Raccoon dog DNA from Wuhan market supports the idea that COVID came from animals

Scientists found the strongest evidence yet that the coronavirus SARS-CoV-2 leapt from animals to humans at a market in China, fueling the first reported outbreak of COVID-19. The genetic data was uploaded to a public database and then promptly removed at the request of the Chinese team that first shared it. 

An international team of scientists reported that swab samples taken in and around the stalls at Huanan Seafood Wholesale Market in early 2020 contained SARS-CoV-2 genetic sequences commingled with the DNA of common raccoon dogs (Nyctereutes procyonoides). The Atlantic first reported the findings on Friday (March 17). Raccoon dogs, a fox relative with dark blotches around their eyes, are known to be able to carry and transmit the coronavirus, The New York Times reported. 

Given when and how the swab samples were collected, and the fact that the virus can't persist indefinitely in the environment without a host, the analysis suggests that raccoon dogs infected with SARS-CoV-2 may have shedding infectious virus while they were being illegally traded at the market in December 2019, the team concluded. 

The analysis, which is not yet complete and has not yet been published, cannot definitely prove that infected raccoon dogs were present at the market. And if the animals were infected, the research cannot show how they caught the virus or how the virus spread from there.

Related: Will we ever find COVID-19's 'Patient Zero?' 

However, the presence of SARS-CoV-2 and raccoon dog genetic material in the exact same swab samples at least suggests that infected wild animals were at the market, and thus, had the potential to spread the virus, the scientists said. 

"This is a really strong indication that animals at the market were infected," Angela Rasmussen, a  virologist involved in the research, told The Atlantic. "There's really no other explanation that makes any sense."

The newly-analyzed genetic sequences were uploaded earlier this month to GISAID, an open-access genomic database, by researchers affiliated with China's Center for Disease Control and Prevention (CDC), according to The Atlantic. Evolutionary biologist Florence Débarre spotted that the raw sequence data had been shared and alerted other researchers.

Just hours after downloading the data from GISAID, scientists led by Kristian Andersen, Edward Holmes, and Michael Worobey uncovered the raccoon dog DNA commingled with SARS-CoV-2 genetic material. The team presented their findings Tuesday (March 14) to the World Health Organization's (WHO) Scientific Advisory Group for the Origins of Novel Pathogens, The Atlantic reported. 

Back in February 2020, the Chinese CDC researchers had analyzed the same data but published only part of it, making no mention of raccoon dog DNA. In a preprint, they reported finding an "abundance" of Homo sapien DNA associated with SARS-CoV-2, which they said suggested infected humans carried the virus into the market. They couldn't find any evidence pointing to an animal host in that data, they wrote. But graphs in the same preprint contradicted that claim, showing animal DNA had been found mixed up with SARS-CoV-2, Science first reported in 2022.

Shortly after Tuesday's WHO meeting, the Chinese research group's 2020 preprint went into review at a peer-reviewed Nature Research journal, suggesting a new version will soon be published. 

The team that presented their findings to the WHO initially reached out to the Chinese researchers to collaborate on the research, but shortly after they made contact, the genetic sequences were removed from GISAID, The New York Times reported.  

GISAID noted that the sequences were removed at the request of the submitter, Science reported. When asked why the sequences weren't shared sooner, the former head of the China CDC George Gao told Science that the data was "[n]othing new. It had been known there was illegal animal dealing and this is why the market was immediately shut down." When asked why GISAID took down the sequence data, Gao did not reply, but indicated that the data did not resolve the question of SARS-CoV-2's origin, which he said is "still scientific and open."

Critics of the widely-supported spillover hypothesis — that SARS-CoV-2 jumped from animals to humans — may ultimately want more conclusive evidence than research can offer, Joel Wertheim, an evolutionary biologist involved in the analysis, told Science.

"You can't observe the zoonotic transmission of a novel virus from animals to humans," he said. "We're just never going to get that level of data."