The acting director of the Centers for Disease Control and Prevention has delayed publication of a CDC report showing the covid-19 vaccine cut the likelihood of emergency department visits and hospitalizations for healthy adults last winter by about half, according to two scientists familiar with the decision. The scientists spoke on the condition of anonymity for fear of retaliation.
The move has raised concerns among current and former officials that information about the vaccine’s benefits are being downplayed because they conflict with the views of Health Secretary Robert F. Kennedy Jr., who has been an outspoken critic of the shots.
The delay, which has not been previously reported, offers a window into how vaccine policy is being shaped behind the scenes, even as the Trump administration has sought to soften its public posture on controversial actions ahead of the midterm elections.
The report had been scheduled for publication March 19 in the CDC’s flagship scientific journal, the Morbidity and Mortality Weekly Report, the scientists said.
Between September and December last year, healthy adults who received the vaccine reduced their likelihood of emergency department and urgent care visits by 50 percent and cut the likelihood of covid-associated hospitalizations by 55 percent, compared with those not receiving a 2025-2026 vaccine dose, according to a summary of the report obtained by The Washington Post.
The report had cleared the agency’s scientific-review process, the scientists said, but now it has been delayed by acting CDC director Jay Bhattacharya over concerns about the methodology, the scientists said. The same methodology has long been used by the CDC to evaluate vaccine effectiveness for respiratory viruses, including influenza. A report about flu vaccine effectiveness this past winter — using the same methodology — was published in the MMWR a week earlier.
That methodology was also used in a 2021 study on covid vaccine effectiveness in clinics and hospitals published in the New England Journal of Medicine. Vaccine effectiveness estimates using the same methodology have also been published in other peer-reviewed journals, including JAMA Network Open, the Lancet and Pediatrics.
Andrew Nixon, a spokesman for the Department of Health and Human Services, which oversees the CDC, said in a statement, “It’s routine for CDC leadership to review and flag concerns about MMWR papers, especially relating to their methodology, leading up to planned publication.” He said Bhattacharya expressed concerns about “the observational method used in the study to calculate vaccine effectiveness, and the scientific team is working to address these concerns.”
Nixon added, “Dr. Bhattacharya wants to make sure that the paper uses the most appropriate methodology for such a study.”
An HHS official, speaking on the condition of anonymity to discuss internal processes, said Bhattacharya was not in a position to review the earlier CDC flu vaccine effectiveness study. Bhattacharya would have raised the same concern over its design, the official said.
Kennedy, the founder of a prominent anti-vaccine group, has been an outspoken critic of covid shots, once referring to them as the “the deadliest vaccine ever made.” Last year, Kennedy posted a video on X directing the CDC to no longer recommend the covid vaccine for healthy pregnant women and children, an unprecedented move that bypassed the CDC’s long-established scientific process that relies on its federal vaccine advisory panel to make recommendations to the agency. Kennedy’s action drew widespread criticism from medical and public health experts.
“The secretary has already taken steps to try and remove the availability of the vaccine from children and others, so if you’re putting out an MMWR that the vaccine is effective at preventing hospitalizations and medical care visits … that message is not line with the direction you’ve been taking with the removal of the vaccine,” said Dan Jernigan, who oversaw the CDC’s vaccine safety office.
He was among three senior leaders who resigned from the agency last summer after then-CDC director Susan Monarez was ousted following clashes with Kennedy over vaccine policy.
Jernigan, who headed CDC’s influenza division for six years, said the methodology used in the covid vaccine report had been routinely used to measure influenza vaccine effectiveness for 20 years.
The methodology, known as test-negative design, looks at people who are already sick enough to seek care, test them and then compare vaccination rates between those who test positive for the disease and those who don’t. That is different from randomized controlled trials in which patients do not know who gets the vaccine and who doesn’t and researchers then compare who gets sick.
Scientists say that approach is impractical for covid vaccines because it is difficult to enroll enough patients and many patients feel strongly enough about the shots that they would not agree to a study in which they might not know whether they received a vaccine. Some scientists say using such an approach would be unethical because the current recommendation is to give the vaccine.
Jernigan said the test-negative design used to measure effectiveness of flu and covid vaccines is not perfect but is well suited for monitoring how the vaccines are performing in the real world.
The design looks only at people seeking medical care, for example, and not those who are not seeking care. “It’s a real-world approach where you can’t control differences between people who get vaccinated and those who don’t, and how that influences their likelihood of getting infected,” Jernigan said.
Another HHS official, speaking on the condition of anonymity to share internal discussions, said the method in question is prone to bias. It analyzed a hospitalized sample of patients, for example, that is not representative of the population at large. Bhattacharya is expected to meet with CDC scientists for additional discussions about the report, the official said.
The episode reflects competing pressures inside and outside the administration over how far to go on vaccine policy. While some officials have tried to hold off on further changes ahead of the midterms, outside allies have been urging Kennedy to go further on questioning vaccines.
Some of Kennedy’s handpicked vaccine advisers had considered moving to stop recommending covid mRNA shots at a planned meeting, The Post previously reported. But that plan was ultimately dropped, according to two people familiar with the discussions.
Lauren Weber contributed to this report
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