March 30, 2023

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New data linking the origins of the epidemic to raccoon dogs in a 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 to the case evidence that the worst pandemic in a century could have triggered it. An injured animal that was handled through the illegal wildlife trade.

The genetic data was obtained from swabs taken in and around the Huanan Seafood Wholesale Market starting in January 2020, shortly after Chinese authorities closed the market over suspicions it was linked to a new virus outbreak. By then, the animals had been evacuated, but the researchers surveyed the walls, floors, metal cages, and carts often used to transport the animals’ cages.

Three scientists involved in the analysis said that in the samples that tested positive for the coronavirus, the international research team found genetic material belonging to the animals, including large amounts that were identical to a raccoon dog.

The mixing of genetic material from the virus and the animal does not prove that the raccoon dog itself is infected. And even if a raccoon dog did become infected, it wouldn’t be clear if the animal transmitted the virus to humans. Another animal could have passed the virus on to people, or an infected person could have spread the virus to a raccoon dog.

But the analysis proved that raccoon dogs — fluffy animals related to foxes and known to be able to transmit the coronavirus — had deposited genetic signatures in the same place where the virus’s genetic material was left, the three scientists said. They said this evidence is consistent with a scenario in which the virus is transmitted to humans from a wild animal.

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

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

The results showed that “samples from the market that had early Covid strains in them were contaminated with DNA reads from wild animals,” said Jeremy Camille, a virologist at Louisiana State University Health Sciences Center Shreveport who was not involved in the study.

Dr. Kamel said that this does not amount to conclusive evidence that the infected animal caused the spread of the epidemic. But, he said, “it really shines a light on the illegal animal trade in an intimate way.”

Chinese scholars A Stady Looking at the same market samples in February 2022. That study reported that the samples tested positive for coronavirus but indicated that the virus came from infected people who were shopping or working at the market, not from the animals sold there.

At some point, those same researchers, including some affiliated with the Chinese Center for Disease Control and Prevention, published raw data from swabs around the market to GISAID, an international repository of virus genetic sequences. (Attempts to contact the Chinese scientists by phone Thursday were unsuccessful.)

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On March 4, Florence Debar, an evolutionary biologist at the French National Center for Scientific Research, happened to be searching this database for information on the Huanan market, when, in an interview, she noticed more sequences than usual. Confused at first as to whether or not it contained new data, Dr. Debarr aside, only to log back in last week and discover they have a trove of raw data.

Virus experts have been waiting for initial sequence data from the market since they learned of its existence in the Chinese report from February 2022. Dr. Debar said she alerted other scientists, including leaders of a team that published a set of studies last year pointing to the market as the origin.

An international team—which included Michael Worby, an evolutionary biologist at the University of Arizona; Christian Andersen, a virologist at the Scripps Research Institute in California; and Edward Holmes, a biologist at the University of Sydney—began mining new genetic data last week.

One specimen in particular caught their attention. It was taken from a cart linked to a particular stall in Huanan Market that Dr. Holmes had visited in 2014, said the scientists involved in the analysis. Dr. Holmes found that this stall contained raccoon dogs caged atop a separate cage holding birds, which is exactly the kind of environment that leads to to the transmission of new viruses.

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

said Stephen Goldstein, a University of Utah virologist who worked on the new analysis. (Nucleic acids are the chemical building blocks that carry genetic information.)

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After the international team found the new data, they contacted the Chinese researchers who uploaded the files with an offer to collaborate, while adhering to the rules of an online repository, the scientists involved in the new analysis said. After that, the sequences disappeared from GISAID.

It is not clear who removed it or why it was removed.

Dr. Debar said the research team was looking for more data, including some of the market samples that were never published. “What is important is that there is still more data,” she said.

The scientists involved in the analysis said that some of the samples also contained genetic material from other animals and humans. Human genome was expected given that people shopped and worked there and that human COVID-19 cases were linked to the market, said Angela Rasmussen, a virologist at the University of Saskatchewan’s Vaccine and Infectious Diseases Organization in Canada who worked on the analysis.

Dr. Goldstein also cautioned that, “We don’t have an infected animal, and we can’t definitively prove that there was an infected animal in this booth.” He said that the genetic material from the virus is stable enough, and it is not clear when exactly it was deposited on the market. He said the team was still analyzing the data and had not intended to publish its analysis before it issued a report.

“But,” he said, “as the animals that were on the market had not been sampled at that time, it is about as good as we can hope to get.”