A Covid vaccine research paper that the acting director of the Centers for Disease Control and Prevention shelved in March has now been published in a peer-reviewed medical journal, revealing that vaccines cut the risk of severe illness by roughly half during last fall and winter.
The study appeared Tuesday in JAMA Network Open, the American Medical Association's respected scientific publication. It was originally slated for release in the CDC's own Morbidity and Mortality Weekly Report, or MMWR, before Jay Bhattacharya raised objections to the methodology after the paper had already passed scientific review and earned the approval of MMWR editors.
The research examined adults who sought care at hospitals and urgent clinics across seven states from September through December with Covid-like symptoms. Investigators compared vaccination rates between those who tested positive for the virus and those who tested negative. The vaccine formulation studied was the 2025-26 version. Results showed a 50% reduction in emergency room or urgent care visits tied to Covid and a 55% drop in hospitalizations.
Bhattacharya's primary concern centered on what researchers call a "test-negative design," a standard epidemiological method that compares the vaccination status of people with confirmed illness to those without it. The acting director argued that longitudinal cohort studies, which track vaccinated and unvaccinated populations over extended periods, represent stronger evidence. Such studies can demand more time and funding than the test-negative approach.
The decision stirred controversy among public health experts who viewed it as political interference in the CDC's scientific independence. The timing amplified those concerns, coming as Health and Human Services Secretary Robert F. Kennedy Jr., who oversees the CDC, has spent years promoting anti-vaccine positions, once describing the Covid vaccine as "the deadliest vaccine ever made."
The Health and Human Services Department defended the delay, with spokesperson Emily Hilliard saying that "applying the highest standards of scientific rigor" required additional review. "Taking time to ensure analyses are methodologically sound and clearly communicated is always preferable to risking error," she said.
In a Washington Post op-ed, Bhattacharya outlined his reservations. Test-negative designs, he argued, exclude people who never sought hospital care and fail to account for variables like prior infections that could skew vaccine effectiveness estimates. He wrote that the method's conclusions could represent either an overestimate or underestimate, making conclusions unreliable.
Yet the scientific community offered a counterpoint. Natalie Dean, an associate professor of biostatistics at Emory University's Rollins School of Public Health who reviewed the JAMA study, noted that researchers have understood test-negative limitations for decades without abandoning the approach as flawed. The study's quality remained unchanged from its CDC review to publication, Dean said. In an editorial accompanying the published paper, she called the test-negative design "an important and practical approach."
Dean acknowledged real constraints in the methodology. People who visit hospitals when sick may trust the medical system more and therefore vaccinate at higher rates than the general population. Study participants who tested negative for Covid carried other respiratory infections, meaning they were not entirely healthy. She proposed that stronger health records documenting who gets tested and why could strengthen such research rather than abandon it.
"I get worried that it's going to get caught up in some culture war, and it's this major tool that we have," Dean said in an interview about the controversy.
The authors of the newly published study defended their methodology as a "convenient and efficient method" for real-world vaccine evaluation. Outside researchers have long recognized the test-negative design's practical merits: cost effectiveness, rapid results, and comparison of groups with comparable healthcare-seeking behavior.
The CDC itself recently hosted a public forum examining the strengths and weaknesses of different vaccine effectiveness study approaches, including cohort studies and randomized controlled trials. The fact that a single methodology became a point of contention significant enough to delay publication struck observers as unusual.
Author Sarah Mitchell: "When a health agency blocks a completed, peer-reviewed study over methodological concerns that experts consider settled, it raises real questions about whether scientific review was the actual issue."
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