administration's looser standards for releasing vaccine-critical material: a memo by Dr. Vinay Prasad, then head of the FDA's vaccine division, had drawn wide coverage by claiming the COVID vaccine was linked to 10 children's deaths—a conclusion the agency never substantiated.

CDC-Funded Study to Generate Doubt About Hepatitis B Vaccine

A Rolling Stone investigation published February 20, 2026, revealed that CDC political appointees allied with Kennedy circumvented scientific and ethical safeguards to rush-fund a $1.6 million research grant for a controversial vaccine study in Guinea-Bissau.

The study, a randomized controlled trial enrolling over 14,000 infants, proposed to give only half the infants a birth dose of the hepatitis B vaccine—proven safe over decades—in a country where one in five adults carries hepatitis B and mother-to-infant transmission rates are high. The research would examine whether the birth dose had potentially negative secondary effects, such as skin ailments or neurodevelopmental disorders.

The grant originated from a direct appeal by Danish researcher Christine Stabell Benn to Lyn Redwood, a Kennedy political appointee at HHS who had previously served as president of Children's Health Defense, the anti-vaccine organization Kennedy founded. Redwood wrote back that "The Secretary has followed your work...over the years."

Rolling Stone found that the proposal bypassed the CDC's standard scientific review process entirely. Rather than being vetted by a scientific center with relevant expertise—a process that can take over a year—it was routed directly from the director's office to grant management officials and approved in just 10 days. The grant listed two non-scientists from the director's office—a 24-year-old former DOGE operative and an anti-vaccine activist—in the role normally filled by subject-matter experts. Seven current and former CDC employees told Rolling Stone that the proposal set off alarm bells internally; one scientist refused to even have it sent to their inbox.

The study's ethical review also failed to meet U.S. standards. Rolling Stone found that the Guinea-Bissau ethics committee that approved the study had a lapsed registration with HHS (expired since 2018), only four active members instead of the required five, and that the approval letter bore the name of a committee president who told Rolling Stone he had resigned three years earlier and that his name was used without his knowledge. The study also did not undergo ethics review by either the CDC or the University of Southern Denmark, the listed grantee.

The World Health Organization released a statement on February 13 expressing "significant concerns" with the study's scientific justification and ethical safeguards. Guinea-Bissau's foreign minister told Reuters on February 18 that the study had been closed, though the lead researcher said she was working to restart it.

Infectious disease specialists drew a direct line between the study and the administration's policy goals. Dr. Jake Scott of Stanford Medicine told Rolling Stone: "They are funding an unsolicited study to generate doubt about a vaccine that they have already decided to pull back." The CDC's former chief medical officer, Dr. Debra Houry, called the study "unjustifiable" and said it was "unfathomable that the CDC's name is even implicated in this."

Expert and Industry Response

Gary Nabel, former head of the NIH Vaccine Research Center and former chief scientist at Sanofi, called the FDA's Moderna rejection "an unprecedented action that really violates the basic principles of a data-driven regulatory agency." He added: "It's a destructive precedent that will undermine the future of vaccine development and the preeminence of American research."

In November 2025, a large group of biotech investors and executives wrote a letter expressing concern about "decisional volatility" and turmoil at the FDA.

As Alex Tabarrok summarized: "An administration that promised medical freedom is delivering medical nationalism: fewer options, less innovation, and a clear signal to every company considering pharmaceutical investment that the rules can change after the game is played."