New data links pandemic origins to raccoon dogs in Wuhan market

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

The genetic data comes from swabs taken in and around the Huanan Seafood Wholesale Market from January 2020, shortly after Chinese authorities shut down the market over suspicions it was linked to the outbreak of a new virus. By then, the animals had been cleaned up, but researchers wiped down walls, floors, metal cages and carts commonly used for transporting animal cages.

In samples positive for the coronavirus, the international research team found genetic material from animals, including large amounts that match the raccoon dog, three scientists involved in the analysis said.

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Mixing up genetic material from the virus and the animal does not prove that a raccoon dog was itself infected. And even if a raccoon dog were infected, it wouldn’t be clear that the animal had spread the virus to humans. Another animal may have transmitted the virus to humans, or someone infected with the virus may have transmitted the virus to a raccoon dog.

But the analysis did show that raccoon dogs — fluffy animals related to foxes and known to transmit the coronavirus — have deposited genetic signatures in the same place where genetic material from the virus is left behind, the three scientists said. That evidence, they said, was consistent with a scenario where the virus had passed to humans from a wild animal.

A report with 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 is sure to shake up the debate over the origins of the pandemic, even if it doesn’t resolve the question of how it started.

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

But the genetic data from the market provides some of the most tangible evidence yet of how the virus could have passed from wild animals to humans outside of a laboratory. It also suggests that Chinese scientists have provided an incomplete account of evidence that could include details of how the virus spread in the Huanan market.

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

Kamil said there was no conclusive evidence that an infected animal had caused the pandemic. But, he said, “it really puts the spotlight on the illegal pet trade in an intimate way.”

Chinese scientists had released a study in February 2022 looking at the same market samples. That study had reported samples positive for the coronavirus, but suggested the virus came from infected people shopping or working in the market, rather than from animals being sold there.

At one point, those same researchers, including some associated with China’s Center for Disease Control and Prevention, posted the raw data from marketed smears to GISAID, an international repository of virus genetic sequences. (Attempts to reach the Chinese scientists by phone on Thursday were unsuccessful.)

On March 4, Florence Débarre, an evolutionary biologist at France’s National Center for Scientific Research, happened to be searching that database for information related to the Huanan market when, she said in an interview, she noticed more sequences than usual. Initially confused as to whether they contained new data, Débarre set them aside, but logged in again last week and found they contained a wealth of raw data.

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

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

One specimen in particular caught their attention. It came from a cart linked to a specific stall at Huanan Market that Holmes had visited in 2014, scientists involved in the analysis said. That shed, Holmes discovered, contained caged raccoon dogs on top of a separate cage of birds, just the sort 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 figure out relatively quickly that there was a lot of raccoon dog nucleic acid in at least one of these samples, along with virus nucleic acid,” said Stephen Goldstein, a virus expert at the University of Utah who worked on the new analysis. (Nucleic acids are the chemical building blocks that contain genetic information.)

After the international team stumbled upon the new data, they contacted the Chinese researchers who uploaded the files with an offer to collaborate, according to the online repository’s rules, scientists involved in the new analysis said. Then the sequences disappeared from GISAID.

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

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

Scientists involved in the analysis said some samples also contained genetic material from other animals and humans. Angela Rasmussen, a virus expert at the Vaccine and Infectious Disease Organization at the University of Saskatchewan in Canada who worked on the analysis, said the human genetic material was to be expected given that people were shopping and working there and that human COVID cases was linked 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 in that barn.” The virus’s genetic material is so stable, he said, that it’s not clear exactly when it was introduced to the market. He said the team was still analyzing the data and it was not intended for the analysis to become public until it had issued a report.

“However,” he said, “since the animals present at the market were not sampled at the time, this is as good as we can hope.”

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