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Covid and flu shots in limbo as Trump administration mulls appeal over vaccine panel

- March 27, 2026


More than a week after a federal judge blocked Health and Human Services Secretary Robert F. Kennedy Jr.’s overhaul of both the nation’s childhood vaccine schedule and a key vaccine advisory committee, the Justice Department has yet to appeal the decision — and ultimately may not.

The Justice Department has 60 days to appeal the decision, which would be by May 15. One HHS official with knowledge of the situation said that no final decision has been made on the agency’s next steps regarding the lawsuit.

It’s the latest example of uncertainty under Kennedy’s leadership. The Centers for Disease Control and Prevention has been without a director for months, with no sign of a new nominee waiting in the wings. And confirmation for his pick for the next surgeon general, Casey Means, appears to have stalled in the Senate.

Meanwhile, work that would normally be ongoing among independent vaccine experts charged with making recommendations to the federal government has stalled indefinitely. Planned meetings about this fall’s flu and Covid shots, for example, are in limbo.

“All the work, as far as I know, has ceased, putting us in a tremendous deficit in recommendations,” said Dr. Jason Goldman, president of the American College of Physicians. “It’s just horrifying to contemplate what damage has been done.”

Over the past year, Kennedy made two major moves in terms of how vaccines are analyzed and ultimately recommended in this country.

In June last year, he abruptly fired members of the Advisory Committee on Immunization Practices (ACIP), a group of independent vaccine experts that advises the CDC. Kennedy tossed aside the usual lengthy vetting process of such members, instead installing a handpicked group of mostly vaccine skeptics. The new group made a series of controversial recommendations, including rolling back long-standing advice to give all newborns a shot to protect against hepatitis B.

Then in January, Kennedy, without formal input from his ACIP group, made sweeping changes to the childhood vaccine schedule, reducing the number of recommended diseases to be vaccinated against from 18 to 11. The change dropped recommendations that all babies should be protected against hepatitis A, hepatitis B, RSV, dengue and two types of bacterial meningitis.

“From a doc’s perspective, we’ve been in limbo for a year,” said Dr. Amy Middleman, an adolescent medicine specialist at UH Rainbow Babies & Children’s in Cleveland. Middleman also serves as the ACIP liaison from the Society for Adolescent Health and Medicine. “We haven’t had a process to look at the evidence. We haven’t had experts vetting the evidence in a public forum.”

The American Academy of Pediatrics and other medical groups sued the Department of Health and Human Services arguing that the changes to the schedule and Kennedy’s ACIP overhaul violated federal law.

On March 16, a federal judge agreed in a decision that put on hold any decisions made by ACIP under Kennedy’s purview, ruling that the health secretary replaced the committee “unlawfully.” Appointments of most ACIP members (13 of 19), were invalidated.

One of those members was Dr. Robert Malone, a Kennedy ally and staunch opponent of Covid vaccines. He decried the ruling on social media, claiming incorrectly the ACIP had been disbanded. He later corrected his statement on X, saying there’d been a “miscommunication” from HHS and posted that he’d resigned from his position.

What happens next?

If the Justice Department appeals, it could also file a motion for emergency relief, requiring the 1st Circuit Court of Appeals to act quickly in deciding whether to stay the March 16 ruling.

Lawrence Gostin, director of the O’Neill Institute for National and Global Health Law at Georgetown University, said the administration’s next move, legally, is tricky. President Donald Trump “does not want HHS to deter vaccinations, at least until the mid-terms,” he said.

Indeed, “the decision to appeal is also a political decision,” said Dorit Reiss, a law professor at the University of California, San Francisco.

As the head of the Department of Health and Human Services, Kennedy still wields power when it comes to vaccines because there is no CDC director or advisory group making recommendations. “One advantage for him is that the decision gives him a ‘get out of jail free card’ for not consulting ACIP right now,” Reiss said.

Timing is key.

A meeting that had been scheduled for this month during which members were expected to discuss Covid shots has been postponed without any indication of it being rescheduled. The committee is supposed to meet again in late June. There is no agenda for that meeting yet. Summer meetings typically involve official recommendations for fall shots, such as those for flu and Covid.

If the vaccine panel doesn’t meet, it’s possible that any recommendation regarding those vaccines could come directly from Kennedy. While the shots would be available to the general public, the recommendations help guide which shots are covered by insurance.

Goldman, who also serves as the American College of Physicians’ liaison to ACIP, said that if and when the group moves forward, there will be a tremendous accumulation of work. It often takes a year or more, he said, for the group to assemble and analyze vaccine information and then present it to the full committee.

“It’s going to be so backlogged,” Goldman said, “it’s going to take an inordinate amount of time to get above water.”



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