New evidence supports the animal origin of the COVID virus through raccoon dogs

Scientists have uncovered new genetic evidence at the market in Wuhan, China, where COVID cases first spiked in late 2019. The results support 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 France’s National Center for Scientific Research, discovered genetic sequences of the virus that researchers in China – led by George Gao, former head of the China Center for Disease Control and Prevention – had uploaded to a public genomic database called GISAID. The sequences were subsequently removed, but not before several other researchers from different countries downloaded and analyzed them. Viral RNA samples collected at the Huanan Seafood Wholesale Market in early 2020 also included genetic material from raccoon dogs — a fox-like type of dog 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 from other animals) and may have been the first to transmit the virus to humans .

The virus sparked a global pandemic that has killed nearly seven million people, and there has been debate as to whether it was caused by a natural spread from wild animals to humans or by a lab leak at a coronavirus research facility in Wuhan. The new evidence doesn’t directly prove SARS-CoV-2 jumped from infected raccoon dogs to humans, but it does add to a growing body of evidence in favor of animal spread.

“These data do not provide a definitive answer as to how the pandemic began, but each and every piece of data is important in bringing us closer to that answer,” World Health Organization director-general Tedros Adhanom Ghebreyesus said in a Friday news conference. The scientists analyzing the data are currently preparing a report of their findings, which they hope to publish in the coming days.

Scientific American spoke to 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 what it adds to our understanding of the origins of COVID.

[An edited transcript of the interview follows.]

What do the new findings reveal and how do they fit into the broader context of the search for the origins of COVID?

First of all I’ve been waiting to see these sequences for more than a year, 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 knew these samples existed, but they weren’t publicly available?

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

But that earlier preprint didn’t mention any animal sequences, right?

Yes, there was no explicit mention of where the non-viral genetic material came from, apart from the samples, which came from humans. I’ve long suspected that at least one of those dots on her chart is from raccoon dogs. And lo and behold, it is so.

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

Well, first I just want to say that even before this data was released, the overwhelming body of scientific evidence points to natural zoonotic spillover [an animal disease jumping into humans] for some time. This new data is fully consistent with this scenario. What’s important here is that I think it’s a mischaracterization to say that these sequences show that raccoon dogs or other mammalian host species were infected with these viruses because all we show is the co-occurrence of genetic material from host environments is . It’s not the same as dabbing a raccoon dog. And it’s not the same as watching a raccoon dog transmit a virus to a human — something we, of course, never see. We never get that evidence. But first and foremost, this is forensic evidence that these putative host animals were present at the market. There is no longer any question. And they were in the same place as the virus.

Well, some of these environmental samples clearly have the virus in them because of infected people. But it’s mind-boggling to say that it was only humans who dumped this virus wherever there were susceptible hosts, and that these are just humans passing it to animals. Given everything we know about the early days of COVID and everything we know about zoonotic viruses, this is fitting. Will this put the lab leak conspiracy to bed? No. Nothing ever will. But I think that should help convince more sane scientists.

Can you elaborate on whether there is any evidence for the lab leak hypothesis at all – at least for the “bona fide” version that regards such a leak as some kind of accident?

The trouble with the bona fide version of a lab leak hypothesis is that there isn’t one. There’s a scientist who gets infected in the field, the scientist who gets infected in the lab with a virus to be described, serial passage or gain-of-function weaponization — I mean, every one of those lab leak hypotheses are mutually incompatible .

If we look at the viral genome, we don’t see anything suspicious related to [some] a kind of laboratory manipulation; we really don’t. The most charitable explanation left here is that you have a lab worker who gets infected with a virus that the lab has yet to characterize, takes it to Huanan Market and possibly dumps it there multiple times, and then the animals, who are sold there are infected. And none of these lab workers are broadcasting [the virus] to no one who would help epidemiologists trace it back to them, nor do they become seroreactive [having antibodies to the virus indicative of previous infection] if later tested.

They say a chain of events seems unlikely. What do you think of the recent Department of Energy report, which concluded “with low confidence” that a lab leak was the most likely cause?

I have no idea what the Department of Energy report said. I cannot comment in detail on an account that has not been described or that I have never seen. But I can’t imagine what real evidence they have. Especially now, given [the new animal evidence].

Those early cases [were] linked to the market. Yes, there was a lot of confusion. But once we cleaned up all the guesswork and data that didn’t stand up to scrutiny, all that was left was the market. And everything we’ve done since then, from the geographic analysis to the genomic analysis to the forensic genetic analysis – everything points to a natural zoonosis in the market.

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

Naturally. I don’t know of any virologist who doesn’t take biosecurity seriously. But when it comes to gain-of-function research and laboratory safety, this discussion should be decoupled from discussions about COVID, as they are two different topics. The circumstances of origin are unrelated and it is a mistake to conflate the two.

Going back to the new genetic evidence, what information are you hoping to glean from it in the coming weeks?

There is genetic material from the [market] Booths that did not have SARS-CoV-2. I would be very interested. There is more genetic data from the market that has not been made available… I think previous sequencing runs may still be available and I think it is imperative that this data be shared with the whole group for the scientists to benefit All stripes can come in and out [study them].

Will you and your colleagues publish these results?

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