Report finds mixtures of Covid and animals in Wuhan – 03/23/2023 – Health

On January 12, 2020, Chinese investigators scouring a market for clues about the outbreak of a mysterious new disease in the city of Wuhan took samples from a cart of the type used to transport animal cages. They tested positive for the coronavirus.

Three years later, a team of international experts analyzed the genetic content of that sample, which was discreetly uploaded to an international database and made public only this year. In a report released late on Monday, the scientists described in detail for the first time evidence from the sample that they say strengthens the case that illegally traded wild animals sparked the coronavirus pandemic.

The Chinese researchers who originally entered the raw data into the database removed it after being contacted by the international team. Now, administrators of the database itself have cut access to international scientists due to rule violations, they say. That raised questions about the database’s role in the dispute over access to data that could shed light on the origins of the virus that killed 7 million people.

Along with the genetic signatures of the coronavirus, the cart sample contained more than 4,500 long fragments of genetic material from raccoon dogs, the report said. There were none of human beings. Some Covid-positive samples taken from other objects and surfaces on the market, the report said, also contained more genetic material from animals than humans.

Finding animal fingerprints in the same location as the virus’s genetic material does not prove that the animals themselves were infected. But some scientists who reviewed the report said the predominance of genetic material from animals — particularly raccoon dogs — suggested that species known for their ability to spread the coronavirus were indeed infected on the market in late 2019.

That scenario, they said, is consistent with the virus spreading from market animals to humans and triggering the pandemic, a similar set of circumstances that gave rise to the first Sars outbreak in China two decades earlier.

“You look at them and say they’re probably infected animals,” Theodora Hatziioannou, a virologist at Rockefeller University in New York who was not involved in the research, said of the latest findings. “If it was a human being spreading the virus, one would expect to find human DNA there as well.”

The samples could still hold more clues about where the viruses came from. The report said, for example, that there was evidence of specific genes that could suggest the material came from the upper respiratory tract of a raccoon dog.

Even if an animal was infected, however, it would not be clear whether it had spread the virus to people. Someone infected with the virus could have passed it on to a market animal. And only by taking samples directly from the animals could scientists prove whether they carried the virus, a step that was prevented because the animals were removed from the market shortly after the outbreak began.

The report has been the subject of intense speculation since international experts presented their findings to the World Health Organization (WHO) last week and then rushed to compile their analyses. At the same time, the discoveries sparked a battle for access to the genetic sequences.

Chinese scientists initially uploaded the raw sequences to a global database some time after they published a study describing them in 2022. But once international experts discovered the data in early March and alerted Chinese researchers to what they had found, the data was removed from the air.

Last week, the WHO chastised China for withholding this crucial information from the rest of the world for three years. Now the Munich-based non-profit organization that runs the database, called Gisaid, is under scrutiny for its role in controlling access to the data.

In the new report, the international team of scientists said that Gisaid had “deviated from its stated mission” by allowing Chinese researchers to retain the data for so long.

Database administrators responded to the report on Tuesday by cutting off team members’ access to their online accounts and saying they had violated their rules by getting ahead of Chinese scientists and posting their own analyses. The scientists said they had fulfilled the Gisaid database access agreement by downloading and studying the sequences, and noted that they had made several proposals to work with the Chinese scientists.

“The ramifications of cutting off access to this group of authors are enormous,” said Michael Worobey, an evolutionary biologist at the University of Arizona and co-author of the new report, noting that Gisaid also undermined the work of team members related to coronavirus variants and flu preparation. “They are making false accusations.”

The international team focused on raccoon dogs — mammals related to foxes and sold for their meat and fur — because of the amount of genetic material from those animals found in the main cart sample and because they are known to spread the virus. They said their findings were consistent with the hypothesis that the animal harbored the virus, which originated in bats, and transmitted it to people at the market.

“This is not an infected animal,” said Joel Wertheim, an evolutionary biologist at the University of California San Diego and co-author of the report, referring to the new genetic data. “But it’s as close as you can get without having the animal in front of you.”

The report, however, also offered the most concrete evidence yet that other animals susceptible to the virus were sold on the market, noted Kristian Andersen, a virologist at the Scripps Research Institute in La Jolla, Calif., and a co-author of the report. Genetic material from these animals — such as the palm civet, a small Asian mammal involved in the SARS outbreak two decades ago — has also been found in samples positive for the coronavirus.

“It’s literally the Disneyland of zoonotic transfer,” said Joseph DeRisi, a professor of biochemistry at the University of California San Francisco and president of the Chan Zuckerberg Biohub, referring to the variety of animals documented in the report.

Several other samples on the market revealed large amounts of human genetic material – an indication, according to the report, that certain virus samples were likely transmitted by infected people. Many of the first known Covid patients worked or shopped at the market.

^{Translated by Luiz Roberto M. Gonçalves}