FDA’s Vaccine Upheaval Has Pharma Worried About the Flu Shot

A whirlwind of new vaccine directives from the Food and Drug Administration has pharmaceutical companies hesitating on new vaccine research — and anxiously waiting to see what the agency does next.

Under increasingly urgent scrutiny are seasonal flu vaccines, which are designed for the following flu season in February and March each year. The FDA is set to release new guidelines describing what will be required for flu vaccine clinical trials, according to an agency planning document.

The Trump administration has been mum on what those requirements will be, but recent decisions and rhetoric from officials have drugmakers worried the government will drop new guidance without warning — and include requirements that could make it difficult or impossible to craft a flu shot each year.

“No one’s told me at this point, ‘We’re getting out of flu, getting out of vaccines,’ but people are certainly concerned about what this means,” one lobbyist in the pharmaceutical space told NOTUS.

Recent FDA decisions, like a request to vaccine manufacturers to put a new label warning of childhood seizures on flu vaccines, have been made on short notice and with little communication, said the lobbyist, who requested anonymity to speak candidly about the industry.

Now, the administration is signaling that it wants to put even more stringent requirements on the annual flu shot.

A 2025 memo written by top FDA official Vinay Prasad called the annual flu vaccine framework an “evidence-based catastrophe of low quality evidence, poor surrogate assays, and uncertain vaccine effectiveness measured in case-control studies with poor methods.”

“We have this pattern of careers being overruled by politicals, and it’s making everybody very concerned about the future of product approvals, or products just staying on the market generally,” the lobbyist said about the dynamics in the FDA.

That newfound unpredictability from the government has already shifted practices at pharmaceutical companies, which have long viewed the FDA as a steady and deliberate decision-maker.

“We have been told by companies where we were supposed to start a clinical trial that it is being delayed,” said Anna Durbin, a professor at Johns Hopkins University who sometimes conducts clinical trials on vaccines for manufacturers. “They are very nervous about submitting any new applications to FDA for this very reason, because they just don’t know.”

Durbin, who declined to name the specific companies on the record, said the pharmaceutical industry is struggling to adapt to the new FDA because its research and development plans can stretch years into the future.

“They look at the risk-return and say, ‘We’re not sure where things are right now … If we wait a year or two until things have sort of become more clear, that’s advantageous to us versus risking it,’” Durbin said of pharmaceutical companies’ decision-making strategy.

At least one company, French pharmaceutical giant Sanofi, has abandoned a planned vaccine entirely. Earlier this year, the company told Fierce Biotech that it had “deprioritized” its mRNA-based seasonal flu vaccine program.

And this week, pharmaceutical company Moderna announced that the FDA had declined to initiate a review of its new mRNA-based influenza vaccine, citing a lack of an “adequate and well-controlled” study that compared the new vaccine against the “best available standard-of-care.”

The FDA notified Moderna of its decision via a “refusal-to-file” letter signed by Prasad, who is a close ally of Secretary Robert F. Kennedy Jr., a critic of the COVID-19 vaccine and the director of the Center for Biologics Evaluation and Research at the FDA.

It is unusual for such a letter to be signed by such a high-level FDA official. Prasad overrode the objections of career scientists at the FDA to reject Moderna’s application, STAT reported.

Moderna called the FDA’s decision “inconsistent with feedback” the company had previously received from the FDA and said it would be requesting a meeting with the agency.

The FDA’s decision to not review a new flu vaccine based on criticism of its study design does not bode well for other seasonal vaccines, one expert told NOTUS.

“If what FDA is trying to do is discourage the industry from investing in trials for respiratory vaccines, this is probably pretty effective,” said Dorit Reiss, a professor at the University of California College of Law, San Francisco, who studies vaccine law. “And it may mean that we won’t have new respiratory vaccines.”

That’s because any delay could have an especially significant impact on seasonal flu vaccines, which are customized each year according to which strains of the virus are circulating.

Prasad, Kennedy and others in the “Make America Healthy Again” movement have pointed to a perceived lack of placebo-controlled, randomized trials on vaccines as evidence that there isn’t enough science to support requiring or even simply recommending vaccines.

Adding new clinical trial requirements could pose a major obstacle to getting a flu vaccine in time for next year’s flu season, one industry source told NOTUS in January.

“Timely flu strain selection depends on robust global surveillance, rapid sharing of viral and genetic data and real-time analysis of how strains are spreading and evolving. It also requires early manufacturing timelines and coordination between public health agencies and vaccine producers to ensure decisions translate quickly into available vaccines,” the source said via email. “Disrupting that process, without clear rationale, is concerning.”

The FDA did not directly answer questions from NOTUS about when the new clinical trial guidance for flu vaccines would be released or what it would entail.

The next month is a critical time of year for seasonal flu vaccines. A World Health Organization committee meets each February to decide which flu strains to recommend for inclusion in that year’s vaccines. After that meeting occurs, a group composed of FDA officials and independent scientists, the Vaccines and Related Biological Products Advisory Committee, meets in early March to decide which strains to direct manufacturers to include in the U.S. seasonal flu vaccine. The strains selected by VRBPAC generally match those recommended by the WHO group.

After strains are selected, manufacturing the seasonal flu vaccine typically takes about six months, so any delay or lengthening of the process could impact its availability next fall.

Last year’s VRPBAC meeting was cancelled; strain selection for the U.S. vaccine was done without the committee’s input. But on Wednesday, a notice posted to the Federal Register announced that this year’s VRBPAC meeting would take place on March 12.

Durbin, who is a member of VRBPAC, said she hadn’t yet received a formal notification from the FDA of the meeting. But so far, she said, “it looks like it’s on track.”