A team of scientists claims it is “beyond reasonable doubt” that the COVID pandemic began with infected animals sold in the market, rather than from a lab leak. They were analyzing hundreds of samples collected from Wuhan, China, in January 2020. The findings suggest that animals like raccoon dogs, civets, and bamboo rats could be among the potential sources of the pandemic.
Despite highlighting a specific stall in the market as a hotspot for both animals and the coronavirus, the study cannot offer conclusive proof. The samples were collected by Chinese officials in the early stages of COVID and represent one of the most valuable scientific sources of information about the pandemic’s origins.
An early link to the Huanan Seafood Wholesale Market was established when patients in Wuhan hospitals appeared with mysterious pneumonia. The market was closed, and teams scanned locations including stalls, inside animal cages, and equipment used to process fur and feathers from slaughtered animals.
Their analysis was published last year, and the raw data was made available to other scientists. Now, a team in the U.S. and France says they’ve conducted more advanced genetic analyses to look deeper into the early days of COVID. This included analyzing millions of short fragments of genetic code—both DNA and RNA—to identify the animals and viruses that were present in the market in January 2020.
Professor Florence Débarre from the French National Center for Scientific Research said: “We see the genetic ‘ghosts’ of these animals in the environmental samples, some of which were taken from the same stalls where [COVID virus] was also found.”
The findings, published in the journal Cell, highlight a series of discoveries that together support their case. They show that both the COVID virus and susceptible animals were detected in the same location, with some individual swabs containing both the animals’ genetic code and the coronavirus. This wasn’t spread evenly across the market, but instead pointed to very specific hotspots.
Professor Kristian Andersen from the Scripps Institute in the U.S. said: “We found a very consistent story, even down to a single stall, pointing to the market as a very likely origin of this particular pandemic.”
However, being in the same place at the same time doesn’t prove that any specific animal was infected.
The animal that appeared most frequently in the samples was the common raccoon dog. It’s known to catch and transmit COVID in experiments. Other animals identified as possible sources of the pandemic include the masked palm civet, which was also linked to the 2003 SARS outbreak, as well as gray bamboo rats and Malayan hedgehogs. “No tests have been done yet to determine if they can spread the virus.”
The depth of genetic analysis was able to pinpoint the specific species of raccoon dogs being sold. These were animals more commonly found in the wild in southern China, rather than those bred for fur. This gives scientists clues about where to search next.
Decoding the Virus
The research teams also analyzed the genetic code of the viral samples found in the market and compared them to samples from patients in the early days of the pandemic. “Examining the different mutations in the viral samples gives us valuable insights.”
The samples suggest, but don’t prove, that COVID might have started more than once in the market, with two potential spillover events from animals to humans. The researchers say this supports the idea of the market being the source, rather than the pandemic starting elsewhere and the market just fueling it with a super-spreader event.
Scientists also used the mutations to build a family tree of the virus and look at its past.
Professor Andersen said: “If we estimate when we think the pandemic most likely started versus when we think the outbreak in the market began, those two things overlap—they’re the same thing.”
In their scientific paper, the full genetic diversity of the coronavirus seen in the early days of the pandemic was found in the market.
Professor Michael Worobey from the University of Arizona said: “Rather than being just a small branch on this big, dense evolutionary tree, the market sequences are found across all the branches of the tree, in a way that fits with the genetic diversity really starting in the market.”
He added that this study, along with other data—such as early cases and hospitalizations linked to the market—point to a zoonotic (animal) origin for COVID.
“There’s no reasonable doubt that this is how it happened,” said Professor Worobey, adding that other interpretations of the data require “truly fanciful, absurd scenarios.”
“I think there’s been an underappreciation of how strong the evidence is.”
Did the Pandemic Start Here?
The “lab leak theory” suggests that instead of the virus spreading from wildlife, it may have originated from the Wuhan Institute of Virology (WIV), which had been studying coronaviruses for a long time. The institute is about a 40-minute drive from the market. The U.S. intelligence community was asked to assess the possibility of a leak—whether accidental or intentional.
In June 2023, all involved agencies stated that either a lab leak or an animal origin were both plausible scenarios. The National Intelligence Council and four other agencies believed animals were the likely source, while the FBI and the Department of Energy thought a lab accident was more probable.
A U.S. intelligence report reveals division over the origins of COVID.
Why the COVID lab leak theory is controversial.
Professor Andersen said, “For many people, this seems like the most likely scenario—‘the lab is right there, of course it was the lab, are you dumb?’ I completely understand that argument.”
However, he says there is now a lot of data that “really points to the market as the true early center” and “even specific sites within that market.”
Identifying the animals that may have been the source of the pandemic provides clues on where scientists can look for more evidence of a zoonotic (animal-based) origin.
However, since farms destroyed their animals in the early days of COVID, this means there may be no remaining evidence to find.
Professor Worobey said, “It’s likely that we missed our chance.”
Professor Alice Hughes, from the University of Hong Kong, who was not involved in the analysis, said it was a “good study.”
“[But] without actual animal samples from the market, which were not collected, we can’t have any higher certainty.”
Professor James Wood, co-director of the Infectious Diseases Division at Cambridge, said the study provided “very strong evidence” that the pandemic began in the wildlife stalls at the market. However, he noted that it couldn’t be definitive because the samples were collected after the market was shut down, and the pandemic may have started weeks earlier.
He warned that “little to nothing” is being done to curb the live wildlife trade, and that “the uncontrolled transmission of animal infections poses a major risk for future pandemics.”