CDC-Blocked COVID Vaccine Study Clears Peer Review, Published in JAMA Network Open

What the Study Found

The COVID-19 vaccine effectiveness study, originally cleared for publication in the CDC's Morbidity and Mortality Weekly Report and scheduled for March 19, showed this season's vaccines reduced the risk of an adult needing an emergency room or urgent care visit for COVID-19 by 50% and reduced the risk of COVID-19-associated hospitalization by 55%, according to Healio.

A 55% reduction in hospitalizations is not a rounding error.

The study used a test-negative design: researchers enrolled patients with COVID-like illness, designated those who tested positive for SARS-CoV-2 as cases, and those who tested negative as controls. That methodology is standard. According to CIDRAP News, the same test-negative approach was used in a CDC flu vaccine effectiveness study that ran in MMWR last month without incident.

How It Got Blocked

Jay Bhattacharya, who currently holds the title of NIH Director but has been performing the duties of acting CDC Director while nominee Erica Schwartz awaits a Senate confirmation hearing, halted the study before publication, citing methodological concerns. The Washington Post first reported the block.

The CDC has not had a confirmed director since Susan Monarez was pushed out on August 27, 2025, according to CIDRAP. Bhattacharya is essentially running two agencies simultaneously.

HHS spokesman Andrew Nixon told Healio that "scientific reports are routinely reviewed at multiple levels to ensure they meet the highest standards before publication" and that "the MMWR's editorial assessment identified concern" with the methodology. Nixon did not specify what the methodological defect was or why it disqualified this study but not the flu study using the same design.

A Former CDC Director Calls It Unprecedented

Demetre Daskalakis, MD, MPH, former director of the CDC's National Center for Immunization and Respiratory Diseases, told CIDRAP he was unaware of any prior instance of a report that had already cleared the agency's scientific review process being blocked by leadership before publication.

"Suppressing the standard of science on VE to wait for a perfect study in a system that cannot support it is not a hallmark of transparent scientific expertise," Daskalakis said. He characterized the cancellation as "cherry picking based on the bias of the director and others at HHS who don't fully understand the importance of the methods used."

Daskalakis is a former official in a Democratic-era CDC, which makes him an interested source. His criticism should be weighed accordingly. But his core factual claim—that this was procedurally unusual—has not been rebutted with a counterexample by HHS or CDC.

The Strongest Case for Bhattacharya's Decision

Test-negative designs can overestimate vaccine effectiveness if health-seeking behavior differs between vaccinated and unvaccinated patients, a well-documented concern in the epidemiology literature. Bhattacharya, who holds both an MD and a PhD in economics from Stanford, has published extensively on health economics and study design. If he concluded the study's controls introduced systematic bias, that is a legitimate scientific objection, not automatically a political one.

HHS has not released a written methodological critique, so the public cannot evaluate whether his objection was substantive or pretextual. That opacity is itself a problem, regardless of whether his underlying concern had merit.

How It Got Published Anyway

Jeremy Faust, MD, MS, attending emergency physician at Brigham and Women's Hospital and assistant professor at Harvard Medical School, obtained a copy of the study through an anonymous source and published it on his Substack, "Inside Medicine," according to Healio. It was subsequently accepted and published April 29 in JAMA Network Open, a peer-reviewed journal published by the American Medical Association.

JAMA Network Open's peer review process is independent of the federal government. The study passed it.

"I want people to ask why the government is suddenly not publishing its own noncontroversial science," Faust told Healio.

Context That Matters

This sits inside a broader pattern. In May 2025, HHS Secretary Robert F. Kennedy Jr. removed the COVID-19 vaccine recommendation for pregnant women and healthy children, according to CIDRAP. Kennedy previously called the COVID-19 vaccine "the deadliest vaccine ever made" — a claim contradicted by the CDC's own vaccine safety surveillance data.

CIDRAP notes the Trump administration has been trying to manage political blowback on vaccine policy ahead of the midterms. That context does not prove Bhattacharya's methodological objection was fabricated. But it does mean the administration has a documented political motive to suppress favorable vaccine data, which is exactly why the lack of a written, public methodological critique is damaging.

The Unresolved Question

The MMWR publication process exists specifically so the CDC can rapidly communicate public health data using standardized, pre-agreed methodology. If the test-negative design is now disqualifying for COVID vaccine studies, HHS needs to explain why it was acceptable for the flu vaccine study published in the same journal last month. Until HHS releases a written methodological critique, the public has no way to judge whether this was rigorous science oversight or selective suppression—and that question will trail Bhattacharya's tenure at CDC regardless of what he ultimately does with the vacancy.