Blocked COVID Vaccine Study Finds a Home in JAMA
A study was cleared for publication. Then it wasn't.
Now, months later, that COVID-19 vaccine research has found its way into print anyway — just not where it was originally headed.
Where the Study Was Supposed to Run
The research was originally scheduled to appear this spring in the Morbidity and Mortality Weekly Report, the CDC's flagship scientific publication.
According to the Associated Press, the paper had already been cleared by the CDC's own Office of Science before acting CDC Director Jay Bhattacharya flagged it.
Althea Grant-Lenzy, the CDC's chief science officer, said in an interview that Bhattacharya's decision didn't mean the paper would never be published — only that its authors needed time to address his specific concerns, while remaining free to submit the work to outside journals instead.
That's exactly what happened. The study has now been published in JAMA Network Open, a peer-reviewed journal from the American Medical Association.
📰 Related: Medicare Launches Pilot Expanding Access to GLP-1 Drugs
What the Research Actually Found
NBC News reported the study examined adults who visited a hospital or urgent care with COVID-like symptoms across seven states between September and December last year.
Researchers tested patients for COVID around the time of their visit, then compared vaccination status between those who tested positive and those who tested negative — a method known as test-negative design.
The findings showed the 2025-26 formulation of the COVID vaccine lowered the odds of a COVID-related ER or urgent care visit by 50%, and lowered the odds of hospitalization by 55%.
Papers using this same test-negative methodology have previously been published, after expert review, in journals including Pediatrics and the New England Journal of Medicine.
📰 Related: HHS Seeks New Warning Labels for Testosterone Therapy
Why Bhattacharya Raised Concerns in the First Place
Bhattacharya's objection centers on the test-negative design itself, not the specific numbers this particular study produced.
He has argued the methodology relies too heavily on underlying assumptions, and could produce results skewed by factors such as patients' prior infection history or differences in how various patient groups seek medical care in the first place.
Supporters of the approach counter that the methodology is specifically built to account for differences in who seeks care, and argue that prior infection shouldn't meaningfully distort results given how widely the virus has already spread through the US population.
They also note that HHS officials haven't proposed a realistic alternative method for producing real-time estimates of vaccine effectiveness, leaving test-negative design as the practical tool available despite its acknowledged limitations.
How This Fits a Larger Pattern
This isn't an isolated dispute over one paper's methodology.
Some public health experts viewed Bhattacharya's decision to pull the study from MMWR as a sign of political interference in the CDC's scientific publishing process, or even an attempt to withhold evidence supporting vaccine effectiveness, according to current and former CDC employees who spoke to NBC News.
Earlier this month, the CDC held a public forum specifically to discuss the strengths and weaknesses of test-negative design studies — a sign the agency recognizes the methodology question extends well beyond this single paper.
The episode also lands within a broader period of scrutiny over vaccine-related research and messaging coming out of HHS under Secretary Robert F. Kennedy Jr.'s leadership.
What This Means Going Forward
The study's underlying findings are now in the public record regardless of where it was ultimately published, since JAMA Network Open carries the same peer-review standard the CDC's own journal would have applied.
What remains unresolved is the institutional question: whether future CDC research using test-negative design will face the same review obstacles, and whether researchers will increasingly route around the agency's own flagship publication when their findings touch on vaccine effectiveness specifically.
For now, the case stands as a concrete example of how a methodology disagreement at the top of a federal health agency can shape not just what gets published, but where.
Key Takeaways
- A COVID-19 vaccine effectiveness study, originally cleared for the CDC's Morbidity and Mortality Weekly Report, was blocked by acting CDC Director Jay Bhattacharya.
- The study has now been published in JAMA Network Open instead.
- It found the 2025-26 vaccine formulation reduced the odds of hospitalization by 55% and ER/urgent care visits by 50%.
- The study used a "test-negative design" methodology, previously published in journals including the New England Journal of Medicine.
- Bhattacharya argues the methodology relies too heavily on assumptions; supporters say no better alternative exists for real-time data.
- Some public health experts view the episode as a sign of political interference in CDC's scientific process.
