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Genetic data links raccoon dogs to covid origin; WHO seeks China cooperation

Vehicles carrying a team from the World Health Organization enter the Huanan Seafood Market in Wuhan, China, in January 2021. (Ng Han Guan/AP)
7 min

The protracted and rancorous debate over the origin of the covid pandemic has added a small but potentially significant data point: A sample taken in a Wuhan market in early 2020 showed genetic traces of both the coronavirus and a raccoon dog, according to scientists who have analyzed newly obtained data from China.

Like so many elements of the mystery, the new data, first reported by the Atlantic, falls short of proving how, where and when people first became infected with the virus. But it boosts the theory that the pandemic started through natural spillover from animals rather than emerging from a laboratory, a theory favored by some researchers.

The director general of the World Health Organization, Tedros Adhanom Ghebreyesus, on Friday renewed his call for China to share scientific data on the origin of the pandemic.

“We continue to call on China to be transparent in sharing data, and to conduct the necessary investigations and share the results,” Tedros said. “Understanding how the pandemic began remains both a moral and scientific imperative.”

The new evidence comes via swabs taken in animal stalls at the Huanan Seafood Market in Wuhan. Investigators collected them in early 2020 after the market had been closed and all the animals removed. One swab contained a mixture of genetic material that included a large amount from a raccoon dog along with traces from the coronavirus, said Stephen Goldstein, a virologist at the University of Utah who was part of the team that analyzed the data.

“We can’t definitively prove that there were infected raccoon dogs who were the first source of the virus going into humans,” Goldstein said, “but it is highly suggestive of that.”

What to know about raccoon dogs, which may be linked to coronavirus’s origin

The data come from Chinese scientists who have submitted a paper to a scientific journal that has not yet been published, Goldstein said. The scientists involved in the new analysis, which has not been peer-reviewed or published in a journal, said they plan to post their work online within the next couple of days.

“I very much wish their paper had come out before news of our analysis broke,” said Michael Worobey, a University of Arizona evolutionary virologist who took part in the new analysis.

“We would have liked to have collaborated with the Chinese scientists, and that still is our intention going forward,” Goldstein said.

Other animals that were probably sold in the market are also capable of being infected with SARS-CoV-2, the virus that causes covid-19. But the new evidence “moves raccoon dogs to the top of the list of animals that started the pandemic,” Robert Garry, a virologist at Tulane University who took part in the new analysis and has long favored the market theory, said Friday in an email.

“It’s just one more brick on this massive wall of evidence that all fits together,” Worobey said. “If it weren’t so politicized, it’s one of the clearest sets of evidence for how a pandemic emerged that we’ve ever had.”

But David A. Relman, a professor of microbiology and immunology at Stanford University who has said both origin scenarios are plausible, called the new data “very inconclusive” in an email. “Frankly, the breathlessness and alacrity with which stories like this one are promoted, in the face of very incomplete and confusing ‘data,’ leaves me frustrated and concerned,” he said.

The virus origin debate has become heavily politicized, and this latest data point, coming from scientists who have long argued for a market origin, is unlikely to shift the views of those who favor the lab leak theory.

“In this case, there is not any smoking gun,” said Peter Hotez, co-director of the Texas Children’s Hospital Center for Vaccine Development. “But if you look cumulatively at the evidence to date, so far it all points to a natural origin of covid.” Settling the origin question, he said, will be critical in helping scientists prepare for any future coronavirus outbreak.

House Republicans are holding hearings on the pandemic’s origin, with Republican lawmakers promoting the lab leak theory and possible culpability among American scientists and government officials. Robert Redfield, the director of the Centers for Disease Control and Prevention during the Trump administration, testified March 8 that the pandemic most likely began with a lab leak.

President Biden two years ago asked his intelligence agencies to dig into the origin of the virus, and they failed to reach a consensus, although they agreed that it was not engineered as a bioweapon. Four of the agencies and the National Intelligence Council favored, with “low confidence,” a natural origin. The FBI favored with “moderate confidence” a lab leak.

But just before the opening of GOP-led House hearings on the pandemic, an updated report from the intelligence community revealed that the Energy Department had shifted from a neutral stance to a conclusion, again with “low confidence,” that a lab origin was most likely. That decision was not accompanied by new data or an explanation of why researchers there had begun to favor the lab leak theory.

Geography has played a huge role in the debate. The covid outbreak began in Wuhan, home to the Wuhan Institute of Virology, which has conducted extensive research on coronaviruses. There has long been a debate within the scientific community over the relative risks and benefits for experiments that, in an attempt to understand viruses, manipulate them in ways that could make them more transmissible or virulent.

But from the start of the Wuhan outbreak, the Huanan Seafood Market has been the focus of attention. Many of the first documented cases of human infection with the virus were clustered in and around the market. Vendors there were among those sickened. And environmental samples showed the presence of the virus preferentially in the part of the sprawling market where animals were sold and butchered.

“It’s a bull’s eye right around the market,” Worobey said. “Clearly in December, the first cases in the community were ones just bleeding out from the epicenter in the market.”

Goldstein said he believes that animals with the virus probably contracted it on a farm, or wherever they were before reaching the market.

China has long denied that the virus came from the market or a lab, and instead has floated conjectures that it originated abroad. Chinese scientists and lab leak proponents have said the clustering of cases at Huanan could be explained as a superspreader event caused by an infected person shopping in the crowded market.

Last summer the journal Science published two papers, written by many of the same scientists producing this new analysis, that contended there were at least two separate spillovers from animals at the Wuhan market. But the authors of the papers acknowledged that their report did not resolve many of the questions about the spillover, including which animal or animals were involved, who sold them or where they were from.

The new research still falls short of doing that. But it ratchets up the plausibility that a raccoon dog or some other animal was infected with the virus in late 2019.

“Top line is that there were animals at the market and they are in the exact location where the virus was,” Angela Rasmussen, a virologist at the University of Saskatchewan who participated in the new analysis, said in an email. “We can’t say for sure that they were infected, but this is very strong evidence supporting that the pandemic’s origin was due to the live animals at Huanan market.”

Benjamin Neuman, a virologist at Texas A&M University who was not part of the new analysis, said the origin of the pandemic may remain forever murky.

“As with any cold case, the evidence isn’t likely to get stronger as time passes, so short of a time machine, this may be the closest we ever get to the origin,” Neuman said in an email. “We still don’t have definitive evidence of animal-to-person spread, but this is a big step in that direction.”

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End of the public health emergency: The Biden administration ended the public health emergency for the coronavirus pandemic on May 11, just days after WHO said it would no longer classify the coronavirus pandemic as a public health emergency. Here’s what the end of the covid public health emergency means for you.

Tracking covid cases, deaths: Covid-19 was the fourth leading cause of death in the United States last year with covid deaths dropping 47 percent between 2021 and 2022. See the latest covid numbers in the U.S. and across the world.

The latest on coronavirus boosters: The FDA cleared the way for people who are at least 65 or immune-compromised to receive a second updated booster shot for the coronavirus. Here’s who should get the second covid booster and when.

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