Scientists have uncovered new genetic evidence in the market in Wuhan, China, where COVID cases first clustered in late 2019. The findings add support for 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, evolutionary biologist at the CNRS 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 genomics database called GISAID. The footage was later deleted, but not before several other researchers from different countries downloaded and analyzed it. 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 type of fox-like canine apparently sold in 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 raccoon dogs may have been infected with the virus (possibly from other animals) and may have been the first to spread the virus to humans. .
The virus has sparked a global pandemic that has killed nearly seven million peopleand debate has raged over whether it was caused by a natural overflow from wildlife to man or a lab leak from an institution studying coronaviruses in Wuhan. The new evidence does not directly prove that SARS-CoV-2 jumped to humans from infected raccoon dogs, but it adds to a growing body of evidence supporting spillover from animals.
“These data do not provide a definitive answer to the question of how the pandemic began, but every piece of data is important in bringing us closer to that answer,” said World Health Organization Director-General Tedros. Adhanom Ghebreyesus. at a press conference on Friday. The scientists analyzing the data are currently preparing a report on their findings, which they hope to publish in the coming days.
American Scientist 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 finding and explained what it adds to our understanding of the origins of COVID.
[An edited transcript of the interview follows.]
What do the new findings show and how do they fit into the larger context of finding the origins of COVID?
First of all, I’ve been waiting for more than a year, maybe two, to see these sequences. 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 that [the Chinese researchers have] performed several sequences of sequencing on the samples. So, I don’t know when they were produced… We know that the Chinese [scientists] had older samples, based on [a] pre-publication from 2022. And we knew these samples existed because of a leaked document in early 2020. [Editor’s note: This preprint is currently under review for possible publication.]
But that earlier preprint didn’t mention the animal footage, did it?
Yeah, he didn’t specifically mention where the non-viral genetic material came from, other than the samples that came from humans. I’ve long suspected that at least one of those dots on their chart came from raccoon dogs. And there it is.
How strong is the evidence for natural spillover causing SARS-CoV-2?
Well, first of all, I would just like to say that even before these data were published, the preponderance of scientific evidence highlighted a natural zoonotic overflow [an animal disease jumping into humans] for a while. These new data are entirely consistent with this scenario. Now, what’s important here is that I think it’s a characterization error to say that these sequences show that raccoon dogs, or any other mammalian host species, were infected with these viruses because everything that we show is the co-occurrence of genetic material from host environments. This is not the same as dabbing a raccoon dog. And that’s not the same as watching a raccoon dog transmit a virus to a human — something, of course, we never see. We never get this level of evidence. But above all, it is forensic evidence that these alleged animal hosts were present in the market. There is no more question about it. And they were there in the same place as the virus.
Now, clearly, some of these environmental samples contain the virus because of infected humans. But it forces the imagination to say that only humans deposited this virus wherever there were susceptible hosts and that it is only humans who transmit it to animals. Given everything we know about the early days of COVID and everything we know about zoonotic viruses, it fits. Will this end the conspiracy against lab leaks? No. Nothing will ever do that. But I think it should help convince more reasonable scientists.
Can you say if there is any evidence for the lab leak hypothesis – at least, for the “good faith” version that considers such a leak to be some kind of accident?
The problem with the good faith version of a lab leak hypothesis is that there isn’t just one. There’s a scientist who gets infected in the field, the scientist who gets infected in the lab with a virus that hasn’t yet been described, mass-switching or gain-of-function weaponization – I mean, each of these laboratories – the leak hypotheses are mutually incompatible.
Looking at the viral genome, we don’t see anything suspicious about [some] sort of laboratory manipulation; truly not. The most charitable explanation left here is that you have a lab worker who is infected with a virus that the lab has not yet characterized, brings it to Huanan Market and drops it there potentially multiple times, then the animals that are being sold there get infected. And none of these lab workers transmits [the virus] to anyone who would help epidemiologists trace them, and they don’t end up being seroreactive either [having antibodies to the virus indicative of previous infection] when tested later.
You say the chain of events seems unlikely. What do you think of the recent Department of Energy report which concluded “with little confidence” that a lab leak was the most likely source?
I have no idea what was in the Department of Energy report. I cannot comment in detail on a report that has not been described or that I have 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. Yes, there was a lot of confusion. But once we sort of stripped away 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, from geographic scans to genomic scans to forensic genetic analysis, all point to natural zoonosis in the marketplace.
Regardless of the true origin of SARS-CoV-2, should we still be concerned about lab safety to prevent potential leaks of deadly pathogens?
Of course. I don’t know any virologist who doesn’t take biosecurity seriously. But when we talk about search for gain of function and lab safety, this discussion should be separated from COVID discussions as they are two different issues. The circumstances of origin are unrelated, and it is a mistake to confuse the two.
Coming back to the new DNA evidence, what further insights do you hope to gain from it in the coming weeks?
There is genetic material from [market] stalls that did not have SARS-CoV-2. I would be very interested to see those. There is more market genetic data that has not been made available…I think previous sequencing rounds may still be available, and I think it is imperative that this data be shared with the public. ‘group so that scientists of all stripes can come in and [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.