Scientists have discovered new genetic evidence from the market in Wuhan, China, where COVID cases first clustered in late 2019. The findings add support to the 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, the former head of the Chinese Centers for Disease Control and Prevention—had uploaded to a public genome database that it is called GISAID. The sequences were then removed, but not before being downloaded and analyzed by several other researchers from different countries. Samples containing viral RNA collected at the Huanan Seafood Wholesale Market in early 2020 also contained genetic material from raccoon dogs — a type of fox apparently sold at the market — as well as other animals. The genetic material came from the same market areas where SARS-CoV-2 was found, suggesting that raccoon dogs may have been infected with the virus (possibly from 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 transmission from wildlife to humans or a laboratory leak from a facility 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 in favor of animal spread.
“These data do not provide a definitive answer to the question of how the pandemic started, but every piece of evidence is important in bringing us closer to that answer,” WHO director-general Tedros Adhanom Ghebreyesus said at a news briefing on Friday. . . The scientists analyzing the data are preparing a report on 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 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 the search for the origins of COVID?
First off, I’ve been waiting to see these sequences for over a year now, maybe two. And we thought for a long time that they would confirm the presence of susceptible hosts and the virus in the same place at the same time in the market.
So did you know these samples existed, but weren’t publicly available?
Yes, it seems so [the Chinese researchers have] multiple sequencing runs were performed on the samples. So I don’t know when these were made…. We know the Chinese [scientists] had earlier samples, based [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 draft didn’t mention animal rows, did it?
Yeah, he didn’t specifically say where the non-viral genetic material came from, other than the samples that came from humans. I have long suspected that at least one of those points on their chart was from raccoon dogs. And lo and behold, it is.
How strong is the evidence now for a natural spread as the origin of SARS-CoV-2?
Well, first, I’d just like to say that even before this data came out, the preponderance of scientific evidence has shown a natural spread of zoonotic [an animal disease jumping into humans] for a long time. This new data is entirely consistent with this scenario. Now, what’s important here is that I think it’s a mischaracterization that these sequences show that raccoon dogs, or any other kind of mammalian host, became infected with these viruses, because all we’re showing is the co-occurrence of genetic material from environments host. . It’s not the same as wiping out a raccoon dog. And it’s not the same as seeing a raccoon dog transmit a virus to a human — which, of course, we never see. We never have that level of evidence. But first and foremost, this is forensic evidence that these alleged host animals were present in the market. There is no other question about it. And it was there in the same place as the virus.
Now, clearly, some of these environmental samples have the virus in them because of infected people. But it’s stretching the imagination to say that it was only humans who deposited this virus in all the places where susceptible hosts were, and that it’s 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. Will this 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 elaborate on whether there is any evidence at all 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 bona fide version of a lab leak case is that there isn’t one. There’s the scientist getting infected in the field, the scientist getting infected in the lab by an as-yet-undescribed virus, the serial pass or the gain-of-function weaponry—I mean, every one of those labs—the leak hypotheses are mutually incompatible with each other. .
Looking at the genome of the virus, we don’t see anything suspicious about it [some] type of laboratory manipulation; we really don’t. The most charitable explanation left here is that you have some lab worker infected with a virus that the lab has not yet characterized, brings it to the Huanan market and deposits it there probably multiple times, and then the animals that are sold there become infected . And none of these lab workers transmit [the virus] to anyone who would help epidemiologists trace it back to them, nor ultimately be HIV positive [having antibodies to the virus indicative of previous infection] when tested later.
You say the chain of events seems improbable. What do you make of the recent Department of Energy report that concluded “with low confidence” that a lab leak was the most likely source?
I have no idea what was in the DOE report. I cannot comment specifically 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 it [the new animal evidence].
These first cases [were] linked to the market. Yes, there was a lot of confusion. But once we somehow removed all the assumptions and data that didn’t hold up to testing, all that was left was the market. And everything we’ve done since then, from the geographic analyzes to the genomic analyzes to, now, the forensic genetic analysis—all point to natural zoonosis in the marketplace.
Regardless of the true origin of SARS-CoV-2, should we be concerned about maintaining safe laboratories to prevent potential releases of deadly pathogens?
Of course. I don’t know any virologists who don’t take biosecurity seriously. But when we talk about profit-operations research and lab safety, that discussion should be disconnected from the discussions about COVID because they are two different issues. The conditions of origin are unrelated and it is wrong to confuse the two.
Back to the new genetics, what insights are you still hoping to glean from these in the coming weeks?
There is genetic material from the [market] counters that did not have SARS-CoV-2. I would be very interested to see them. There’s more genetic data from the market that hasn’t become available… I think the earlier sequencing runs may still be out there, and I think it’s imperative that that data be shared across the board so that scientists all stripes can be entered as well [study them].
Will you and your colleagues publish these findings?
We will publish a report summarizing our findings. I would say [the time frame will be] closer to days, maybe even hours.