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The findings are not particularly surprising: Researchers have repeatedly found that COVID-19 vaccines work. But the paper drew public attention after Trump administration political appointees decided in a Centers for Disease Control and Prevention publication.

They argued that the study's design was too vulnerable to false assumptions that could produce flawed results. But many public health researchers maintain it's a reliable design that's been used for decades and offers the best way to understand how well a vaccine is working currently.

“It is critical that we continue to characterize and publish estimates of vaccine effectiveness in populations with changing immunity against evolving viral strains,” wrote Natalie Dean, an Emory University biostatistics expert, in that accompanied the study's publication Tuesday.

The research originally was scheduled to be published this spring in Morbidity and Mortality Weekly Report, the CDC's flagship publication. It had been cleared by the agency's Office of Science but was flagged by acting agency Director Jay Bhattacharya, said Althea Grant-Lenzy, the CDC's chief science officer, in a recent interview.

His decision did not mean the paper would never be published, she said, but rather that the authors had to take time to address his concerns. The authors had the freedom to take the study instead to outside journals, she added.

The study approach, called “test-negative design,” looks at people who were admitted to hospitals or visited emergency rooms with respiratory illnesses. The researchers checked whether patients were vaccinated and then calculated the odds of a positive COVID-19 test among vaccinated patients vs. those who were unvaccinated.

Papers using that methodology have been published — after review by experts in the field — in a number of esteemed journals, including and the .

Bhattacharya has argued the methodology relies too heavily on assumptions and could produce results that were skewed by factors such as prior infections and how different groups of patients behave.

Proponents of the study design say the methodology is built to address differences related to who seeks care, and prior infection shouldn’t be much of an issue because so many Americans have already been infected by the coronavirus. They say no study design is perfect but that U.S. Department of Health and Human Services officials haven’t proposed a realistic alternative for getting real-time estimates of how well vaccines are working.

Earlier this month, the CDC held a forum to discuss the pros and cons of such studies. A panel of speakers at the front of a CDC auditorium included Dean and two others who mostly focused on the methodology's strengths.

But the panel also included one critic: , a Swedish-born biostatistician who — along with Bhattacharya — was a co-author of the Great Barrington Declaration, an October 2020 letter maintaining that pandemic shutdowns were causing irreparable harm.

U.S. Health Secretary Robert F. Kennedy Jr. last year appointed Kulldorff as head of a federal vaccine advisory committee before the biostatistician stepped down to become chief science officer at the HHS planning and evaluation office.

Kulldorff argued that studies with that design can — but shouldn't — include people with different diseases. He also questioned why longer-term studies weren't used to evaluate COVID-19 vaccines.

“We were in a pandemic! That's why!” one person called from the audience.

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The Associated Press Health and Science Department receives support from the Howard Hughes Medical Institute’s Department of Science Education and the Robert Wood Johnson Foundation. The AP is solely responsible for all content.