Last month, JAMA Network Open published an article led by researchers from the Centers for Disease Control and Prevention examining the effectiveness of the 2025-26 covid-19 vaccine. This would not be especially noteworthy, except this was the same research rejected by the CDC’s own flagship journal after objections from its acting director. Moreover, his reasoning could have major implications for future vaccine recommendations.
The study was authored by members of a research collaborative between the CDC and multiple health systems, including Kaiser Permanente, Intermountain Health and Columbia University. Established in 2019, the network evaluates the effectiveness of vaccines and treatments against respiratory viruses across different age groups and populations. Previous reports have assessed the flu vaccine’s effectiveness during pregnancy and antibody treatment to protect newborns against respiratory syncytial virus.
Since the beginning of the covid pandemic, the collaborative contributed to pivotal reports in the CDC’s Morbidity and Mortality Weekly Report as well as in leading medical journals such as JAMA and the Lancet. These studies have helped answer practical questions about how well a vaccine matches circulating strains and how long protection lasts. They have also guided recommendations about who should receive updated vaccines and how often.
As with many of the collaborative’s previous reports, researchers analyzed data from more than 100,000 adults who sought care for respiratory illnesses at emergency departments, urgent care centers and hospitals between September and December 2025. They found that the updated booster reduced covid-related emergency visits by 50 percent and hospitalizations by 55 percent.
These findings, which were consistent with past years’ studies, provided strong support for the continued usefulness of the vaccine. They also aligned with a separate JAMA Network Open study from five European countries, which concluded that the 2025-26 booster reduced health care visits for symptomatic covid by 59 percent among older adults during the first two months after vaccination, with waning protection over time.
Yet, as my Post colleagues reported, its publication in the MMWR, initially slated for March, was delayed and then ultimately blocked. Acting CDC director Jay Bhattacharya said this was because of the study’s methodology, specifically its “test-negative” design.
This research method compares vaccination rates among people who seek medical care for similar symptoms and test positive for the virus with those who test negative. To be sure, it is not as rigorous as following large groups of vaccinated and unvaccinated people over time to compare who becomes infected, but it is much faster and far more practical. For viruses such as the coronavirus and influenza, which evolve quickly and require frequent updates to vaccines, waiting years for answers would leave health officials without crucial up-to-date information.
Plus, as an accompanying editorial explained, the test-negative design has been widely used for decades to evaluate vaccines for respiratory viruses in real-world settings. Like any study design, it has limitations, but these are well-understood and researchers have developed ways to mitigate them.
The study’s eventual publication is the right outcome, but the process leading up to it raises three concerns. First, the delay has consequences. The MMWR exists to rapidly publicize findings with immediate public health importance. Historically, the CDC has published estimates for interim vaccine effectiveness there first to provide real-time guidance to clinicians and patients. Had these findings been disseminated in March, more people might have decided to receive the updated covid vaccine in the spring.
Second, this episode did not occur in isolation. Earlier this year, the Department of Health and Human Services altered the childhood immunization schedule by removing universal recommendations for six diseases. HHS Secretary Robert F. Kennedy Jr., who has called covid shots “the deadliest vaccine ever made,” replaced all 17 members of the CDC’s influential vaccine advisory committee and is now rewriting its charter to exert greater influence over vaccine access. Against that backdrop, it seems the problem was less the methodology than the findings.
Third, even if Bhattacharya’s complaint about the study design is taken at face value, it raises troubling questions. The test-negative design forms the backbone of vaccine effectiveness monitoring. If the CDC starts rejecting this approach, how will researchers evaluate vaccines against common respiratory viruses going forward? And what other vaccine studies will be considered methodologically unacceptable?
Unless, of course, that is the goal. If every study showing vaccines work can be dismissed as flawed, then no amount of evidence will ever be enough.
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