Fifty percent. That is how much the 2025–2026 COVID-19 vaccine reduced emergency department and urgent care visits among healthy adults between September and December of last year, according to a CDC study that had cleared the agency’s full scientific review process. Hospitalizations dropped by 55 percent in the vaccinated group compared to those who skipped the shot.

The findings were scheduled for publication March 19 in the Morbidity and Mortality Weekly Report, the CDC’s flagship journal. The study never appeared. Acting CDC director Jay Bhattacharya personally intervened to block its release.

A methodology the CDC has used for decades

Bhattacharya objected to the study’s methodology, arguing it produced an inaccurate picture of vaccine effectiveness, an administration official told the New York Times. The approach — known as test-negative design — examines patients sick enough to seek medical care, tests them, and compares vaccination rates between those who test positive and those who test negative.

The CDC has used this same design to evaluate flu vaccine effectiveness for roughly 20 years, according to Dan Jernigan, who headed the agency’s influenza division for six years. Estimates derived from the method have been published in the New England Journal of Medicine, the Lancet, JAMA Network Open, and Pediatrics.

A flu vaccine effectiveness report using the identical methodology was published in the MMWR a week before the COVID study was pulled.

HHS spokesperson Andrew Nixon said in a statement that Bhattacharya wants “to make sure that the paper uses the most appropriate methodology.” An HHS official added that Bhattacharya was not in a position to review the earlier flu study — but “would have raised the same concern over its design.”

Political appointees don’t normally do this

Dr. Debra Houry, who served as the CDC’s chief medical officer before resigning in August, described the intervention as highly unusual. “A political appointee at CDC would be very rarely involved in a review or decision regarding MMWR,” she said.

The MMWR has historically operated with significant editorial independence. Studies clear a rigorous internal scientific review before publication. Bhattacharya intervened after that process was complete.

Jernigan, one of three senior CDC officials who resigned last summer after then-director Susan Monarez was ousted following clashes over vaccine policy, connected the dots. The study’s conclusions — that COVID shots significantly reduce hospitalizations — run counter to the direction Health Secretary Robert F. Kennedy Jr. has taken the department. Kennedy, who founded a prominent anti-vaccine group before his cabinet appointment, once called COVID shots “the deadliest vaccine ever made.” Last year, he directed the CDC to stop recommending the vaccine for healthy pregnant women and children, bypassing the agency’s established scientific advisory process.

What happens now

Bhattacharya, who also serves as director of the National Institutes of Health, is expected to meet with CDC scientists to discuss the report. His acting CDC directorship expired last month when the administration failed to nominate a permanent replacement, though he retains broad oversight authority.

Some of Kennedy’s handpicked vaccine advisers had considered recommending an end to COVID mRNA shots entirely, according to two people familiar with the discussions, though that plan was ultimately dropped. The White House has indicated it wants to tamp down vaccine-related controversy ahead of the midterm elections.

As of this week, the study remains unpublished. The data inside it is now more than three months old.

Sources