Beijing controls and shapes information as a matter of course, particularly in moments of crisis. But some of the censorship changed the timeline of early infections, a delicate topic as the government faced criticism over whether it responded to the outbreak quickly enough.

There is no evidence that the censorship is designed to conceal a specific scenario for the origins of the pandemic. Some scientists believe that Covid-19 spread naturally from animals to humans. Others argue that it may have spread from a Chinese laboratory. Both sides have pointed to censored data to support their theories.

A man in a Chinese security uniform and a blue medical mask holds a clipboard and gestures with his arms stretched wide. Outside the Wuhan Institute of Virology while a World Health Organization team was visiting in February 2021. The agency’s relationship with China has drawn criticism. Credit...Ng Han Guan/Associated Press

But they have come to agree on one point: The Chinese government’s grip on science has stifled the search for truth.

“I think there’s a major political agenda that is impacting the science,” said Edward Holmes, a University of Sydney biologist who was part of the group that analyzed the sequences containing raccoon dog DNA.

Soon after the group alerted Chinese researchers to their findings, the genetic sequences temporarily disappeared from a global database. “It’s just pathetic that we’re in this stage where we’re having cloak-and-dagger conversations about deleted data,” Dr. Holmes said.

Ever-Changing Dates For a brief moment, the coronavirus appeared to challenge China’s notoriously tough hold on information. On Feb. 6, 2020, when averting a pandemic still seemed possible, the Chinese internet lit up with the death of Li Wenliang, a Wuhan doctor who had been punished for warning about the outbreak before falling ill himself.

Anger boiled over. People sensed that officials had withheld lifesaving information. Across China, they asked: How many had caught the virus in December? Who had known? Why hadn’t more been done?

Around that time, researchers confirmed that the virus had been spreading for weeks from human to human, a fact that Chinese officials had initially dismissed.

The Chinese government reacted by tightening online censorship and wresting control of research. The censorship was piecemeal at first. The Ministry of Science and Technology told scientists to prioritize handling the outbreak, not publishing papers. One European scientist recalled his Chinese collaborators asking him to sign a nondisclosure agreement promising not to share data — on research that had already been published.

Soon, Chinese researchers were asking journals to retract their work. Journals can withdraw papers for a number of legitimate reasons, like flawed data. But a review of more than a dozen retracted papers from China shows a pattern of revising or suppressing research on early cases, conditions for medical workers and how widely the virus had spread — topics that could make the government look bad. The retracted papers reviewed by The Times had been flagged by Retraction Watch, a group that tracks withdrawn research.

Among them were a study that included infected children in southern China; a survey of depression and anxiety among Chinese medical workers who had been treating Covid-19 patients; and even a letter published in The Lancet Global Health by two nurses who described the desperation they felt while working in hospitals in Wuhan.

“Even experienced nurses may also cry,” they wrote.

Journals are typically slow to retract papers, even when they are shown to be fraudulent or unethical. But in China, the calculus is different, said Ivan Oransky, a founder of Retraction Watch. Journals that want to sell subscriptions in China or publish Chinese research often bend to the government’s demands. “Scientific publishers have really gone out of their way to placate the censorship requests,” he said.

As the virus spread, China formalized its controls. A government task force was put in charge of all coronavirus research. Officials in the eastern province of Zhejiang discussed “strengthening the management” of scientific results, records show.

Then on March 9, scientists from top Chinese laboratories published a paper about how the coronavirus might be mutating. The research appeared in Clinical Infectious Diseases, a prestigious journal published by Oxford University Press.

The topic was seemingly apolitical, but it relied on samples collected from patients in Wuhan starting in mid-December 2019. That added to evidence that the virus was spreading widely before the Chinese government took action.

A hospital worker in head-to-toe white gear closes a plastic protective sheath behind a patient lying on a gurney wearing a puffy green winter jacket with a fur collar. In a hospital in Wuhan in January 2020. A letter about the stress of nursing in Wuhan was pulled from a scientific journal.Credit...Hector Retamal/Agence France-Presse — Getty Images

The paper landed just as the government formalized its censorship policy. The following day, China’s Ministry of Education ordered universities to submit research topics to the government task force for approval, according to a directive posted on a university’s website.

Those who did not vet their scientific projects or who caused “serious adverse social impacts” would be punished, the directive said.

The move sent a chill through Chinese science. Schools tightened restrictions on faculty media interviews and instructed professors to comply with the directive, university notices show.

The journal retractions continued, and for unusual reasons.

One group of authors noted that “our data is not perfect enough.” Another warned that its paper “cannot be used as the basis for the origin and evolution of SARS-CoV-2.” A third said its findings were “incomplete and not ready for publication.” Several scientists promised in retraction notices to update their findings but never did.

Because Chinese scientists have been muzzled, it is difficult to neatly distinguish between censored papers and those retracted for legitimate scientific reasons.

The censorship helped the government tell a story.

“China emerged from the pandemic as an early winner,” said Yanzhong Huang, a global health expert at Seton Hall University. “They started to present a new narrative on the outbreak, in terms of not just the origin, but also in terms of the government’s role in responding to the pandemic.”

Two months after posting the paper on coronavirus mutations, Clinical Infectious Diseases published an update. The new version said that the Wuhan samples were not collected in December after all, but weeks later, in January.

The paper’s corresponding author, Li Mingkun of the Beijing Institute of Genomics, did not respond to requests for comment.

After Jesse Bloom of the Fred Hutchinson Cancer Center in Seattle tweeted about the discrepancy, the journal’s editors posted a third version of the paper, adding yet another timeline. This revision says the samples were collected between Dec. 30 and Jan. 1.

A correction merely says that the previous dates had been “unclear.”

In an email to The Times, the journal editors said the correction was “the most appropriate approach to clarify the scientific record.”

An Origin Mystery Chinese scientists ignored requests for years to release information about swabs taken from surfaces at the Wuhan market. That refusal has hindered efforts to determine how the pandemic began.

Dr. Holmes, the University of Sydney biologist, said that as far back as two years ago, he stressed to Chinese researchers the importance of those samples. He even sent them a raccoon dog genome sequence, hoping they would compare it with samples from the market. The researchers did not make the data public until this year.

The World Health Organization, the supposed repository for reliable information about the virus, has only added to confusion about the pandemic’s origins. After errors were found in a major March 2021 report from the organization and China, an agency spokesman, Tarik Jasarevic, promised that officials would correct the mistakes.

Two years later, they have not. The flawed report remains online, painting an inaccurate timeline of the earliest known cases. Mr. Jasarevic now refers questions about the report to the scientists who prepared it.

“That’s a deep and in many ways unforgivable mystery, when the data were demonstrated to be false,” said Lawrence Gostin, the faculty director of Georgetown University’s O’Neill Institute for National and Global Health Law and a longtime W.H.O. adviser. “It either shows that W.H.O. wasn’t insistent enough with China, or that China simply didn’t cooperate.”

Some scientists have become similarly suspicious that China’s censorship has affected the genetic databases that underpin worldwide research.

Dr. Bloom, the Seattle evolutionary virologist, was poring over tables in a scientific paper in June 2021 when he discovered that dozens of gene sequences had been deleted from the Sequence Read Archive, a U.S. government database. The sequences, from early 2020, had been submitted by scientists from Wuhan University. But they had curiously vanished.

The U.S. government’s National Library of Medicine, which manages the database, said at the time that the Wuhan researchers had asked that the sequences be withdrawn — and implied that it was the only instance during the pandemic in which data was removed at the request of scientists in China.

But a March 2022 review by an outside consultant showed that the scientists withdrew another, unrelated sequence on the same day. After Dr. Bloom published a paper about the deleted Wuhan University sequences, they reappeared online — but most had been moved to a database affiliated with the Chinese government.

This controversy and the recent dust-up over the discovered-then-deleted-then-recovered raccoon dog DNA from a separate database have prompted calls for transparency from these genetic archives.

On a cloudy day, a man stands outside a gray stone building with a traditional East Asian-style roof. A building of Wuhan University in 2020. Chinese scientists have been urged to publish at home, rather than in international journals.Credit...Roman Pilipey/EPA, via Shutterstock

Virginie Courtier-Orgogozo, an evolutionary biologist at the French National Center for Scientific Research, said all pandemic-related sequences should be released to global health experts, particularly from early samples. “Among people who were sick in December, we have less than 20 sequences,” she said. (The National Library of Medicine said that sharing withdrawn data was against its policy.)

The Chinese government’s grip on science continues.

The laboratory of a Chinese scientist who studies the wildlife trade was recently shuttered while the authorities investigated unfounded concerns that its research related to the origins of the pandemic, according to a scientist outside China who collaborated on the work.

On April 1, Beijing limited foreign access to the China National Knowledge Infrastructure, an academic portal, curtailing insight into research there. Leaders have urged Chinese scientists to publish in domestic journals rather than international publications.

And this month, Chinese government scientists said it was time to start investigating outside China for the virus’s origins.

It was a nod to the widely refuted claim that the pandemic began somewhere else.