The Centers for Disease Control and Prevention (CDC) has delayed publication of a report indicating that the COVID-19 vaccine reduced emergency department visits and hospitalizations among healthy adults during the 2025-2026 winter season by roughly half, according to two scientists familiar with the matter who spoke on the condition of anonymity. The report, originally slated for release on March 19 in the CDC’s Morbidity and Mortality Weekly Report (MMWR), had already passed the agency’s scientific review process but was held back by acting CDC director Jay Bhattacharya over methodological concerns.

The unpublished study assessed vaccine effectiveness between September and December of last year, finding that vaccinated healthy adults were approximately 50% less likely to seek emergency or urgent care and 55% less likely to be hospitalized due to COVID-19 compared with unvaccinated individuals. The methodology in question, known as a test-negative design, is commonly used by the CDC to evaluate respiratory vaccine effectiveness, including annual influenza vaccines. In fact, a flu vaccine effectiveness report based on the same method was published in the MMWR just a week prior. This approach has also been employed in peer-reviewed journals such as the New England Journal of Medicine and the Lancet.

A spokesperson for the Department of Health and Human Services (HHS), which oversees the CDC, characterized the review and flagging of methodological issues in MMWR papers as routine. They stated that Bhattacharya wants to ensure the study employs the most appropriate methodology and that the agency’s scientific team is working to address his concerns. An HHS official noted that Bhattacharya had not previously overseen the review of the recent flu vaccine report, but suggested he likely would have raised similar questions about its methodology had he done so.

Bhattacharya’s leadership has been marked by tensions surrounding COVID-19 vaccine policy, especially given Health Secretary Robert F. Kennedy Jr.’s outspoken opposition to COVID-19 vaccines. Kennedy, head of a well-known anti-vaccine advocacy group, has publicly questioned the safety and efficacy of the vaccines and criticized the CDC’s existing recommendations. Last year, he bypassed the CDC’s established scientific advisory process by directing the agency not to recommend COVID-19 vaccines for healthy pregnant women and children, drawing widespread criticism from public health experts.

Former CDC officials expressed concern that the delay in publishing data supporting vaccine effectiveness reflects an effort to downplay benefits that contradict the messaging preferred by the current administration. Dan Jernigan, a former CDC senior leader who resigned last summer following conflicts over vaccine policies, noted that the test-negative design method has been a longstanding, accepted tool for evaluating vaccine performance in real-world settings despite inherent limitations. Jernigan emphasized that while not perfect, the method provides valuable insight into vaccine effectiveness by comparing vaccination rates among symptomatic individuals who test positive versus negative for the virus.

Conversely, some internal voices within HHS have questioned the appropriateness of the methodology in this particular study, citing concerns that the hospitalized sample analyzed may not be representative of the broader population and that the test-negative design may introduce bias. Bhattacharya is reportedly scheduled to engage further with CDC scientists to resolve these issues.

Bhattacharya’s temporary appointment as acting CDC director expired on March 25, but he continues to lead the agency as the White House searches for a permanent nominee. The delay in releasing the report highlights ongoing internal debates and external pressures surrounding COVID-19 vaccine policy, especially amid a politically sensitive environment ahead of the midterm elections. Discussions among vaccine advisory groups reportedly considered but ultimately abandoned moves to cease recommending COVID-19 mRNA vaccines.