A scientific sleuth in France has identified previously undisclosed genetic data from a food market in Wuhan, China, that she and colleagues say support the theory that coronavirus-infected animals there triggered the COVID-19 pandemic. Several of the researchers presented their findings on Tuesday to the Scientific Advisory Group for the Origins of Novel Pathogens [SAGO], an expert group convened last year by the World Health Organization [WHO].

“The data does point even further to a market origin,” says Kristian Andersen, an evolutionary biologist at Scripps Research who attended the meeting and is one of the scientists analyzing the new data. If so, the findings weaken the view of a vocal minority that a virology lab in Wuhan was the likely origin of SARS-CoV-2, perhaps when the coronavirus infected a lab worker who spread it further.

Florence Débarre, a theoretician who specializes in evolutionary biology and works at CNRS, the French national research agency, unearthed the data, which consist of genetic sequences posted in GISAID, a virology database, by Chinese researchers. The Chinese team had collected environmental samples from the Huanan Seafood Wholesale Market, which was connected to a cluster of early COVID-19 cases and despite its name also sold a variety of mammals for food. Since Débarre spotted the sequences, GISAID has removed them, noting that this was at the request of the submitter.

Given that the mystery of SARS-CoV-2’s origin has been a matter of intense global interest and divisive debate, the data’s discovery and subsequent disappearance will certainly raise questions about why the Chinese team—which includes the former head of the Chinese Center for Disease Control and Prevention [China CDC], George Gao—did not make the sequences public earlier. Contacted by Science, Gao said the sequences are “[n]othing new. It had been known there was illegal animal dealing and this is why the market was immediately shut down.”

But Andersen and his colleagues hope Gao’s team will now make the sequences widely available. “We have urged China CDC and our colleagues there to release this data as soon as possible,” he says.

Gao’s team used swabs to collect environmental samples from many of the stalls of the Huanan market between 1 January 2020, the day it was shut down, and 2 March 2020. The group reported last year that some of the samples that tested positive for SARS-CoV-2 also had human genetic material, but no DNA from other animals. The team concluded in a preprint posted on Research Square on 25 February 2022 that this “highly suggests” humans brought the virus to the market; Gao and his co-authors said this meant the marketplace was not the origin of the pandemic but simply amplified early spread of SARS-CoV-2.

To some Chinese researchers and officials, that scenario suggested the virus originated outside China and somehow found its way to Wuhan. To lab-leak supporters, it implied the pandemic might have started at the Wuhan lab.

The study has not yet been published in a peer-reviewed journal, and Science first reported last year that some scientists questioned why a graph in the preprint seemed to show animal sequences had been found in the market’s virus-positive environment samples, but offered no data of their identity. The analysis presented to the WHO panel this week now suggests some coronavirus-positive samples collected contained DNA or RNA from raccoon dogs, civets, and other mammals now known to be highly susceptible to SARS-CoV-2.

Débarre says on 4 March she “randomly” came across the previously unknown sequence data while doing other research on GISAID. It took her 5 days to recognize the extent of data available and its potential importance.

Débarre quickly reached out to Andersen and other co-authors of two preprints posted in February 2022 that supported the marketplace origin theory, papers she says helped shift her away from the lab-leak origin to thinking the virus likely came from animals at the Huanan seafood market. Michael Worobey, an evolutionary biologist at the University of Arizona who was a lead author of one of the papers, says he and his collaborators are still analyzing the new genetic information, but it has so far solidified his own view that SARS-CoV-2 had a zoonotic origin. [The two preprints on which he is a co-author were later published by Science.]

“Flo and I have been traveling the same road of being very open to lab-leak ideas, but becoming more and more convinced as more and more evidence comes in that’s just not how it happened, and that it did happen at the Huanan market via the wildlife trade,” Worobey tells ScienceInsider.

Worobey also attended the SAGO meeting with Andersen and virologist Edward Holmes of the University of Sydney, who captured a picture of a raccoon dog for sale in the Huanan market in 2014. [China denied the market traded in live mammals until a June 2021 paper documented their sale for 2 years preceding the pandemic.] “We are hoping to be able to talk more about our analyses once they’re completely wrapped up very soon,” Worobey says.

The group says it reached out to Gao and colleagues to collaborate on analyzing the unearthed market sequences, and soon after that, the data disappeared from GISAID. When Science asked Gao why GISAID removed the sequence data, he did not reply, but he indicated that the data did not resolve the question of SARS-CoV-2’s origin, which he said is “still scientific and open.”

The team’s preprint recently had its status on Research Square—which is linked to the Nature family of journals—change from “posted” to “under review.” Journals often require data deposition before publication, so an imminent publication might originally have prompted Gao’s team to submit the data to GISAID.

Débarre and colleagues plan to post a report of their findings once their analysis is complete, but they hope the Chinese researchers will revise their preprint to include the full sequence data from the Huanan market and repost it first. “As scientists, we can work together on this,” Andersen says.

Andersen adds that he does not expect the new data to convince everyone that the virus originated at the market. He suspects some people may interpret the new information to mean simply that humans infected with SARS-CoV-2 transmitted the virus to the animals at the market.

Joel Wertheim, an evolutionary biologist at the University of California, San Diego, who is collaborating with Andersen and others in the analyses of the newly discovered sequences, says some critics of the spillover hypothesis want more conclusive evidence than science can possibly deliver. “You can’t observe the zoonotic transmission of a novel virus from animals to humans,” Wertheim says. “We’re just never going to get that level of data.”

Maria Van Kerkhove has had a crazy, busy week.

The infectious disease epidemiologist who oversees the World Health Organization’s (WHO’s) program on emerging diseases and zoonoses began Sunday morning with a start: A researcher contacted her and said colleagues had uncovered crucial new data from China that speak to the origin of the pandemic. The researcher told Van Kerkhove—who was preparing to leave her home in Geneva for a flight to Oman—that a team led by George Gao, former head of China’s Center for Disease Control and Prevention, had sat on potentially important genetic sequences from samples it collected in early 2020 at a Wuhan food market where the first cluster of COVID-19 cases occurred.

Last night, The Atlantic and Science published the first news stories about the previously undisclosed data, which was Topic A at a WHO press conference this morning. “These data could have—and should have—been shared 3 years ago,” WHO Director-General Tedros Adhanom Ghebreyesus said. “We continue to call on China to be transparent in sharing data, and to conduct the necessary investigations and share the results.”

The group that contacted Van Kerkhove found that in June 2022, the Chinese researchers had deposited in a virology database called GISAID never-before-seen genomic information from samples taken from stalls at the Huanan Seafood Wholesale Market in Wuhan. The sequences, which GISAID told WHO only became publicly viewable to other researchers this year on 30 January, show mixtures of SARS-CoV-2 and different animal species, including racoon dogs and civets, that China at one point insisted were not for sale at the market. The samples do not prove the pandemic began at the market, but the research team that contacted WHO says they offer support for the theory that the virus likely jumped from animals there into humans.

“All pieces of evidence so far go in the same direction,” says Florence Débarre, an evolutionary biologist who stumbled across the market data from Gao’s team while doing searches on GISAID. Many who instead argue that SARS-CoV-2 leaked from a virology lab in Wuhan reacted to the new findings by saying humans could have infected animals at the market. But to Débarre, such scenarios “rest only on speculation.”

At today’s press conference, Tedros complained that the China market data were recently taken down. (Débarre says that happened after she and others notified Gao that they had found the sequences and wanted to collaborate on an analysis. Gao did not respond to Science’s attempt to clarify what happened.) “These data do not provide a definitive answer to the question of how the pandemic began, but every piece of data is important in moving us closer to that answer,” Tedros said. “And every piece of data relating to studying the origins of COVID-19 needs to be shared with the international community immediately.”

Van Kerkhove had reached out to Gao for an explanation right after she was called Sunday morning, and quickly organized a confidential meeting that took place on Tuesday between Chinese researchers, the team that found the new data, and WHO’s Scientific Advisory Group for the Origins of Novel Pathogens (SAGO) on Tuesday.

This morning her time, she stepped out of the COVID-19 meeting she was attending in Oman to speak with Science about this surprising turn in the origin probe. Foreshadowing her boss’s concern about the apparent lack of data disclosure, she said, “It’s inexcusable. The scientific imperative, the public health importance, the moral importance of this should override everything else that’s happening and it’s not.”

This interview has been condensed for brevity and clarity.

Q: What do you think of what [Débarre and her collaborators] found?

A:It confirms what has been suspected: There were animals at the market that were susceptible to SARS-CoV-2 infection, that the market of course played a really important role, certainly in the amplification of viral spread in the early days of the pandemic. The questions that remain are questions that have yet to be answered. Where did these animals come from? What additional sampling of animals and of environments in markets across Wuhan were done in December 2019 and in January, February, and March 2020? What were the trade routes of these animals? What mixing occurred with other species? Was there any serology done, either in animals or in people that worked at these markets? None of that information is available. This provides more evidence of intermediate hosts, but it doesn’t answer everything, and it doesn’t take away other hypotheses yet.

Q: Why weren’t these data made available sooner?

A:That is the question. Why weren’t these data shared and analyzed with Chinese scientists? We have been calling for any and all data to be made available. Clearly there is more data that is out there. What is not clear is what else is out there.

Q: You and WHO are in a position of saying all hypotheses about the origin are on the table, and having sort of a neutral position. But at what point do the data make WHO ask, “Hey, what it is difference between the two leading hypotheses?”

A:Saying that all hypotheses are on the table doesn’t mean that all hypotheses have equal weight. We have to look at what we have access to, all of the available data that exists. There’s a changing narrative. We know that there’s more information that is out there. But looking at all available data, of course, it suggests that it’s much more likely that we have a zoonotic origin. The challenge is we cannot take the other hypotheses off the table without having evidence to do so.

Q: There’s also the problem of not being able to prove a negative.

A:There are so many additional pieces of information that would be really helpful to understand the story. The fact is we have we have very little information or anything new coming from the Wuhan lab that was working with coronaviruses—it’s just enough to sort of keep that alive and we don’t have the cooperation from China to be able to evaluate and take it off the table or not.

Q: Do these new data have any impact on how you weigh this?

A:Sure. But to date, we have been told by Chinese colleagues that not a single animal has tested positive for SARS-CoV-2 in China.

Q: China told an international team of scientists on a WHO-sponsored COVID-19 origin mission in 2021 that it had tested some 80,000 animals for the pandemic virus, but many were zoo animals and livestock that have nothing at all to do with this. How many raccoon dogs are in that report?

A: We’re pushing for more information through SAGO. We were told that there were additional surveys that were done, including animals that are susceptible to SARS-CoV-2. For them to tell us that not a single animal has tested positive? There are mink farms there, the raccoon dogs, the civets, there are huge numbers of animals there. It calls into question their credibility, which I’ve said to them as well. It is beyond infuriating and frustrating to be in this position and learning later that these data exists, learning that this analysis could have been done in March 2020, if we had had an environment in which collaboration could have taken place. We still don’t have that. And that is scary as hell.

Q: The team that found the new data reached out to Gao to collaborate on this?

A: We facilitated the interaction through SAGO so that they could have that conversation directly. They haven’t responded to them as far as I’m aware. But the fact that we have individuals that were in a situation where it’s this clandestine searching, it shouldn’t be like this. And this shouldn’t be playing out in social media and in media. This should be playing out with a robust debate with everything on the table.

Q: The evidence has consistently suggested to me that China’s message is it didn’t have anything to do with the origin, whether as a lab leak or from an infected animal.

A:They’ve flat out said that. To me, as a scientist, as a public health professional, as someone who works for the World Health Organization, where our only goal is to keep people safe and to prevent these things from happening in the first place, the fact that we’ve had tens of millions of people die from something like this and that there’s the continued fighting and politicization of this does not actually allow us to do our work. It is a distraction and it is unconscionable to me.

Q: How would knowing the origin make a difference?

A:By understanding the exact conditions in which this happened, we can get more refined about how we prevent this happening from the future. Yes, we already know we have to address biosecurity on farms, biosafety and biosecurity in labs. Yes, we know about live animal markets and disinfection within the markets themselves. There’s surveillance that needs to happen there. Yes, we know all of that. But we need to understand how this particular one happened as well, in a country that has excellent lab systems, that has fever surveillance system in place post-SARS [severe acute respiratory syndrome], that has capable scientists that can do this. And why aren’t we looking at the incentives and disincentives for addressing all that?

Q: The new data revealed this week challenge people who say, “Oh, we’re never going to know the origin.”

A:Nobody knows if we will or not. And we’ve learned through the pandemic that anyone who speaks with absolute certainty really doesn’t know. This is a clue and it’s an important one.

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WHO officials said they first learned of the sequences on Sunday. They appear to indicate what many scientists have long suspected: that the seafood market where the first cluster was recorded in the city of Wuhan was also selling wild mammals, including species such as raccoon dogs that are susceptible to Covid-19. They are less clear on whether those animals were infected with the virus.

“We knew raccoon dogs were present in the market. What this shows is that raccoon dogs were present in the same stall where the virus was also deposited,” said Stephen Goldstein of the University of Utah, who belongs to a group of scientists that downloaded the sequences for analysis before they were removed.

A report by the scientists hasn’t yet been published. The Atlantic first reported the scientists’ initial analysis this week.

Dr. Goldstein said that in a stall where five Covid-19 virus samples were found, the amount of raccoon dog genetic material encountered was substantial. That doesn’t prove the animals were infected,he said, but “I think it is quite likely they were infected.”

Dr. Goldstein said there is no proof that even if animals in the market were infected with the virus, that they gave it to humans. Humans could have given the virus to the animals, he said.

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