A new analysis of samples taken from a market in Wuhan, China, during the early days of the pandemic are the strongest evidence yet that the COVID-19 virus jumped from animals to humans, some researchers say.
The samples found evidence of the presence of the novel coronavirus along with genetic material from multiple animals — including raccoon dogs, which are susceptible to the disease — according to a report published Monday on the Zenodo.org open science website, which builds a case for the Huanan Wholesale Seafood Market as the epicenter of the pandemic.
In some samples there was more animal genetic material than human genetic material indicating possible SARS-CoV-2 infections in animals, the report says. Like many studies released quickly during the pandemic, it has not yet undergone review by the scientific community.
Those involved worked to finish the report after early findings garnered intense interest and a flurry of media coverage last week. The World Health Organization has called on China to fully share the genetic data the researchers analyzed, which appeared briefly in a public database before being taken down March 11. The raw data have still not been made available.
For some outside experts, the situation has sparked concerns.
“I worry a lot about our jumping on tidbits that are incomplete and cannot be verified,” said David Relman, a professor of microbiology and immunology at Stanford University. “I think we need to take a deep breath and insist on the kind of process and science that any important issue, especially this one deserves.”
Relman said this is true on both sides of the debate over COVID-19’s origins. He’s long advocated for both theories — a laboratory accident or natural spillover — to be investigated with equal rigor.
The report is the latest chapter in a fraught search for answers about how the pandemic began. On Monday, President Joe Biden signed into law a bill to declassify intelligence on the origins of COVID. The U.S. intelligence community remains split in its findings, with the the FBI and Department of Energy concluding that the virus likely came from a lab accident.
The latest report further complicates the picture.
“These data do not provide a definitive answer to the question of how the pandemic began,” WHO Director-General Tedros Adhanom Ghebreyesus said Friday in a press conference, “but every piece of data is important in moving us closer to that answer.”
The scientists generated their report after samples uploaded by Chinese scientists briefly appeared in the open-access genomics database GISAID. Florence Débarre, an evolutionary biologist at the French National Centre for Scientific Research, fortuitously spotted the data on March 4 and reached out to an international group of scientists who have authored papers supporting the hypothesis that COVID-19 originated at the Huanan Market. The scientists had been hunting for what they’ve called “invaluable” sequencing data for more than a year.
“It’s the first time we’ve been able to identify a genetic fingerprint of the virus and a potential intermediate host in the exact same place,” Stephen Goldstein, a University of Utah virologist who contributed to the analysis and is an author of the report, said in an interview. “It’s completely consistent and expected from what you’d see in a zoonotic spillover event.”
No Smoking Gun
The samples show that DNA from raccoon dogs — a distant relative of foxes sometimes sold in Chinese markets like the one in Wuhan — appeared in environmental samples taken from the Wuhan market linked to the earliest COVID cases in 2019. In a sample taken from a cart, more raccoon dog DNA was apparent than human.
Natural SARS coronavirus infections were previously detected in raccoon dogs at another market in China after SARS emerged there in 2002. The animals are also capable of shedding the virus, studies have shown. Seeing that raccoon dog DNA was indicated in the samples was “one of the most incredible moments of my career,” Goldstein said.
DNA from several other animal species were also found in the samples, including Malaysian porcupines, Siberian weasels, Amur hedgehogs and bamboo rats, among others, the report said.
This strongly supports the idea that animal-to-human transmission spawned the pandemic, according to the scientists who performed the analysis.
“The presence of virus and potential host genetic material in the market is exactly what one would expect under the zoonotic origins hypothesis,” said Joel Wertheim, an associate professor at the University of California, San Diego, who was involved in analyzing the samples.
Others are less convinced. The rush to draw conclusions when very little information was initially available “is not the way careful and thoughtful science is done,” Relman said.
Access to the data analyzed by the researchers is key, as it “will allow for a more informed discussion about the strength of the new evidence,” Francois Balloux, director of University College London’s Genetics Institute, wrote on Twitter.
The existence of the data wasn’t a secret. Disease detectives that arrived from Beijing during the early days of the pandemic ordered environmental samples to be collected from drains and other surfaces at the market, which closed on Jan. 1, 2020.
“All current evidence points to wild animals sold illegally,” China Center for Disease Control Director George Gao and colleagues wrote in the agency’s weekly bulletin in January 2020. All but two of the positive specimens came from a section of the market’s western wing, where many shops sold animals.
“We have found out which stalls on the seafood market in Wuhan had the virus,” Tan Wenjie, a researcher at China CDC’s viral disease control and prevention institute, was quoted telling the state-owned China Daily newspaper at the time. “It is an important discovery, and we will investigate which animal was the source.”
But those samples were never shared, until they emerged in GISAID earlier this month. And after Goldstein and his team reached out to Gao’s, the sequences again disappeared from the GISAID site.
“We were surprised to see it taken down,” Goldstein said. “The questions of timing are questions that the China CDC can answer.”
The records are currently being updated with newer, additional data as part of a review of a manuscript that’s been submitted for publication, GISAID said in a statement. While existing records may be temporarily invisible while they are being updated, the group doesn’t delete records, it said.
The WHO is encouraging researchers using the data to collaborate with their Chinese counterparts, according to the statement.
“The story isn’t over,” said Gerald Parker, director of the Pandemic and Biosecurity Policy Program at Texas A&M University’s Bush School of Government and Public Service. “We still need an objective, transparent investigation with forensic vigor that brings together the intelligence community and the scientific community.”
(Bloomberg staff writer Jason Gale contributed to this report.)