CDC’s chief blocked a COVID vaccine study. Now it’s in a top medical journal.

A COVID vaccine study that the CDC’s chief halted this spring over methodological concerns was published Tuesday in JAMA Network Open, a leading peer-reviewed medical journal.

The analysis used the same methodology that CDC’s interim director had criticized when the paper was not allowed to be published in the weekly scientific report of the Centers for Disease Control and Prevention.

The study, which had been slated for publication in March in the CDC’s Morbidity and Mortality Weekly Report, found that the COVID-19 vaccine reduced the risk of emergency department visits and hospitalizations among healthy adults by about half last winter. The findings were consistent with what researchers have found in past years, that the vaccine can help reduce the risk of severe illness in adults even after accounting for immunity from prior vaccination or infection.

“Science was never the issue,” said Michelle Barron, one of the study’s authors and senior medical director of infection prevention and control for UCHealth, a nonprofit health system in Colorado. “Certainly it was within [the CDC’s] purview to keep it out, for whatever reason, but it was clearly not for scientific reasons that the study was withheld from publication in the MMWR.”

Jay Bhattacharya, CDC’s interim director, delayed publication of the study before it was subsequently not published in the MMWR at all, The Washington Post previously reported. Bhattacharya had concerns about the methods used to calculate vaccine effectiveness, a Health and Human Services spokesman said at the time.

Barron said she believed the study was not published because the findings did not support Health Secretary Robert F. Kennedy Jr.’s agenda that wants to limit the use of COVID vaccine specifically.

Kennedy, the founder of a prominent anti-vaccine group, has been an outspoken critic of COVID shots, once referring to them as the “deadliest vaccine ever made.”

A spokeswoman for the Health and Human Services Department did not directly address the author’s allegation Tuesday that the paper was withheld because it conflicted with the administration’s vaccine agenda. Spokeswoman Emily Hilliard said the CDC evaluates studies using rigorous scientific methods and reviews methodological concerns before publication.

“The CDC does not make scientific determinations based on predetermined conclusions,” Hilliard wrote in an email. “We evaluate the weight of evidence using rigorous methods, communicate uncertainty and limitations, and subject our work to scientific scrutiny before publication.”

A commentary accompanying Tuesday’s JAMA Network Open report said the methodology in question, known as test negative design, has limitations, like any study. But those shortcomings are well understood, actively studied, and outweighed by the method’s practicality for routine vaccine-effectiveness monitoring, wrote Natalie Dean, associate professor of biostatistics and epidemiology at Emory University’s Rollins School of Public Health.

“This is not a controversial study design — this is [the] same design that has been churning out vaccine results for a long time,” Dean wrote in an email. “And from a highly experienced group — CDC plus a network of top vaccine researchers across the country. They are a well-oiled machine.”

She added: “There was no scientific reason to reject this paper. It had undergone internal review, and it clearly meets the standards of peer-reviewed science. It makes my colleagues on edge to see political interference in the scientific process.”

Dean said the methodology is being “unfairly maligned” and worried that efforts to discard it could weaken the nation’s vaccine surveillance system. “Then we’ll be flying blind with respect to influenza, COVID, and RSV vaccine monitoring,” she said.

Between September and December last year, healthy adults who received the COVID-19 vaccine reduced their likelihood of emergency department and urgent care visits by 50% and cut the likelihood of COVID-associated hospitalizations by 55%, compared with those not receiving a 2025-26 vaccine dose, the report found.

Researchers analyzed data from a CDC-funded surveillance network to compare data on adults who sought medical care for COVID-like symptoms and compared outcomes between those who received the updated 2025-26 vaccine and those who had not.