The Search for the Origins of SARS-CoV-2 "The Results on My Screen Were: Raccoon Dog, Raccoon Dog, Raccoon Dog!"
Raccoon dogs at a fur farm in Zhangjiakaou, China
Foto: Greg Baker / AFPDER SPIEGEL: Ms. Débarre, you have achieved quite a bit of acclaim by stumbling across evidence for the origins of the coronavirus pandemic in a database. Was it just luck?
Débarre: It was Louis Pasteur who said that chance favors the prepared mind. I found the data by chance in the sense that I was not expecting to find it on this database, called GISAID. It’s not the usual database for this kind of data. But I was looking for these sequences in general. We knew the data existed. I was not looking for that data, but it’s not totally random, because I was looking for related information.
Florence Débarre
Foto: Angelika Leuchter / WissenschaftskollegBiologist Florence Débarre, from the National Center for Scientific Research in France, works on mathematical and computational models in evolutionary ecology, genetics and epidemiology at the Institute of Ecology and Environmental Sciences in Paris. She was long open to the possibility that SARS-CoV-2 could have escaped from a laboratory - until an increasing volume of evidence pointed to a natural origin. On Twitter, under the handle @flodebarre, she has more recently been disproving a number of myths propagated by the lab-leak theory.
DER SPIEGEL: What were you specifically looking for?
Débarre: I was looking for information on a genetic sequence that had been shared before and was from the Huanan Seafood Market in Wuhan. You have two ways of accessing a sequence. If you know the identifier, you just enter the identifier, but I was too lazy to look for the identifier, so I just used the search function. I just entered something like "sequences from China. January 2020. Environmental.” And there were more sequences than usual. I thought: Wow!
The article you are reading originally appeared in German in issue 13/2023 (March 25th, 2023) of DER SPIEGEL.
DER SPIEGEL: Did you immediately realize what you had found?
Débarre: The results are displayed in a table, and you have a column for sequence length. In each sequence length field, a very short sequence was entered, only three nucleotides. It made no sense. I thought they were placeholders and that the data hadn’t been entered yet.
DER SPIEGEL: As you and your co-authors write in the recently released report, this happened on March 4. But you only found the actual data five days later?
Débarre: I immediately contacted the people who became my co-authors – as well as multiple other researchers – and asked them about the placeholders. They were surprised, but not much more. I really wanted to know what was going on. Then, on March 9, I went back to the database and just clicked on one of the entries – and I realized that there was data associated with them!
DER SPIEGEL: Genetic sequences from samples taken by Chinese researchers in the Huanan market shortly after the outbreak of the pandemic -- samples containing the SARS-CoV-2 virus. What went through your mind when you found them?
Débarre: It was 11:30 p.m. and I was at home on my couch. It was: Wow! I had been waiting for a year, and then suddenly seeing them. But the greatest emotion was the next day …
DER SPIEGEL: What happened then?
Débarre: My co-authors started downloading the data and my colleague, Alex Crits-Christoph started analyzing it, focusing first on samples that he found particularly interesting. He sent us a file the next day, a sequence he had assembled from one of the samples. He didn’t tell us what it was, to give us the pleasure of seeing it for ourselves. I entered it into a program we use to identify sequences, and the result was: raccoon dog, raccoon dog, raccoon dog! So I don’t swear, but I didn’t just say "wow!”
DER SPIEGEL: During the SARS-1 pandemic from 2002-2003, raccoon dogs were, along with civet cats, intermediary hosts from which the virus jumped to people. For that reason, they are a primary suspect when it comes to SARS-CoV-2, but absolute proof has yet to be found. The genetic material that you have now discovered indicates the presence of coronavirus-infected raccoon dogs at the Wuhan market – meaning they could be the connection between bats and humans this time as well. Did it come as a surprise to you?
Débarre: It’s very interesting. Back in December, I had email exchanges with Michael Worobey about his study …
DER SPIEGEL: … the evolutionary biologist from the University of Arizona, who had found indications that the pandemic had started in the Huanan Seafood Market.
Débarre: Exactly. And I basically told him that, while his paper was very convincing, he was slightly overselling the result. They were presenting it as being too decisive. I recently looked back and found a postscript in one of my emails, where I wrote: If genetic material from a raccoon dog is ever found in the positive coronavirus tests from the market, I will say the evidence is decisive.
DER SPIEGEL: Still, the sequences you found are not clear proof that the animals were infected, and that SARS-CoV-2 jumped from them to humans at the market.
Débarre: That is basically impossible to determine for sure, for now. But this is close to the best that we can have. We can now say that the presence of corona-infected racoon dogs at the market is a plausible scenario. Especially since we have found genetic material from other species that could have served as an intermediary host for SARS-CoV-2.
DER SPIEGEL: How much more likely does your data make it that the virus has a zoonotic origin?
Débarre: It is an additional element in an already big body of evidence – and all the available evidence is consistent and goes in the same direction. But more important than that confirmation is the fact that the genetic material allows us to place the infected animals in the genealogical tree.
DER SPIEGEL: Why is that important?
Débarre: That allows us to see where the infected animals from the Huanan Seafood Market come from. The raccoon dog, for example, doesn’t seem to be part of the subspecies used for the fur trade in northern China.
DER SPIEGEL: The suspicion held by many experts, that the virus could have jumped to humans at a fur farm, is therefore likely inaccurate?
Débarre: It looks like that might not be correct. But now, using the genetic information, we can be more precise in the search for the intermediary host of the SARS-CoV-2 virus. A future investigation could sequence samples from wild and farmed raccoon dogs. The closer they are to the market animals that we found, the more likely it is that that’s where the market animals came from.
DER SPIEGEL: Is it not possible that the raccoon-dog DNA in the positive sample from the market is much older than the outbreak in China? DNA endures for quite some time.
Débarre: But RNA degrades more quickly. And we found both nucleic acids from the animals, DNA and RNA.
DER SPIEGEL: There is also the so-called lab leak theory, according to which the virus could have escaped from a Chinese research laboratory. You were part of the Paris Group, a collection of researchers that demanded the theory be investigated. What changed your mind?
Débarre: I was never in favor of that theory, I was agnostic. I thought both the natural origin and the lab origin were possible. And I never signed the open letter of the Paris Group because I think that science and politics shouldn’t mix.
DER SPIEGEL: But what made you turn away from the lab leak hypothesis.
Débarre: I started seeing contradictions. I realized that many of the key stories that made the lab leak sound plausible were actually false, and that many of the things I had been told didn’t stand up to scrutiny. The only thing that is in favor of the lab-origin idea is the coincidence that the lab is located in Wuhan. But all the facts go in the direction of the market and of a natural origin.
DER SPIEGEL: Could you give us an example?
Débarre: The fact that the closest known relative to SARS-CoV-2 doesn’t come from scientists at the Wuhan Institute of Virology, but from Laos. That even at the Huanan Seafood Market, there were two different virus lineages, so virus diversity was present there. And then there are the early cases: Whether they can be traced definitively to the market or not, they are grouped geographically around it. And now, another strong indication, the raccoon dog DNA.
DER SPIEGEL: Do you think your findings will be enough to put the lab leak theory to bed? In the U.S., more than half the population believes it.
Débarre: Hard to say. The most important role in shaping public opinion is played by the media, and they unfortunately haven’t always been a productive participant in the discussion over the origins of the virus. Even a serious newspaper like Le Monde reported things that were incorrect. Ultimately, though, science is science, and not a beauty contest. Scientific truth may not always be popular, but it is the truth. And the truth is not influenced by what people think.
DER SPIEGEL: The samples taken from the cages, walls and floor of the Huanan Seafood Market were collected between January and March 2020. Why didn’t the Chinese publish their own results long ago?
Débarre: You’d have to ask them.
DER SPIEGEL: We did, but we didn’t get an answer.
Débarre: I don’t know the Chinese scientists personally. I don’t really know what their reasons are.
DER SPIEGEL: Could it be possible that the researchers simply missed the raccoon dog DNA in the samples, with no ill intentions or political agenda?
Débarre: There are a number of plausible reasons for why the world heard nothing about it for so long. But I don't want to speculate.
DER SPIEGEL: Amid the search for the source of the pandemic, China has spent the last three years trying to cast suspicions on other countries. They claimed the virus, for example, could have come into China via frozen foods from Vietnam, or during military exercises in 2019. In their pre-print from February 2022, scientists from the Chinese Center for Disease Control and Prevention wrote that they had been unable to find any indications of a zoonotic intermediary host …
Débarre: … though they also indicated that they had collected data on it. Scientists from around the world have been talking about it for the last year.
DER SPIEGEL: The conclusion of the Chinese pre-print was that the origins of the pandemic could not be traced to the Huanan Seafood Market. Doesn’t that make it clear that the scientists were adhering to their country’s political agenda?
Débarre: I do not want to go into politics. I know there is a political aspect. But I am a scientist and I stick to my field of expertise.
DER SPIEGEL: Though you now find yourself in a rather sensitive situation as a scientist. Those responsible for the GISAID database have accused you and your co-authors of stealing data. Are you facing negative consequences?
Débarre: My access to the GISAID database was revoked recently.
DER SPIEGEL: It was?
Débarre: Yes, as was that of my co-authors. We weren’t able access any part of the entire database. It was an extremely serious situation for us, but also for public health in general. I work with the French sequencing consortium, for example, which follows whether new variants are appearing. I can’t do that work without access to GISAID. I am extremely relieved that my access was restored.
DER SPIEGEL: The platform was established to allow for the rapid exchange of important data pertaining to public health. Could that have been the intention of the Chinese researchers?
Débarre: The metadata indicates that it was uploaded last June. But it was apparently only made accessible on January 30. That is essentially an embargo, which is contrary to the spirit of GISAID.
DER SPIEGEL: Was it clear to you that you would be attacked when you came out with your results.
Débarre: It was clear to us that we were in a challenging ethical situation. On the one hand, we wanted to adhere to the rules of science and not publish the data of others under our names. On the other hand, the world has been obsessing over the origin of this pandemic for three years. Being silent when we had part of the answer was morally indefensible. In the end, we decided not to write a paper for a scientific journal, but a report in which we merely communicated our most important findings. We of course want to give our Chinese colleagues an opportunity to publish a scientific paper first.
DER SPIEGEL: One of the Chinese scientists involved gave you advance permission to analyze the data …
Débarre: … that went through (the British evolutionary biologist and virologist) Eddie Holmes, who has had good contacts in China for many years …
DER SPIEGEL: … but after you found the raccoon dog DNA, the data was suddenly no longer accessible. GISAID said in a statement that data could become temporarily "invisible” when being updated.
Débarre: I was shocked when it was no longer possible to access the data. But I wasn’t surprised.
DER SPIEGEL: You offered to cooperate with the Chinese researchers, but thus far, no cooperation has materialized. Are you still interested in working with them?
Débarre: The Chinese scientists are in possession of more data that would be useful. We don’t want to burn bridges.
DER SPIEGEL: Though it currently looks like the Chinese scientists, at the very least, slowed down the search for the origins of the pandemic, if not actively hindered it. Has the announcement of your team’s findings exposed them?
Débarre: I don’t know what the world now thinks about the Chinese researchers. I basically stayed at home all week. I had three all-nighters in the week, basically just taking 20-minute naps here and there. In the morning I would speak with Eddie Holmes in Australia and in the afternoon with my colleagues in California. I didn’t even know what was going on with the political situation in France with the strikes. At some point, I started wondering why garbage was piling up on the street outside. It was probably the most exhausting week of my life. But it’s exciting to have found such an important piece of the puzzle, the answer to a question I have been obsessed with for the last three years.
DER SPIEGEL: What happens next?
Débarre: I’m just living from day to day. I’m not even thinking about what might happen in the coming weeks and months. Either way, we have to wait and see what is in the scientific paper the Chinese researchers have now submitted to a journal of the Nature publishing group. A lot depends on that. Beyond that, I hope that the riddle about the origin of SARS-CoV-2 might ultimately be solved.
