How raccoon dog DNA fits into the COVID-19 origins debate

It’s been three years since the COVID-19 pandemic began. Yet the mystery of how it got started continues to make headlines again and again and to fuel a heated, and oft-time political, debate.

While what exactly happened in the earliest days of the pandemic remains an ongoing question, some genetic studies have tipped the scales in favor of the pandemic originating from a viral spillover from animals (SN: 10/4/22). A hypothesis, but no evidence, suggests the virus could have been leaked, either accidentally or deliberately, from a lab.

U.S. intelligence agencies are split over which scenario they deem more likely. The Department of Energy and the FBI lean more toward the possibility of a lab leak, while the National Intelligence Council and others suspect a natural origin. It is important to note that most of these agencies drew their conclusions with “low confidence,” which means the available data the intelligence community had to rely on is “scant, questionable or very fragmented,” according to the National Intelligence Council.

Very soon, we will see what that intelligence looks like. President Joe Biden signed a bill into law on March 20 to declassify government information on the virus’s origins within 90 days.

Meanwhile, a new genetic analysis adds another piece to the puzzle in favor of the spillover scenario, this time with a possible suspect: raccoon dogs.

“These data do not provide a definitive answer to how the pandemic began,” World Health Organization Director-General Tedros Adhanom Ghebreyesus said in a March 17 news briefing. “But every piece of data is important to moving us closer to that answer.”

Here’s what to know about the latest data and what they mean for pinning down the events that sparked the pandemic.

What is the latest line of evidence for a natural origin?

The first cluster of coronavirus cases in humans was linked to the Huanan Seafood Wholesale Market in Wuhan, China (SN: 1/24/20). Environmental samples taken in 2020 from the southwest corner of the market, where live animals were sold, carried genetic material from both the coronavirus and animals, the Atlantic first reported on March 16.

In some virus-positive samples, computational biologist Alex Crits-Christoph and an international team of colleagues also found DNA from the common raccoon dog (Nyctereutes procyonoides). The foxlike animal native to Asia is susceptible to coronavirus infections, including SARS-CoV-2, the virus that causes COVID-19.  

The fact that traces of both animal and coronavirus were uncovered in the same samples suggest that the virus may have jumped from bats to raccoon dogs or other animals at the market and then to people, the team writes (SN: 7/12/21). It posted its analysis March 20 on Zenodo, a repository where scientists can post research results that have not yet been reviewed by their peers.

This analysis builds on evidence from two studies published in Science in July 2022. In the first study, researchers reported that the genetic diversity of SARS-CoV-2 variants from the pandemic’s early days suggest that there may have been two separate jumps from animals to people: one in late November 2019 and another weeks later. The second study used the first known COVID-19 cases and coronavirus-positive environmental samples from the seafood market to identify the southwest part of the market with live animal vendors as the likely epicenter of the pandemic’s spread.

In the new analysis, Crits-Christoph, who works from Baltimore for the nonprofit Cultivarium, and colleagues analyzed public genetic data that had been released in early March from the Chinese Center for Disease Control and Prevention. That data, linked to a February 2022 preliminary study from the China CDC (which is now under review at a scientific journal), allowed the team to zoom in on an animal stall in the southwest part of the market that had the most virus-positive samples. A sample from a cart in that stall also contained plenty of genetic material from raccoon dogs, as well as a handful of other animals such as ducks.

There was no evidence of human DNA in that sample, a finding that hints that animals, not necessarily people, were close to the coronavirus in that spot. Raccoon dogs or another animal, the results suggest, might have served as a bridge to take the coronavirus from bats to humans.

Does this finding confirm where the coronavirus originated?  

No. As Tedros said on March 17, the findings aren’t a nail in the coffin to confirm the spillover hypothesis. Finding evidence of animal and coronavirus together in samples hints that the two were mighty close to one another. But this particular spillover story is still circumstantial. It’s unclear if animals housed in the stalls might have been infected with the virus, and if these animals then passed the virus on to humans.

It would have been better to have a positive swab from a live animal that was for sale at the market in late November or December 2019. Or to find the virus in wild animals. But both of those things may now be almost impossible.

By the time officials came to investigate the market in early 2020, any infected animals were probably long gone. And the virus has evolved since then. It’s morphed in people — giving us the alpha and delta variants as well as omicron and its spawn (SN:10/17/22). And it’s still evolving in animals, too. Coronaviruses circulating in animals now, or even two years ago, probably won’t look the same as SARS-CoV-2 did at the end of 2019, so viruses from nature won’t be an exact match. 

“It’s like a cold criminal case,” says Michael Osterholm, an epidemiologist at the University of Minnesota in Minneapolis. “There may be mounting evidence that, you know, John Doe did it. But not conclusive enough to try John Doe for the crime.”

That isn’t unusual when it comes to pinning down the source of an outbreak. Such investigations can take years and may never provide a definitive answer (SN: 3/18/21). Eventually, we may reach a point where we’re relying on the best evidence available and will have to accept that it’s as close as we’re going to get.

Do we need to know COVID-19’s origins to prepare for the next pandemic?

Not really. While the evidence we have leans toward spillover, we’re “mired in the mud,” says Osterholm, who notes that he’s agnostic for how the pandemic got started. He says it’d be better to focus on preparing for the next pandemic, rather than paying attention to only this one.  

It’s unavoidable that another pandemic is in our future; whether it will be another coronavirus, bird flu or something else entirely is anyone’s guess (SN: 3/6/23).

What we can do now is think more carefully about how we use land and do research.

As wildlife habitats disappear, humans come across animals more often, perhaps introducing more opportunities to exchange pathogens. Farming animals in tight quarters provides more opportunities too. Fixing those problems could help prevent spillover, or at least make it less likely.

Lab regulations — making sure potentially risky work is done safely or not done at all — can help to stop a lab leak.

There’s no reason we can’t start doing these things now, Osterholm says. “I wish we’d move on and start addressing … what we’re going to do to be better prepared” for the next potential spillover or lab leak, he says. “Because we’re not.”