New data links the origins of the pandemic to raccoon dogs in the Wuhan market

An international team of virus experts said Thursday they found genetic data from a market in Wuhan, China, linking the coronavirus to raccoon dogs for sale there, adding evidence in case the worst pandemic since a century ago by an infected animal trafficked through the illegal wildlife trade.

The genetic data was collected from swabs taken in and around the Huanan seafood wholesale market beginning in January 2020, shortly after Chinese authorities shut down the market on suspicion that it was linked to an outbreak of a new virus became. By then, the animals had been cleared out, but researchers wiped down walls, floors, metal cages, and carts that are often used to transport animal cages.

In samples that came back positive for the coronavirus, the international research team found animal genetic material, including large amounts, that matched the raccoon dog, said three scientists involved in the analysis.

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The jumble of genetic material from the virus and the animal does not prove that a raccoon dog was itself infected. And even if a raccoon dog had been infected, it would not be clear that the animal transmitted the virus to humans. Another animal could have transmitted the virus to humans, or someone infected with the virus could have transmitted the virus to a raccoon dog.

But the analysis found that raccoon dogs – fluffy animals related to foxes and known to be able to transmit the coronavirus – deposited genetic signatures in the same place where genetic material of the virus was left, the three scientists said. That evidence, they said, was consistent with a scenario in which the virus had passed from a wild animal to humans.

A report with the full details of the international research team’s findings has not yet been published. Their analysis was first reported by The Atlantic.

The new evidence will certainly shake up the debate about the origins of the pandemic, even if it doesn’t settle the question of when it started.

In recent weeks, the so-called lab leak theory, which suggests the coronavirus originated in a research lab in Wuhan, has gained traction thanks to a new intelligence assessment by the US Department of Energy and hearings led by the new leadership of the Republican House of Representatives.

But the genetic data from the market offers some of the most tangible evidence yet of how the virus might have spread from wild animals to humans outside of a laboratory. It also suggests that Chinese scientists have presented an incomplete account of evidence that could fill in details on how the virus is spreading in the Huanan market.

Jeremy Kamil, a virus expert at the Louisiana State University Health Sciences Center at Shreveport, who was not involved in the study, said the results showed that “the samples from the market, which contained early COVID lineages, were contaminated with DNA readings from wild animals “.

Kamil said there was a lack of conclusive evidence that an infected animal caused the pandemic. But, he said, “it really puts the spotlight on the illegal pet trade in an intimate way.”

Chinese scientists published a study in February 2022 examining the same market samples. That study had reported samples positive for the coronavirus, but suggested the virus came from infected people shopping or working at the market, not animals sold there.

At one point, the same researchers, including some associated with the Chinese Center for Disease Control and Prevention, sent the raw data from swabs in the market to GISAID, an international archive of viral genetic sequences. (Attempts to reach the Chinese scientists by phone on Thursday were unsuccessful.)

On March 4, Florence Débarre, an evolutionary biologist at the French National Center for Scientific Research, was randomly searching this database for information about the Huanan market when, as she said in an interview, she noticed that more sequences than usual were popping up. Initially confused as to whether they contained new data, Débarre put them aside, only to log back in last week to find that they contained a wealth of raw data.

Virus experts had been waiting for this raw sequence data from the market since learning of its existence in the February 2022 Chinese report. Débarre said she alarmed other scientists, including leaders of a team that published a series of studies last year pointing to the market as originating.

An international team – including Michael Worobey, an evolutionary biologist at the University of Arizona; Kristian Andersen, virus expert at the Scripps Research Institute in California; and Edward Holmes, a biologist at the University of Sydney – began collecting the new genetic data last week.

One sample in particular caught her attention. It had been taken from a cart linked to a specific stall at the Huanan market that Holmes visited in 2014, scientists involved in the analysis said. This pen, Holmes found, contained caged raccoon dogs on top of a separate cage with birds, just the kind of environment conducive to the transmission of new viruses.

The swab taken from a cart there in early 2020, the research team found, contained genetic material from the virus and a raccoon dog.

“We were able to find out relatively quickly that in at least one of these samples there was a lot of raccoon dog nucleic acid along with virus nucleic acid,” said Stephen Goldstein, a virus expert at the University of Utah who collaborated on the new analysis. (Nucleic acids are the chemical building blocks that carry genetic information.)

After coming across the new data, the international team reached out to the Chinese researchers who uploaded the files with an offer to collaborate, while abiding by the online repository’s rules, said scientists working on the new analysis were involved. After that, the sequences from GISAID disappeared.

It is not clear who removed them or why they were removed.

Débarre said the research team is looking for more data, including some from market samples that have never been released. “What’s important is that there’s more data,” she said.

Scientists involved in the analysis said some of the samples also contained genetic material from other animals and from humans. Angela Rasmussen, a virus expert at the Vaccines and Infectious Diseases Organization at the University of Saskatchewan in Canada who worked on the analysis, said the human genetic material is to be expected given that people shop and work there and that there have been human COVID cases was connected to the market.

Goldstein also warned that “we don’t have an infected animal and we can’t definitively prove that there was an infected animal at this booth.” The virus’s genetic material is stable enough, he said, that it’s not clear exactly when it was deposited on the market. He said the team was still analyzing the data and that they had no intention of having their analysis published before they published a report.

“But,” he said, “given that the animals on the market have not been sampled at this time, this is as good as we can hope.”

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