New crown retrospectively: a French genetic researcher’s weighty questions

A group of 31 internationally renowned scholars from the fields of virology, genetics and computer science issued a joint appeal on June 28 for an in-depth investigation into the source of the new coronavirus. While not the first of its kind, this appeal is unique in that it proposes a plan B that could lead to a thorough investigation into the source of the virus even if China continues to refuse to cooperate.

The signatories of the open letter believe that there is a lot of important information outside of China that could help trace the true source of the virus, and they explicitly call on laboratories and research institutions that have collaborated with the Wuhan lab to release the information they have, especially those that study coronaviruses, including the EcoHealth Alliance in the United States and the European Several research institutions, notably the Institut Pasteur in France, the Institut National de la Santé et de la Recherche Médicale (INSERM) in France, and the Fondation Mérieux in Lyon, France, as well as several foundations that provide research funding to the Wuhan laboratory.

Ms. Virginie Courtier, a researcher in genetic evolution at the Institut Jacques Monod (CNRS UMR7592 -Université de Paris), is one of the leading authors of this appeal, having signed several similar appeals. In an interview with RFE/RL, she explained in detail why she signed several similar open letters calling for the tracing of the origin of the virus and why she had doubts about the origin of the virus from the beginning. In particular, she raised various questions in the interview about the RaTG13 virus, the closest to the new coronavirus announced by the Wuhan laboratory. She also stated that she wrote directly to Ms. Zhengli Shi, the head of the Wuhan laboratory, on June 11, but did not receive any response from Shi.

The following is the text of an interview with Ms. Virginie Courtier on June 29th.

First of all, this is not the first time you are involved in publishing an open letter calling for tracing the source of the virus, why are you so insistent?

Virginie Courtier: The New Coronavirus has affected people all over the world, and none of us want a similar outbreak to happen again, so I think it’s important to find out the source of the virus so that we don’t have to deal with it again and know what to do if it happens in the future. So for me, this is a very important issue, especially today when the epidemic is still not over and continues to have very serious consequences. I’m very shocked that the international community has not investigated more deeply into a virus that has had such serious consequences. I don’t think there is any contradiction between the fact that some researchers can work on the epidemic, develop a vaccine and find an effective cure, and others can work on finding the root cause of the virus to avoid repeating the same mistakes.

RFK: We have noticed that the new coronavirus is mutating, is this related to the source of the virus? Is it possible to deduce from the rate of mutation whether the virus is naturally occurring or has been modified in the laboratory?

Virginie Courtier: It doesn’t tell us much, I know the media focuses a lot on the mutation of the virus, but the flu virus is also mutating very rapidly, depending on the properties of the virus. As the number of people infected with a new coronavirus grows, the chance of the virus mutating increases. However, there is no need to worry too much about this, because so far many vaccines still carry some resistance.

FG: The mutated virus we are talking about now, for you, did the earliest virus come from Wuhan? Because Chinese officials are still emphasizing that although the outbreak first occurred in Wuhan, that doesn’t mean that the virus necessarily came from Wuhan. Do you think that is a possibility?

Virginie Courtier: As of now, we don’t have a definitive picture of the earliest outbreak, what we know is that the outbreak was in Wuhan at the end of 2019, and not knowing anything about the situation before that, we have found some possible traces of the virus in Italy, in Spain, and probably in France. However, we have not yet done genetic tests on samples of these viruses because the presence of antibodies to the virus in blood samples is not enough to tell, because sometimes there is crossover between viruses, but if we can compile genetic samples of the viruses that appeared at the end of 2019, compile their genetic sequences and analyze them, we should be able to gain further insight into the origin of the virus.

RFE: Are these samples of the virus in China?

Virginie Courtier: Not only in China, but also in hospitals in Europe and the United States. We know that France and Italy have started to compile the genetic sequences of these viruses, but we don’t know much about other countries. As for China, this is a big problem. We were unable to obtain samples from patients at the beginning of the outbreak. It is likely that Chinese hospitals have samples from the early outbreak that have not been analyzed and studied. Even the WHO has not been able to obtain these samples. The reason for compiling the genetic samples of the first viruses is that it is possible to gradually piece together the genetic sequences of the viruses at their earliest appearance, and as far as we know, it appears that the first viruses infected a large wave of people with the same virus, so tracing the first traces of the virus can help to understand when the virus started to mutate and under what circumstances, and also where the virus actually first appeared.

RFE: If I understand correctly, for you, it is not unreasonable for Chinese officials to say that the virus did not necessarily first appear in Wuhan, although the outbreak occurred there?

Virginie Courtier: Well, after all, the new coronavirus is very similar to that of bats, which live mainly in Southeast Asia, especially in the south of China. Forty years ago, these coronaviruses existed in bats. After that, what exactly happened these viruses began to infect humans. From the point of view of logical reasoning, it would be the simplest way to spread the coronavirus from the bats living in Asia that infected the local population, followed by an outbreak. Of course, it is also conceivable that the virus could have passed through another country and then infected China, which is significantly less likely because it would have left a trail. Of course, until the truth is known, and until all the data from the study is carefully analyzed, it is certainly impossible to rule out any of these possibilities 100% of the time. The truth is that we cannot be sure whether the virus came from nature or from the laboratory.

We have noticed the reaction of the Chinese official media after France assisted in the construction of the P4 laboratory in Wuhan, suggesting that China could henceforth rival the United States in the field of biological virus research, and that the Chinese military was playing up the endless possibilities that the laboratory could offer. The lab leak theory, which was initially denounced as a conspiracy theory, is gaining more and more support from experts today.

Virginie Courtier: Actually, from the very first moment of the outbreak, I had doubts about whether the virus was of natural origin. This is still a question for me today. Because we have to admit that we don’t have conclusive evidence. Of course, the reasons for our suspicion are first of all geographical, because the outbreak first broke out in Wuhan, where the Wuhan laboratory is located, and also, the Sass virus that the laboratory is studying happens to be the same type of virus as the new coronavirus. Another big reason, for me the most important one, is that the Chinese side is withholding a lot of important information from the outside world, and of course, the Chinese side may have his own reasons, and it may be unfair for us to condemn it without knowing why. So, for me, it’s important to continue to follow up until we find the real source of the virus.

RFE: Yes, Chinese official media often refuse to provide information on the grounds of Chinese sovereignty and refuse to accept requests from the WHO, the U.S. or other countries, but in the face of a pandemic that has killed millions of people, national sovereignty or national pride and so on do not seem to be sufficient to explain the Chinese official position. I remember last year I interviewed a virologist from China who believed that the new coronavirus must have come from a laboratory, and she reasoned that the presence of the S protein in the virus gene, which can infect humans, showed that it was an artificially processed virus, because it is unlikely that the virus gene would have appeared in such a short time under normal natural genetic evolution. For her, this is very obvious, but, surprisingly, the French virologists do not seem to be surprised by this, what do you think?

Virginie Courtier: It is her personal opinion and perhaps very obvious to her. Actually, from an objective point of view, it is not impossible. Previously, when researchers created new viruses, they tended to add together the genomes of viruses that already existed, and the new coronavirus contains sequences that were unprecedented in its genetic sequence, which was the primary basis put forward by those who first refuted the idea that the virus came from a laboratory, although that basis is no longer valid today because we know today that the Wuhan laboratory is working on a virus that is close to the new coronavirus. Another major argument against the laboratory leak theory is that man-made viruses generally bear traces of molecular cleavage, whereas there are no traces on the genetic sequence of the new coronavirus. Of course, proponents of the laboratory origin of the virus emphasize that the virus is particularly susceptible to human infection and seems to be specifically designed for humans, which I do not think is the case because pandemics that ravage the world often occur only once every few decades, and the virus that caused this catastrophe is certainly not an ordinary virus, so it is conceivable that a chain of factors led to today’s consequences. Of course, the new coronavirus carries an enzyme entry point, which is known to make the coronavirus more transmissible, but this enzyme entry point on the new coronavirus is not the usual method used by researchers, so the possibility that the virus is the result of natural evolution still exists. This is why we must conduct more in-depth studies.

RF: Were you surprised when Zhengli Shi announced in February 2020 the genetic sequence of RaTG13, the closest virus to the new coronavirus, to the public? How do you understand that a researcher waits several years after discovering an important virus before releasing it?

Virginie Courtier: I was not surprised by this, because it takes time to publish a scholarly research article. However, I was surprised that the samples of the RaTG13 virus were not left in a negative form. In an academic article, the Wuhan lab claimed that all virus samples had been used up and that there were no samples to verify the genetic compilation. This is very surprising to me, because usually people who do research leave some samples behind. It is also very surprising because the RaTG13 virus once appeared under another name RA4991 in a PhD thesis in June 2019. Why would the same virus have two names? Why did she publish the RaTG13 virus without mentioning the virus that had already appeared before?

FW: Have you found possible answers to these questions today or have you been unable to understand them so far?

Virginie Courtier: I really can’t understand. I wrote to Zhengli Shi a few weeks ago and asked her a series of questions, but I haven’t received any answers so far. Of course, I also understand that she should not have any freedom at the moment.

FG: Yes, any public statements she makes should be strictly controlled. Do you know her personally? Because she used to study at the University of Montpellier in the south of France, perhaps you had the opportunity to meet.

Virginie Courtier: No, I studied genetic evolution and worked on flies for 20 years, and only started studying coronaviruses after the outbreak of the new crown epidemic.

FaQ: I once interviewed a virologist of Chinese descent who thought that the RaTG13 virus was probably a man-made virus, and she said that it was actually an easy thing to make up the genetic sequence of a virus in just a week. At that time, I thought that this idea was perhaps a bit fanciful, so I did not make this interview public, but today, it seems that the idea of a human-made genetic sequence could at least explain the reason why the Wuhan laboratory was not able to provide the virus samples that you just mentioned. Do you think that this possibility exists?

Virginie Courtier: She thinks that the genetic sequence of the virus was completely fabricated! This is a possibility that never occurred to me. Because as biologists, this is completely beyond our imagination. However, technically, it is entirely possible, just by sitting in front of a computer, to make up a genetic sequence of a virus artificially. In fact, the people in the Drastic investigation team were skeptical about the authenticity of the RaTG13 virus from the beginning because we lacked much information related to the virus. For example, at the beginning, the top 15 nucleotides (nucleotide) on the gene sequence of the virus were not published, and Jung-Li Shih said at the beginning, in response to a question from Science Magazine, that there was a lack of genetic samples and therefore the gene sequence of the top 15 nucleotides (nucleotide) could not be compiled. Therefore, this part of the gene sequence was not included in the first published sequence of RatG13 virus, but later, for some reason, the sequence of these 15 nucleotides appeared, and it was identical to the sequence of the new coronavirus. This was all very puzzling to us. Several colleagues and I sent a list of questions to Zhengli Shi, as she was the only one who knew the answers to these questions.

French: You actually doubted the credibility of the natural origin of the new coronavirus from the very beginning, why did you have such doubts?

Virginie Courtier: I was skeptical of the origin of this virus from the beginning, but what I find most bizarre is why so much important information has not been released to the public. For example, the entry point of the S protease of the new coronavirus, this information was probably already known by the Wuhan virus laboratory, so why wasn’t it released to the public? And they deliberately kept the information about the entry point in the announcement. Also, what exactly are some of the connections between the new coronavirus and the bat cave in Yunnan and the previous pneumonia that appeared in 2012. So, all of this, for me, I’m skeptical about the origin of the virus primarily because of the important news related to the production of the new coronavirus, not because of the genetic sequence of the virus or anything else. However, I would like to point out here that a complete in-depth analysis of the viral genetic sequence has not yet been completed and I look forward to completing this work with my colleagues.

Questions focus on RaTG13 virus

RFG: There are indeed many doubts surrounding the RaTG13 virus, and many experts believe that this virus has a lot of important doubts, do you think so too? What do you think are the biggest questions about the RatG13 virus?

Virginie Courtier: Yes, I agree. There are indeed many major doubts about this virus; first of all, why did Zhengli Shi not mention the previously known RA4991 when she first published this virus in Nature; secondly, how exactly was the gene sequence of this virus obtained? Why were we not able to obtain a sample of the first 15 nucleotides of the compilation? Also, why did they not leave a sample of the virus in order to verify the gene compilation procedure? If we take a closer look at the gene sequence of RaTG13, there is not a lot of bacterial data in it, whereas in general, the gene sequence of a virus from bat guano should have many bacterial sequence sets in it. So, this is also very strange. Instead, we found many sequences of human genes in the sequence. Finally, RaTG13, being a virus from bats, so far no laboratory has recombined the RaTG13 virus, but someone has recombined the S protein in it, and it turns out that the S protein is hardly accepted by the bat receptor, whereas it should be a virus from a bat. So it’s all very strange.

RF: The questions you raised should have been objective questions from the beginning, but we noticed that the virology community publicly raised these questions only last summer, and that many well-known research institutions are still silent today.

Virginie Courtier: Many international research institutions have worked with the Wuhan lab, and it is not easy to publicly raise doubts about a trusted colleague, especially when there is no evidence for the lab leak theory.

FAG: In the early days of the outbreak, the prestigious British journal The Lancet and Nature immediately published articles that ruled out the possibility of a lab leak and characterized similar suspicions as conspiracy theories, leading to a halt to similar comments, which many of us found puzzling at the time, because lab leaks do not happen every day, but they do happen from time to time. Scientists can vouch that it hasn’t happened in their own labs, but how can they vouch for a lab thousands of kilometers away! What is your comment on the withdrawal of Peter Daszak, president of the American Association of Health Care Coalitions, as a member of the New Coronavirus Research Committee by the Lancet today?

Virginie Courtier: Yes, The Lancet considered Peter Daszak’s work to be of a conflict of interest nature, but did not take action against others who were also suspected of having a conflict of interest. Of course, one should not let this lead one to believe that the scientific community is also in the dark. The latest article on Jesse Bloom’s latest findings published in Nature is valuable!

Finally, you must have noticed, as many people interested in virus tracing, the comments made by Peter Daszak about coronavirus research at a symposium in Singapore shortly before the Wuhan outbreak.

Virginie Courtier: In general, I have reservations about the comments he made, for example, about RaTG13, where he said that the virus was stored in a freezer and the lab only compiled the genetic sequence of the virus at the time of the outbreak, whereas today the Wuhan lab says that the genetic sequence of the virus was completed as early as 2018.

FW: Thank you very much for the interview with FW!

Annex: Email from Virginie Courtier to Zhengli Shi on June 11

Email from Virginie Courtier, a French researcher in genetic evolution, to Zhengli Shi on June 11

From:COURTIER Virginie

Sent:Friday,June 11,2021 2:28 PM

To:[email protected]

Subject:questions around SARS-CoV-2

Dear Pr. Shi Zheng-Li,

These ongoing times are probably putting a lot of pressure on you and I imagine that the situation must be very difficult in the present context. I sincerely hope that you can cope with it well. As shown by the recentScience letter,many people in the scientific community are currently not satisfied with the conclusions of theWHO-China joint reportand are asking for amore thorough investigationin order to unravel how SARS-CoV-2 spread into the human population. To try to put an end to the discussions about a possible lab origin of the virus,I think that it would be important to clarify the few elements below. Maybe you could help in this process.

In April 2012,after clearing bat guano in an abandoned mine in Mojiang(Yunnan),six men contractedsevere pneumonia with COVID-19-like symptoms. All were sent to Kunming hospital where three eventually died. Unspecified samples from these patients were sent to different labs including the Wuhan Institute of Virology(WIV)in 2012. You recently announced that theWIV tested the serum samples again.

Why were these six miners sent to clean guano in the mine in April 2012?Who hired them and sent them all to the same Kunming hospital?

Why were these lethal pneumonia cases not mentioned in any scientific research article from the WIV,except theNature‘sAddendumfrom last November?

What samples were taken from these six patients and sent to the WIV?Are any of these samples still available for independent analysis?

Were any SARS-like coronaviruses isolated from the patient samples or were any RdRP or spike sequence obtained by RT-PCR?

Is it possible to provide to the WHO serum samples from the three surviving miners in order to better understand in which condition these miners fell sick and what their exact pathology was?

2You stated that Wuhan Institute of Virology virus databases were taken offlineduring the pandemic. However the keybat virus databasewas taken offline in September 2019,three months before the official date of outbreak started.

Can you provide further details on why the database was shut down?

Can all the databases,in their state as of September 2019,be shared with selected expert scientists?

Do you have any information concerning the reasons why thescientific paperdescribing thekey database(digital object identifier:10.11922/csdata.2019.0018.zh)was takenofflinefrom the corresponding Chinese journal website“China Science Data”mid-2020?

Did you know that even thefull websiteof“China Science Data”,where the database is described,becameinaccessiblein March-April 2021?

3。A bat coronavirus sampled in the Mojiang mine in 2013(’RaTG13‘)is a virus most closely-related to SARS-CoV-2. In your interview withSciencein July 2020,you said that“Ra4991”was renamed to“RaTG13”,the virus was not isolated,and that there is“no more sample”,so no further sequencing is possible. Unfortunately,based on the raw data provided,it has not been possible toassemblethe RaTG13 genome sequence.

How was the RaTG13 genome sequence assembled and how was the5’sequence determined?

Was“Ra4991”renamed to“RaTG13”for yourarticle,as theAddendumseems to indicate,or are these 2 viruses divergent in some regions such as the spike protein?

When was the RaTG13 sample fully depleted?

Why are a few of theRaTG13 ampliconsdated as of June 2017and named“7896”,which is thenameof another closely related virus collected in the same mine?

As the row data contains low levels of bacterial sequences,wasRaTG13sampled from bronchoalveolar lavage fluid or from bat feces?

Given that RaTG13 showsweak bindingto bat receptor ACE-2 and binds only to one of the ACE2 orthologs ofRhinolophus affinis,is RaTG13 the true whole genome sequence of the sample BtCoV/4991 collected in 2013 by the WIV?

Did the WIV or any other laboratory ever attempt to recreate RaTG13 or any other coronaviruses by assembling them from synthetic gene sequences?

4。A striking feature of the SARS-CoV-2 genome is the presence of the furin cleavage site. This site was noted as a“cleavage site”in your January 2020publication.

Why was this so-called“furin cleavage site,”clearly an important and novel feature of the SARS-CoV-2 virus,not mentioned in your February 2020 Naturepublication?

5.You acknowledgedisolating three strains of live SARS-related coronaviruses,but based on the WIV namingconventionfor their live viruses isolates it appears that the WIV did not disclose two potential isolates,WIV6(not WIV06)andWIV15,as these names are not mentioned in the literature.

Do these isolates exist?If not,what is the explanation for why these isolate names were skipped in the series?

6.Chinese authorities have statedthat all staff at Wuhan labstested negative for SARS-CoV-2 antibodies.

How many people were tested,in which Wuhan labs,on which days,and as part of which teams or services within these labs?

Were any of these serum samples retained?

Are independent international investigators able to retest the samples of the lab staff to confirm the results?

7.You previouslywrotethat:‘Recently we tested the sera from all staff and students in the lab and nobody is infected by either bat SARSr-CoV or SARS-CoV-2. To date,there is“zero infection”of all staff and students in our institute’. This statement is statistically unlikely(roughly less than one chance in a billion)given that there are more than 590 staff and students at the WIV and about 4.4%of the Wuhan urban populationtested positiveat around that time. Even if only 85 people were tested,the chance of no positive test would still be less than 4%.

How can this unexpected observation be explained?

Is it possible to have more information on the“one or two”WIV‘s workers that fell ill in late 2019,as evoked by amember of the WHO-China jointmission?

8.Recently,you published apreprintpresenting the 8 coronaviruses that were mentioned in Nature’sAddendum,in November 2020.

The preprint indicates that these 8 new coronaviruses,including RaTG15,are constituting a novel lineage of SARSr-CoV from bats:“we report the identification of a novel lineage of SARSr-CoVs,including RaTG15 and seven other viruses,form bats”. When did exactly this identification take place?

Do you confirm that the lineage called“lineage 4”in a phylogenetic tree(Figure 3.1)in the MS thesis by Yu Ping,“Geographic Evolution of Bat SARS-related Coronaviruses”(June,2019),is the same lineage as that of the 8 new coronaviruses?

The preprint mentions that these 8 viruses have been collected in“the same location where we found RaTG13 in 2015”. Why is the 2012 Mojiang mine‘s outbreak that occurred at the same location not mentioned,which is important information to understand the context of your research?

The preprint claims that none of the known viruses in bat SARSr-CoV-2 lineage or the novel lineage discovered so far use human ACE2 efficiently compared to SARSr-CoV-2 from pangolin or some of the SARSr-CoV-1 lineage:“We show that none of the known viruses in bat SARSr-CoV-2 lineage or the novel lineage discovered so far use human ACE2 efficiently compared to SARSr-CoV-2 from pangolin or some of the SARSr-CoV-1 lineage viruses.”To support this statement,is it possible to share the complete list of unpublished viruses that are present in your institute,as well as the raw data and the experimentation records related to them?

Are these 8 new viruses still kept in your institute,in what condition,and if they are physically available can they be made available to other researchers?

Can you clarify whether the Bat Ra ACE2 sequenceMT394204used in the pre-print comes from the same Mojiang mine?

How can you explain that the eight viruses are almost identical?How can you explain that each sequence was found only once along the 7 visits to the mine?Doesn’t it contradict your findings of a“rich gene pool”in the longitudinal study in the caves of Jinning?Did you retest all the 1,322 samples?

Can you provide the raw sequencing data of the 8 viruses?

Why do the 8 virus sequences display a few nucleotide changes in their RdRp sequences compared to the previous versions that were submitted to NCBI Genbank for the publication of the Latinne et al. paper?Can you explain the methods employed then and now?

There is some confusion in the nomenclature of these viruses:in the slide of 2 different presentations from your lab,they were labeled Ra or Rs. Can you confirm the bat species infected with such viruses?Isn’t it surprising that RaTG15 is found in one bat species while the extremely close viruses are from another bat species?Could there be an issue regarding the bat species assignment based on COI sequence?

With my sincere and warmest regards,


Virginie Courtier-Orgogozo

Institut Jacques Monod -CNRS UMR7592 -Université Paris Diderot

Bâtiment Buffon -4eétage -420B

15 rue Hélène Brion

75013 Paris


tél:(33)1 57 27 80 43

fax:(33)1 57 27 80 87