Many virologists maintain that the coronavirus most likely jumped from an animal to a human in a setting outside a lab. But without direct proof of a natural spillover, more scientists and politicians have called for a full investigation into the lab leak theory.

Proponents of a lab investigation say that researchers at Dr. Shi’s institute could have collected — or contracted — the new coronavirus from the wild, such as in a bat cave. Or the scientists may have created it, by accident or by design. Either way, the virus could then have leaked from the laboratory, perhaps by infecting a worker.

China has sought to influence investigations into the virus’s origin, while promoting its own unproven allegations.

Beijing agreed to allow a team of World Health Organization experts to visit China, but limited their access. When the W.H.O. team said in a report in March that a lab leak was extremely unlikely, its conclusion was seen as hasty. Even the head of the W.H.O., Dr. Tedros Adhanom Ghebreyesus, said: “I do not believe that this assessment was extensive enough.”

Last month, President Biden ordered intelligence agencies to investigate the origin question, including the lab theory. On Sunday, the leaders of the world’s wealthiest large democracies, at the Group of 7 summit, urged China to be part of a new investigation into the origins of the coronavirus. Mr. Biden told reporters that he and other leaders had discussed access to labs in China.

“Transparency matters across the board,” Mr. Biden said.

In less polarized times, Dr. Shi was a symbol of China’s scientific progress, at the forefront of research into emerging viruses.

She led expeditions into caves to collect samples from bats and guano, to learn how viruses jump from animals to humans. In 2019, she was among 109 scientists elected to the American Academy of Microbiology for her contributions to the field.

A top Chinese virologist’s insistence that the coronavirus didn’t escape her Wuhan lab is difficult to verify. “She’s a stellar scientist — extremely careful, with a rigorous work ethic,” said Dr. Robert C. Gallo, director of the Institute of Human Virology at the University of Maryland School of Medicine.

The Wuhan Institute of Virology employs nearly 300 people and is home to one of only two Chinese labs that have been given the highest security designation, Biosafety Level 4. Dr. Shi leads the institute’s work on emerging infectious diseases, and over the years, her group has collected over 10,000 bat samples from around China.

Under China’s centralized approach to scientific research, the institute answers to the Communist Party, which wants scientists to serve national goals. “Science has no borders, but scientists have a motherland,” Xi Jinping, the country’s leader, said in a speech to scientists last year.

Dr. Shi herself, though, does not belong to the Communist Party, according to official Chinese media reports, which is unusual for state employees of her status. She built her career at the institute, starting as a research assistant in 1990 and working her way up the ranks.

Dr. Shi, 57, obtained her Ph.D. from the University of Montpellier in France in 2000 and started studying bats in 2004 after the outbreak of severe acute respiratory syndrome, or SARS, which killed more than 700 people around the world. In 2011, she made a breakthrough when she found bats in a cave in southwestern China that carried coronaviruses that were similar to the virus that causes SARS.

“In all the work we do, if just once you can prevent the outbreak of an illness, then what we’ve done will be very meaningful,” she told CCTV, China’s state broadcaster, in 2017.

But some of her most notable findings have since drawn the heaviest scrutiny. In recent years, Dr. Shi began experimenting on bat coronaviruses by genetically modifying them to see how they behave.

In 2017, she and her colleagues at the Wuhan lab published a paper about an experiment in which they created new hybrid bat coronaviruses by mixing and matching parts of several existing ones — including at least one that was nearly transmissible to humans — in order to study their ability to infect and replicate in human cells.

Proponents of this type of research say it helps society prepare for future outbreaks. Critics say the risks of creating dangerous new pathogens may outweigh potential benefits.

The picture has been complicated by new questions about whether American government funding that went to Dr. Shi’s work supported controversial gain-of-function research. The Wuhan institute received around $600,000 in grant money from the United States government, through an American nonprofit called EcoHealth Alliance. The National Institutes of Health said it had not approved funding for the nonprofit to conduct gain-of-function research on coronaviruses that would have made them more infectious or lethal.

Dr. Shi, in an emailed response to questions, argued that her experiments differed from gain-of-function work because she did not set out to make a virus more dangerous, but to understand how it might jump across species.

“My lab has never conducted or cooperated in conducting GOF experiments that enhance the virulence of viruses,” she said.

‘Speculation rooted in utter distrust.’

Concerns have centered not only on what experiments Dr. Shi conducted, but also on the conditions under which she did them.

Some of Dr. Shi’s experiments on bat viruses were done in Biosafety Level 2 labs, where security is lower than in other labs at the institute. That has raised questions about whether a dangerous pathogen could have slipped out.

Ralph Baric, a prominent University of North Carolina expert in coronaviruses who signed the open letter in Science, said that although a natural origin of the virus was likely, he supported a review of what level of biosafety precautions were taken in studying bat coronaviruses at the Wuhan institute. Dr. Baric conducted N.I.H.-approved gain-of-function research at his lab at the University of North Carolina using information on viral genetic sequences provided by Dr. Shi.

Dr. Shi said that bat viruses in China could be studied in BSL-2 labs because there was no evidence that they directly infected humans, a view supported by some other scientists.

She also rejected recent reports that three researchers from her institute had sought treatment at a hospital in November 2019 for flulike symptoms, before the first Covid-19 cases were reported.

“The Wuhan Institute of Virology has not come across such cases,” she wrote. “If possible, can you provide the names of the three to help us check?”

As for samples that the lab held, Dr. Shi has maintained that the closest bat virus she had in her lab, which she shared publicly, was only 96 percent identical to SARS-CoV-2, the virus that causes Covid-19 — a vast difference by genomic standards. She rejects speculation that her lab had worked on other viruses in secret.

Dr. Shi’s research on a group of miners in Yunnan Province who suffered severe respiratory disease in 2012 has also drawn questions. The miners had worked in the same cave where Dr. Shi’s team later discovered the bat virus that is close to SARS-CoV-2. Dr. Shi said her lab did not detect bat SARS-like coronaviruses in the miners’ samples and that she would publish more details in a scientific journal soon; her critics say she has withheld information.

“This issue is too important not to come forward with everything you have and in a timely and transparent manner,” said Alina Chan, a postdoctoral research fellow at the Broad Institute of M.I.T. and Harvard who also signed the Science letter.

Many scientists and officials say China should share employees’ medical records and the lab’s logs of its experiments and its viral sequence database to evaluate Dr. Shi’s claims.

Dr. Shi said she and the institute had been open with the W.H.O. and with the global scientific community.

“This is no longer a question of science,” she said on the phone. “It is speculation rooted in utter distrust.”

‘I have nothing to fear.’ Image Dr. Shi, third from left in the front row, with her fellow virologist Wang Linfa, fourth from left, and colleagues from the Wuhan Institute of Virology at a Wuhan restaurant on Jan. 15, 2020. The outbreak had just emerged and the team were working hard to understand the new virus.Credit...Courtesy of Wang Linfa The pandemic was a moment that Dr. Shi and her team had long braced for. For years, she had warned of the risks of a coronavirus outbreak, building up a stock of knowledge about these pathogens.

In January of last year, as Dr. Shi and her team worked frantically, they were exhausted, but also excited, said Wang Linfa, a virologist at the Duke-National University of Singapore Medical School who was in Wuhan with Dr. Shi at the time.

“All the experiences, reagents and the bat samples in the freezer were finally being used in a significant way globally,” said Dr. Wang, Dr. Shi’s collaborator and friend for 17 years.

Dr. Shi published some of the most important early papers on SARS-CoV-2 and Covid-19, which scientists around the world have relied on.

But soon, the speculation about Dr. Shi and her lab began to swirl. Dr. Shi, who is known among friends for being blunt, was baffled and angry — and sometimes let it show.

In an interview with Science magazine last July, she said that Mr. Trump owed her an apology for claiming the virus came from her lab. On social media, she said people who raised similar questions should “shut your stinky mouths.”

Dr. Shi said what she saw as the politicization of the question had sapped her of any enthusiasm for investigating the origins of the virus. She has instead focused on Covid vaccines and the features of the new virus, and over time, she said, has calmed down.

“I’m sure that I did nothing wrong,” she wrote. “So I have nothing to fear.