Covid-19 found in raccoon dogs in China, strengthens natural origin theory: Report

The first coronavirus case was reported in China’s Wuhan Province in December 2019

Scientists have uncovered new genetic evidence from the market in Wuhan, China, where Covid cases first clustered in late 2019. The findings add support to an animal origin of SARS-CoV-2, the virus that causes Covid. They were presented to an advisory group convened by the World Health Organization earlier this week.

Florence Débarre, an evolutionary biologist at the French National Center for Scientific Research discovered genetic sequences of the virus that researchers in China—led by George Gao, former head of the Chinese Center for Disease Control and Prevention—had uploaded to a public genomic database called GISAID. The sequences were subsequently taken down but not before several other researchers from different countries downloaded and analyzed them. Samples containing viral RNA, which had been collected at the Huanan Seafood Wholesale Market in early 2020, also contained genetic material from raccoon dogs—a foxlike type of canid apparently sold at the market—as well as other animals. The genetic material came from the same areas of the market where SARS-CoV-2 was found, suggesting that the raccoon dogs may have been infected with the virus (possibly by other animals) and could have been the first to spread the virus to humans.

The virus sparked a global pandemic that has killed nearly seven million people, and debate has raged over whether it was caused by a natural spillover from wildlife to humans or a lab leak from a facility studying coronaviruses in Wuhan. The new evidence does not directly prove that SARS-CoV-2 jumped into humans from infected raccoon dogs, but it adds to a growing body of evidence in favor of a spillover from animals.

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“These data do not provide a definitive answer to the question of how the pandemic began, but every piece of data is important in moving us closer to that answer,” said the World Health Organization’s director general Tedros Adhanom Ghebreyesus in a news briefing on Friday. The scientists who are analyzing the data are currently preparing a report on their findings, which they hope to release in the coming days.

Scientific American spoke with one of the researchers who analyzed the samples: Joel Wertheim, an evolutionary biologist at the University of California, San Diego. He described the new discovery and explained what it adds to our understanding of Covid’s origins.

[An edited transcript of the interview follows.]

What do the new findings show, and how do they fit into the broader context of the search for Covid’s origins?

First of all, I have been waiting to see these sequences for more than a year now, maybe two. And we have long thought that they would confirm the presence of susceptible hosts and the virus in the same place at the same time in the market.

So you were aware that these samples existed, but they weren’t publicly available?

Yeah, it seems that [the Chinese researchers have] done multiple sequencing runs on the samples. So I don’t know when these were produced.... We know that the Chinese [scientists] had older samples, based on [a] preprint from 2022. And we knew that those samples existed because of a leaked document from early 2020. [Editor’s note: This preprint is currently under review for possible publication.]

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But that earlier preprint did not mention animal sequences, right?

Yeah, it specifically didn’t mention where the nonviral genetic material was from, aside from the samples that were from humans. I’ve long suspected that at least one of those points on their graph was from raccoon dogs. And lo and behold, it is.

How strong is the evidence now for a natural spillover as the origin of SARS-CoV-2?

Well, first, I’d like to just say that even before these data came out, the preponderance of scientific evidence has pointed to a natural zoonotic spillover [an animal disease jumping into humans] for quite some time. These new data are entirely consistent with that scenario. Now, what’s important here is that I think it’s a mischaracterization to say that these sequences show that raccoon dogs, or any other mammal host species, were infected with these viruses because all we’re showing is co-occurrence of genetic material from host environments. It’s not the same as swabbing a raccoon dog. And it’s not the same as watching a raccoon dog transmit a virus to a human—something, of course, we never see. We never get that level of evidence. But first and foremost, this is forensic evidence that these putative host animals were present at the market. There’s no more question about that. And they were there in the same place as the virus.

Now, clearly, some of these environmental samples have the virus in them because of infected humans. But it strains the imagination to say it was only humans who were depositing this virus all over places where susceptible hosts were and that this is just humans giving it to animals. Given everything else we know about the early days of Covid and everything we know about zoonotic viruses, this fits. Is this going to put the lab-leak conspiracy to bed? No. Nothing will ever do that. But I think this should help convince more reasonable scientists.

Can you address whether there is any evidence at all for the lab-leak hypothesis—at least, for the “good faith” version that views such a leak as some kind of accident?

The problem with the good faith version of a lab-leak hypothesis is that there isn’t a single one. There is a scientist who gets infected in the field, the scientist who gets infected in the lab by a virus that has yet to be described, the serial passage or gain-of-function weaponization—I mean, every single one of these lab-leak hypotheses are mutually incompatible with each other.

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Looking at the viral genome, we don’t see anything suspicious with regard to [some] sort of lab manipulation; we really don't. The most charitable explanation here that’s still left is that you have some lab worker who gets infected with a virus that the lab has yet to characterize, brings it over to the Huanan market and deposits it there potentially multiple times, and then the animals that are being sold there get infected. And none of these lab workers transmit [the virus] to anyone who would help epidemiologists trace it back to them, nor do they end up being seroreactive [having antibodies to the virus indicative of previous infection] when tested later.

You are saying that chain of events seems unlikely. What do you make of the recent Department of Energy report that concluded “with low confidence” that a lab leak was the most likely origin?

I have no idea what was in the Department of Energy report. I can't comment in specifics about a report that hasn’t been described or that I’ve never seen. But I can’t imagine what real evidence they have. Especially now, in light of [the new animal evidence].

These early cases [were] linked to the market. Yeah, there was a lot of confusion. But once we sort of stripped away all of the supposition and the data that didn’t hold up to scrutiny, all that was left was the market. And everything that we’ve done since, from the geographical analyses to the genomic analyses to, now, the forensic genetic analysis—it all points to natural zoonosis at the market.

Regardless of the true origin of SARS-CoV-2, should we still be concerned about keeping labs secure to prevent possible leaks of deadly pathogens?

Of course. I don’t know any virologist who doesn’t take biosecurity seriously. But when talking about gain-of-function research and lab safety, that discussion should be decoupled from the discussions of Covid because they’re two different issues. The circumstances of the origin are unrelated, and it’s a mistake to conflate the two.

Getting back to the new genetic evidence, what information are you still hoping to glean from that in the coming weeks?

There’s genetic material from the [market] stalls that didn’t have SARS-CoV-2. I'd be very interested in seeing those. There are more genetic data from the market that haven’t been made available.... I think previous sequencing runs may still be out there, and I think that there’s an imperative to have those data shared with the entire group so that scientists of all stripes can come in and [study them].

Will you and your colleagues be publishing these findings?

We are going to be releasing a report summarizing our findings. I would say [the time frame will be] closer to days, maybe hours.