The Food and Drug Administration’s recent decision to turn away Moderna’s application for a new flu shot for older Americans is a troubling development in health officials’ piecemeal dismantling of the U.S. vaccine infrastructure.

The biotech firm’s shot had been tested in a huge, late-stage trial of more than 40,000 adults aged 50 and older, where it appeared more effective than the standard flu vaccine most of us take. That should have been enough to at least merit an FDA review — in the past, that is. But it landed at U.S. regulators’ desk at a time of incredible scrutiny of both its underlying mRNA technology and vaccines in general.

This type of dismissal from FDA is rare and typically reserved for applications that have some glaring deficiency. Yet the agency didn’t identify any safety or efficacy problems with the shot, Moderna says.

Stat News reported that Vinay Prasad — who oversees the FDA’s vaccines arm, and in December put out a controversial memo foreshadowing changes to vaccine oversight — had overruled career scientists in turning away the application. Prasad’s critique centered on the study’s design, which he said failed to compare Moderna’s shot to “the best-available standard of care,” or a higher-dose flu vaccine that is recommended for the elderly.

In an interview with Fox News on Wednesday, FDA Commissioner Marty Makary commented on the controversy. “Some say that the trial they conducted was unethical,” he said, because it did not use the high-dose shot in seniors. Yet he also appeared to soften the agency’s stance, suggesting the application could eventually be considered in parts.

It’s fair for the FDA to question aspects of the study, but those concerns typically are aired out during the review, when agency experts spend months poring over the details of an application. Any implications for a vaccine’s use — in this case, whether the shot should be recommended for people over the age of 65 — are then typically determined by the CDC. Prasad’s extreme move upends that open process, and suggests an agency intent on changing the rules midgame.

Prasad’s decision is particularly galling amid this severe flu season, which has underscored the need for more innovative products. The current shots work well at keeping people out of the hospital and saving lives, but they take a long time to make, and that can limit their effectiveness. In order for shots to be ready for the fall, global health agencies must pick the strains that go into the shots in February. But the current outbreak was driven by a new flu strain that emerged over the summer.

An mRNA vaccine, which can be manufactured in just a few months, could in theory yield a vaccine that is better matched to what’s circulating when people actually roll up their sleeves. Now, the arrival of such a shot is at best delayed. At worst, it might not happen at all.

But the issue is much bigger than this one shot. Drug and vaccine developers — not to mention investors — rely on regulatory certainty. Consider the immense size and cost of a late-stage trial for a new vaccine. Moderna’s Phase 3 trial for its flu shot likely cost about $1 billion. (The company declined to give an exact figure, but noted in an interview that Blackstone Life Sciences publicly committed to investing up to $750 million in the shot.)

FDA’s shifting standards for vaccines make such investments far riskier. “The next people, whether it’s us or others, that want to go have a conversation with the agency about a billion-dollar, Phase 3 investment, they’re going to have in the back of their mind, ‘Are they misleading me?’” Moderna President Stephen Hoge told me. “You can imagine the incredible dampening effect that will have on the appetite for investment.”

Moderna’s CEO Stéphane Bancel told Bloomberg last month that U.S. health officials’ attitudes toward vaccines have prompted the company to curtail investment in late-stage studies. It’s not hard to imagine others could follow suit.

The FDA’s decision marks another escalation in Health Secretary Robert F. Kennedy Jr.’s anti-vaccine crusade. So far, his most visible moves have been at the Centers for Disease Control and Prevention, where he replaced the agency’s vaccine advisers with a panel that shares his agenda. That panel made several changes to the CDC’s advice, most notably rescinding the decades-long recommendation that newborns receive the hepatitis B vaccine. The most shocking shift occurred last month, when HHS unveiled a dramatically pared back childhood vaccination schedule.

Those decisions influence insurance coverage of vaccines, affect public perception of their safety and value, and encourage states to make it easier for people to forgo them. That ultimately makes the country more vulnerable to preventable diseases. The result? Needless infections and deaths.

Despite all of that, individuals still can get the shots that CDC has opted against recommending. The barriers might be higher — a vaccine might be harder to find or too expensive to afford, for example — but so far, access still exists.

The FDA, with its oversight of what products can be marketed in the U.S., has power to directly change that. The Moderna flu debacle offers a first glimpse of how that might unfold more broadly for routine shots. The situation already puts a second Moderna vaccine in limbo. That’s because the FDA wanted to consider Moderna’s flu vaccine application before reviewing its combination flu-covid shot, Hoge says.

Regulators in other countries, meanwhile, have continued to review vaccines with the same level of scrutiny and surety as in the past. Moderna, for example, says its flu shot is now under consideration for approval in Australia, Canada and Europe.

Where does that leave the public? Americans might soon find that instead of being the first in line for medical innovations, they will have to wait — or worse, can’t get them at all. That could be because the FDA refuses to approve them, or because companies decide it’s too risky to develop them. Either way, that’ll compromise both America’s innovative edge and its people’s health.

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This column reflects the personal views of the author and does not necessarily reflect the opinion of the editorial board or Bloomberg LP and its owners.

Lisa Jarvis is a Bloomberg Opinion columnist covering biotech, health care and the pharmaceutical industry. Previously, she was executive editor of Chemical & Engineering News.

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