Genetic sequences discovered from China market may suggest animal origin of COVID-19 | Science

A scientist in France has identified previously undisclosed genetic data from a food market in Wuhan, China, which he and his colleagues support the theory that coronavirus-infected animals there caused the COVID-19 pandemic. Several of the researchers presented their findings Tuesday to the Scientific Advisory Group on the Origin of New Pathogens (SAGO), an expert group convened last year by the World Health Organization.

“The data point even more to the origin of the market,” says Christian 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 a vocal minority view 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 theorist specializing in evolutionary biology who works at France’s National Center for Scientific Research, discovered the data, which consists of genetic sequences published in GISAID, a virology database, by Chinese researchers. The Chinese team had collected environmental samples from the Huanan Seafood Market, which was linked to a cluster of early COVID-19 cases and despite its name also sold a variety of mammals for food. Since Débarre identified the sequences, GISAID has removed them, noting that this was done at the submitter’s request.

Since the mystery of the origin of SARS-CoV-2 has been a matter of intense global interest and divisive debate, the discovery and subsequent disappearance of the data will certainly raise questions about why the Chinese team—which includes the former head of the Center China’s Center for Disease Control and Prevention (CDC), George Gao–did not release the sequences earlier. Contact from ScienceGao said that sequences are “[n]something new. It was known that there was illegal trade in animals, so the market was closed immediately.”

But Andersen and his colleagues hope Gao’s team will now make the sequences widely available. “We have urged the 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 Huanan market stalls between January 1, the day it closed, and March 2, 2020. The team reported last year that some of the samples tested positive for SARS-CoV-2 it also had human genetic material, but no DNA from other animals. The team came up with a preprint published on Research Square on Feb. 25, 2022, that this “strongly suggests” that people brought the virus to the market — a finding Gao and co-authors wrote meant that the market was not the origin of the pandemic but merely enhanced the early spread of SARS — CoV-2.

To some Chinese researchers and officials, this scenario suggested that the virus originated outside China and somehow found its way to Wuhan. For lab leak advocates, it implied that the pandemic may have started in 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 chart in the preprint appeared to show animal sequences had been found in marketed virus-positive environmental samples but offered no data on their identity. Analysis presented to the WHO panel this week now shows that some of the coronavirus-positive samples collected contained DNA or RNA from raccoon dogs, muskrats and other mammals now known to be highly susceptible to SARS-CoV-2.

Edward Holmes visited the Huanan Seafood Market in 2014 and took this photo of a raccoon dog for sale. New evidence that helped the analysis suggests the site had both SARS-CoV-2 and this susceptible species.Edward C. Holmes

Débarre says she found the previously unknown sequence data “accidentally” on March 4 while doing other research for GISAID. It took her five days to recognize the extent of the available data and its potential significance.

Débarre quickly approached the genetic sequences with Andersen and other co-authors of two preprints published in February 2022 who supported the market origin theory, the documents she says helped her to distance herself from the origin of the laboratory spill and to believe that the virus likely came from animals at the Huanan Seafood Market. Michael Worobey, an evolutionary biologist at the University of Arizona who was the lead author of one of the papers, says he and his colleagues are still analyzing the new genetic information, but so far he has established his own view that SARS-CoV – 2 had zoonotic origin. (The two co-authored preprints were later published by Science.)

“Flo and I are on the same path of being very open to ideas about lab leaks, but increasingly convinced as more and more evidence comes to light that this is not exactly what happened, and that it happened in the Huanan market through the wildlife trade ,” says Worobey ScienceInsider.

Worobey also attended the SAGO meeting with Andersen and University of Sydney virologist Edward Holmes, who captured a photo of a raccoon dog for sale at the Huanan market in 2014. (China denied the market traded live mammals until documented of June 2021 Their sale for 2 years before the pandemic.) “We hope to be able to talk more about our analyzes once they are fully completed very soon,” says Worobey.

The team says they contacted Gao and their colleagues to collaborate on analyzing the discovered market sequences, and soon after the data disappeared from GISAID. when Science asked Gao why GISAID removed the sequence data, he did not respond, but said the data did not resolve the question of the origin of SARS-CoV-2, which he said is “still scientific and open.”

The team’s preprint recently had its status on ResearchSquare—which is linked to Nature journal family—change from “published” to “under review”. Journals often require data to be submitted before publication, so an impending publication could initially prompt Gao’s team to submit the data to GISAID.

Missing data;

Chinese researchers in February 2022 published a preprint that presented this graph to show that several environmental samples from the market that contained SARS-CoV-2 also had human genetic material, but did not offer data on virus samples mixed with other animal species .

A graph depicting environmental genetic samples from the Huanan seafood wholesale market
G. Gao et al., Research Square, 25 February 2022,

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

Andersen adds that he doesn’t expect the new data to convince everyone that the virus came from the market. He suspects that some people may interpret the new information as simply that humans infected with SARS-CoV-2 transmitted the virus to market animals.

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

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