Several shots lost their recommendation from the US Centers for Disease Control and Prevention (CDC) after a judge’s stay against changes made by the Trump administration – which may affect access to the shots in some states. And no new vaccine recommendations may be made as long as the vaccines committee is halted.

Access to existing vaccines – and the future development of new vaccines – has been increasingly called into question under the second Trump administration, as the now-halted Advisory Committee on Immunization Practices (ACIP) made controversial recommendations and health officials made unilateral changes to routine vaccines, with long-term and global implications.

Recommendations for the current annual flu and Covid shots no longer exist, and the recommendation for a new shot to protect babies against RSV (respiratory syncytial virus) is also on hold. It’s not clear if new shots will be recommended in coming months, even in anticipation of respiratory virus spikes.

“We could see delays in updates of vaccines,” said Jen Kates, senior vice-president and director of the Global and Public Health Policy Program at KFF, a health policy non-profit. “We’re going into some pretty uncharted territory.”

America’s vaccines landscape has been thrown into greater tumult after a judge essentially overturned all decisions made by the vaccine advisers, who were hand-picked by Robert F Kennedy Jr, the secretary of the US Department of Health and Human Services (HHS) and a longtime vaccine opponent.

Brian Murphy, a US district court judge, issued a stay on vaccine changes after a lawsuit brought by the American Academy of Pediatrics (AAP) against decisions made both by ACIP and directly by health officials. Although the lawsuit didn’t challenge recommendations for new shots, the stay appears to have included them.

“The whole thing got thrown out,” said Sarah DesPres, a former counselor to the HHS secretary for public health and science during the Biden administration and a consultant to nonprofits on vaccines.

In addition to recommendations for the most recent season’s flu and Covid shots, the recommendation for Merck’s RSV monoclonal antibodies also ended, in the midst of RSV season – though another RSV shot for babies, Beyfortus, is still recommended.

Some insurance providers said they would continue to cover all vaccines recommended as of September 2025, “but this is a new recommendation”, DesPres pointed out, so it’s not clear if insurers will cover it.

The tumult also has implications for vaccines in the pipeline, like Moderna’s new flu shot and Pfizer’s new Lyme vaccination, which has shown promising results in trials.

Although the US Food and Drug Administration (FDA) has not made a decision on Moderna’s new flu shot – after initially rejecting the application outright – vaccine advisers usually review the data before approval in case they need to make a recommendation quickly. Typically, the ACIP working group on flu vaccination would already be reviewing the confidential data from Moderna, for example, DesPres said.

If the new flu shot is approved by the FDA but not recommended by the CDC or ACIP, it’s not clear if insurers (also known as payers) will cover it.

“I don’t know how the payers will respond to that,” DesPres said.

Professional organizations have stepped into the gap to make vaccination recommendations based on publicly available data – but data on vaccines not yet on the market is often shared with ACIP confidentially.

“When you’re talking about a new vaccine, it just becomes a little more challenging, because you’re not going to have as much data about it,” DesPres said.

There are also questions about whether pharmacists may administer Covid and flu vaccines without existing recommendations. Pharmacists and providers are protected against liability in administering Covid shots under the Prep Act – but the shots must be recommended by ACIP, so they may not be able to continue administering Covid shots with Prep Act protections.

Flu shots don’t have the same obstacle.

“As long as the payers are prepared to pay for it, and the professional societies can make recommendations, I think that the public will be able to have access to flu vaccines” – at least, to existing flu shots, DesPres said.

‘Increased level of confusion’

About 29 states and Washington DC have moved to decouple their vaccination processes from the ACIP following the committee’s controversial decisions to end recommendations for certain routine childhood vaccines.

But other states still have laws tied to CDC or ACIP recommendations, which means providers and pharmacists may be unable to administer flu or Covid shots. Residents of those states could face challenges accessing them – both now and when the formulations are updated in the fall.

“There’s a lot of uncertainty on this,” Kates said. “We just don’t have the answers right now.”

With no functioning ACIP, new recommendations – for shots that are updated each year or for new vaccines coming out of the pipeline – can’t be made.

There is no confirmed or acting director of the CDC who could make recommendations without the committee’s input. Kennedy, as HHS secretary, has the legal authority to sign off on recommendations, but the AAP lawsuit challenged officials’ abilities to make unilateral decisions on vaccines.

“Potentially Kennedy could make the recommendation, but it would have to meet the satisfaction of what’s laid out in the court ruling,” Kates said.

Health officials could also simply ignore the stay. “This administration has certainly done that in other cases where a judge has ruled one way and they’ve continued to do the behavior. So there’s a lot of different ways this could go,” Kates added.

Last week, the CDC released a new charter for ACIP, elevating the committee’s existing focus on potential vaccine side-effects and adding new expertise areas for members. It also brought in liaison groups that have challenged scientific evidence, especially around vaccines, such as the Association of American Physicians and Surgeons, Physicians for Informed Consent and Independent Medical Alliance.

The new charter seems unlikely to address the judge’s concerns about the way advisers were selected and onboarded. And even if the administration brings on new advisers in a way that isn’t subjected to legal challenges, that process can take months.

For annual respiratory vaccines like the flu and Covid, ACIP usually meets in June to make recommendations that are published by August.

In some ways, the damage is already done, Kates said. Polling already indicates decreased trust in the CDC, and confusion abounds over which vaccines are safe and recommended.

“The increased level of mistrust among the public, among parents, the increased level of confusion – that’s happened. The genie is not going to go back in the bottle,” Kates said. “In a way, it’s partially too late because what has happened in the last year has contributed to this increasing context of confusion and mistrust.”

The loss of trust amid continued misinformation from officials could have serious long-term consequences, Kates added. “If there’s going to be some kind of public health emergency at any point, it would be pretty challenging if more and more people are not trusting the federal government to provide advice about what to do.”

It was clear that the administration is “undermining confidence in vaccines and creating confusion”, DesPres said. “The confusion is really part of the overarching strategy of undermining confidence.” These moves also make it harder for vaccine developers to bring new shots to the public by “creating an uncertain climate”, she said.

The role played by trusted independent advisers in assessing vaccine safety and effectiveness is integral to the process, DesPres said: “We need a functioning ACIP to put out recommendations that providers and patients and the public can trust.” Yet it was not clear when ACIP would function correctly again, she said.