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An appeal for an open scientific debate about the proximal origin of SARS-CoV-2

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This letter was submitted to The Lancet on January 6, 2021. It re-evaluates the scientific evidences that have been invoked at the very beginning of the COVID-19 pandemics to support the hypothesis of a natural zoonosis, and shows that these arguments were inconclusive and felt under some logical flaws. It thus requests scientific journals to open their columns to an evidence-based, prejudice-free evaluation of all the reasonable hypotheses about the origins or SARS-CoV-2. The letter was rejected by the editorial committee. We asked the editors whether this refusal meant that they consider this scientific evaluation of the alternative hypotheses should not be hosted by scientific journals, and advocated that leaving it to social media and politicians was the best way to fuel conspiracy theories. The submission was reassessed by the chief editor, who confirmed the decision to reject the letter without peer review. One argument for the rejection was that our appeal was a response to Calisher's statement ( ), published in Jan 2020, whereas The Lancet policy is to accept responses within 15 days after the publication of an article. On July 5th, 2021, Calisher and colleagues published a new statement ( ). We revised our Appeal and submitted as a response to this second statement, and this version was accepted, and finally published in Sept 17 ( ).
An appeal for an open scientific debate about the proximal origin of SARS-CoV-2
Jacques van Helden1,2,*, Colin D Butler3, Bruno Canard4, Guillaume Achaz5,6, François Graner7,
Rossana Segreto8, Yuri Deigin9, Fabien Colombo10, Serge Morand11, Didier Casane12,13, Dan
Sirotkin14, Karl Sirotkin14, Etienne Decroly,4,* José Halloy15,*
1. CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
2. Aix-Marseille Univ, Inserm, laboratoire Theory and approaches of genome complexity (TAGC),
Marseille, France; ORCID: 0000-0002-8799-8584
3. National Centre for Epidemiology and Population Health, Australian National University, Canberra,
4. Aix-Marseille Univ, CNRS, UMR 7257, AFMB, Case 925, 163 Avenue de Luminy, 13288 Marseille Cedex
09, France. ORCID: 0000-0002-6046-024X
5. Eco-Anthropologie (UMR7206 Université de Paris-CNRS-MNHN), Muséum National d’Histoire
Naturelle, Paris, France
6. Center for Interdisciplinary Research in Biology (UMR7142 Collège de France-CNRS-INSERM), Collège
de France, Paris, France
7. MSC, Université de Paris, CNRS UMR 7057, 10 rue Alice Domon et Léonie Duquet, 75205 Paris Cedex
13, France
8. Department of Microbiology, University of Innsbruck, Austria
9. Youthereum Genetics Inc., Toronto, Canada.
10. Université Bordeaux Montaigne, Mediation, Information, Communication, Art (MICA, EA 4426), 10
esplanade des Antilles, Pessac, France.
11. Montpellier Université, CNRS, Institut des Sciences de l'Évolution (ISEM), 34290 Montpellier, France,
ORCID: 0000-0003-3986-7659
12. Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198,
Gif-sur-Yvette, France
13. Université de Paris, UFR Sciences du Vivant, F-75013 Paris, France
14. Karl Sirotkin LLC. ORCID: 0000-0002-9685-0338
15. Université de Paris, LIED, CNRS UMR 8236, 85 bd Saint-Germain, 75006 Paris, France.
ORCID: 0000-0003-1555-2484
* Corresponding authors
One year after the onset of the COVID-19 pandemic, the origin of SARS-CoV-2 still eludes humanity.
Early publications firmly stated that the virus was of natural origin, and the possibility that the virus
might have escaped from a lab was discarded in most subsequent publications. However, based on a
re-analysis of the initial arguments, highlighted by the current knowledge about the virus, we show
that the natural origin is not supported by conclusive arguments, and that a lab origin cannot be
formally discarded. We call for an opening of peer-reviewed journals to a rational, evidence-based
and prejudice-free evaluation of all the reasonable hypotheses about the virus’ origin. We advocate
that this debate should take place in the columns of renowned scientific journals, rather than being
left to social media and newspapers.
On February 19, 2020, three weeks after the publication of the SARS-CoV-2 genome,1
twenty-seven scientists signed a Statement in support of the scientists, public health professionals
and medical professionals of China combatting COVID-19
in The Lancet.
2They took an authoritative
position about the origin of the novel coronavirus behind the pandemic: “Scientists from multiple
countries have published and analysed genomes of the causative agent, SARS-CoV-2, and they
overwhelmingly conclude that this coronavirus originated in wildlife”
. This statement has since
attracted 23,000 additional signatures, and was used throughout the international press as proof
that SARS-CoV-2 emerged due to a natural zoonosis.
We share our colleagues’ annoyance about various unfounded theories spreading over social
networks which seemed to be aimed at increasing geopolitical tensions. However, on the basis of
the current scientific literature, complemented by our own analysis of coronavirus genomes and
proteins,3–5 we hold that there is currently no compelling evidence to definitively arbitrate between
a completely “natural” origin (i.e. a virus that has evolved and been transmitted to humans solely via
contact with wild or farmed animals) and a “laboratory” origin (which might involve one or more
steps such as transport of animal samples to Wuhan, viral evolution, an index case occurring through
viral exposure in a laboratory, accidental laboratory escape, faulty autoclaving equipment, or any
other possible escape pathway ...).
Of the nine references cited in the statement to support the natural origin hypothesis, eight
consist of trees showing phylogenetic relationships between SARS-CoV-2 and other coronaviruses. A
distinction has to be made between the general ancestry and the proximal
origin of the virus, i.e. the
last step of its transmission chain from its original animal reservoir (putatively bats) to humans. To
the best of our knowledge, the fact that the causative agent of COVID-19 descends from natural
viruses has not been questioned by anyone, but this distal origin does not explain how it came to be
able to infect humans. This step is still unknown, since the closest animal virus at our disposal
(RaTG13) shows a 4% difference with SARS-CoV-2, genetic distance which has been estimated to
reflect 4 to 7 decades of evolutionary divergence6. Pangolins are no longer considered a plausible
intermediate host based on the molecular evidence.7–10 We thus still need to trace the animal
intermediates between the bat reservoir, locate the places of transmissions, characterize the viral
strains, trace back the outbreak from the first COVID-19 patients, and then finally understand the
ultimate conditions of the transfer from animals to humans.
The proximal origin was explicitly addressed in one reference in the Lancet statement: a preprint
by Andersen et al.
, later published in Nature Medicine in April 202011. This article was highly
influential: within 9 months it was cited in 2,000 scientific publications, and the vast majority of
scientists, including many of us, initially took it for granted that this novel coronavirus was of natural
origin. However, upon re-analysis, we realised that a conclusive proof of the proximal origin is still
lacking. The initial method of reasoning, endorsed in many subsequent papers, was to contrast two
opposing possibilities: natural origin versus “laboratory construct or purposefully manufactured
virus”. Two main arguments were presented against the latter possibility: (i) the specific mutations
that confer their particular affinity to the SARS-CoV-2 spike protein were unknown before COVID-19
emergence, and thus could not have been designed ; (ii) the SARS-CoV-2 genome has no evidence
for reverse engineering (e.g. a previously used viral backbone). The lab construct hypothesis was
thus rejected, leaving a natural proximal origin as the only possibility. However, this reasoning
suffers from a logical fallacy. Proving a hypothesis by discarding its alternative is only valid if the two
hypotheses are mutually exclusive, and cover all conceivable possibilities. In this case, these
conditions are not met, since other mechanisms are plausible, for example serial passage
experiments, 12 which consist of testing and measuring the ability of a virus to infect different animal
models or cultured cells. Such experiments exert an artificial selection of the random mutations that
increase the fitness of the virus to the new host, thereby resulting in a fast evolution of genomic
sequences. As in many virology labs, passage experiments are routinely performed in the Wuhan
Institute of Virology (WIV)13–15, consistently with their mission to collect and monitor viral strains
having epidemic potential into humans. Selection during passage is dismissed by Andersen, based on
the argument that it would be less parsimonious than the pangolin origin. However, the pangolin
hypothesis has since been abandoned. 7–10 Regarding the hypothesis of a laboratory construct,
absence of evidence is not evidence of absence, and a viral genome might be engineered with a yet
unpublished backbone. Also, the expectation of finding traces of engineering in the sequences does
not account for the seamless technologies currently used to synthesise nucleic acids, which have
been around for about 20 years16.
Experiments involving pathogenic viruses require highly secure laboratory conditions.17,18 There
are, however, many well-documented cases of pathogen escapes from laboratories, including
viruses.12,19–22 This scenario was a priori discarded in the February statement: We stand together to
strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin
”. 2
We, like The Lancet authors, condemn conspiracy theories. However, an accident is not a conspiracy,
and we think that scenarios involving a potential lab accident should be evaluated rigorously, along
with the other hypotheses. Even more, it is precisely because actual conspiracy theories are so
rapidly spreading on social media and via some politicians that we ought, as a scientific community,
to evaluate all hypotheses on a rational basis. We need to weigh their likelihood, based on facts and
evidence, devoid of speculation concerning alleged political intent. This approach seems consistent
with the views presented near the conclusion of the Lancet statement “to promote scientific
evidence and unity over misinformation and conjecture
”, but a little word makes a whole difference:
a scientific question has never been solved, and should never be approached, by asking scientists to
promote unity. Science, by definition, explores and embraces alternative hypotheses, contradictory
arguments, verification, refutability, and even controversy. Departing from this principle risks
establishing dogmas, and abandoning science.
Unfortunately, the unitary view promoted in the Lancet statement has, to date, been widely
adopted, with few exceptions.3,4,12,23–25 Scientific evaluations of alternative hypotheses for the origin
of COVID-19 are, as yet, absent from the most prominent scientific journals. This lacuna may even
fuel conspiracy theories. Instead, the scientific community should bring this debate to the place it
belongs: the columns of renowned scientific journals26. An evidence-based, independent and
prejudice-free evaluation of all the reasonable origin scenarios will require collecting samples and
data in all the potentially relevant places, including wildlife sites and farms (as scheduled for the
WHO mission) but also in hospitals and in laboratories. This effort is crucial, not only to solve many
currently unanswered questions and elucidate the cause of the current pandemic, but also to take
appropriate measures of prevention.
1 Zhou P, Yang X-L, Wang X-G, et al.
A pneumonia outbreak associated with a new coronavirus of
probable bat origin. Nature
2020; 579: 270–3.
2 Calisher C, Carroll D, Colwell R, et al.
Statement in support of the scientists, public health
professionals, and medical professionals of China combatting COVID-19. The Lancet
2020; 395:
3 Segreto R, Deigin Y. The genetic structure of SARS-CoV-2 does not rule out a laboratory origin:
SARS-COV-2 chimeric structure and furin cleavage site might be the result of genetic manipulation.
2020; : 2000240.
4 Sallard E, Halloy J, Casane D, Decroly É, van Helden J. Tracing the origins of SARS-COV-2 in
coronavirus phylogenies. Environmental Chemistry Letters
2021; in press.
5 Sallard E, Halloy J, Casane D, Decroly E, van Helden J. Tracing the origins of SARS-CoV-2 in
coronavirus phylogenies. Med Sci (Paris)
2020; 36: 783–96.
6 Sironi M, Hasnain SE, Rosenthal B, et al.
SARS-CoV-2 and COVID-19: A genetic, epidemiological, and
evolutionary perspective. Infection, Genetics and Evolution
2020; 84: 104384.
7 Lee J, Hughes T, Lee M-H, et al.
No Evidence of Coronaviruses or Other Potentially Zoonotic Viruses
in Sunda pangolins (Manis javanica) Entering the Wildlife Trade via Malaysia. EcoHealth
published online Nov 23. DOI:10.1007/s10393-020-01503-x.
8 Choo SW, Zhou J, Tian X, et al.
Are pangolins scapegoats of the COVID-19 outbreak-CoV
transmission and pathology evidence? CONSERVATION LETTERS
2020; 13. DOI:10.1111/conl.12754.
9 Frutos R, Serra-Cobo J, Chen T, Devaux CA. COVID-19: Time to exonerate the pangolin from the
transmission of SARS-CoV-2 to humans. Infection, Genetics and Evolution
2020; 84: 104493.
10 WHO-convened Global Study of the Origins of SARS-CoV-2.
2 (accessed Dec 20, 2020).
11 Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of
SARS-CoV-2. Nature Medicine
2020; 26: 450–2.
12 Sirotkin K, Sirotkin D. Might SARS-CoV-2 Have Arisen via Serial Passage through an Animal
Host or Cell Culture?: A potential explanation for much of the novel coronavirus’ distinctive
genome. BioEssays
2020; : 2000091.
13 Hu B, Zeng L-P, Yang X-L, et al.
Discovery of a rich gene pool of bat SARS-related
coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog
2017; 13:
14 Ge X-Y, Li J-L, Yang X-L, et al.
Isolation and characterization of a bat SARS-like coronavirus
that uses the ACE2 receptor. Nature
2013; 503: 535–8.
15 Yang X-L, Hu B, Wang B, et al.
Isolation and Characterization of a Novel Bat Coronavirus
Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coronavirus.
Journal of Virology
2016; 90: 3253–6.
16 Yount B, Denison MR, Weiss SR, Baric RS. Systematic assembly of a full-length infectious
cDNA of mouse hepatitis virus strain A59. J Virol
2002; 76: 11065–78.
17 Moritz RL, Berger KM, Owen BR, Gillum DR. Promoting biosecurity by professionalizing
biosecurity. Science
2020; 367: 856–8.
18 Xia H, Huang Y, Ma H, et al.
Biosafety Level 4 Laboratory User Training Program, China.
Emerg Infect Dis
2019; 25. DOI:10.3201/eid2505.180220.
19 Sewell DL. Laboratory-associated infections and biosafety. Clinical Microbiology Reviews
1995; 8: 389–405.
20 Heymann DL, Aylward RB, Wolff C. Dangerous pathogens in the laboratory: from smallpox to
today’s SARS setbacks and tomorrow’s polio-free world. The Lancet
2004; 363: 1566–8.
21 Siengsanan-Lamont J, Blacksell SD. A Review of Laboratory-Acquired Infections in the
Asia-Pacific: Understanding Risk and the Need for Improved Biosafety for Veterinary and Zoonotic
Diseases. Tropical Medicine and Infectious Disease
2018; 3: 36.
22 Klotz LC, Sylvester EJ. The Consequences of a Lab Escape of a Potential Pandemic Pathogen.
Front Public Health
2014; 2. DOI:10.3389/fpubh.2014.00116.
23 Rahalkar MC, Bahulikar RA. Lethal Pneumonia Cases in Mojiang Miners (2012) and the
Mineshaft Could Provide Important Clues to the Origin of SARS-CoV-2. Front Public Health
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24 Seyran M, Pizzol D, Adadi P, et al.
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25 Butler CD. Plagues, Pandemics, Health Security, and the War on Nature. Journal of Human
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26 Relman DA. Opinion: To stop the next pandemic, we need to unravel the origins of
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ResearchGate has not been able to resolve any citations for this publication.
Full-text available
This editorial presents a brief review of pandemics from antiquity to COVID-19. Although all large-scale epidemic diseases ("pandemics") can be considered ecological "checks" on human population size, and although COVID-19 is the biggest such pandemic since HIV/AIDS emerged it is not likely to approach the deathtoll of earlier pandemics, such as the plague. There are two major hypotheses to explain the origin of COVID-19. One is the "natural origin" hypothesis, the other is that it might have escaped from a laboratory, with its origin subsequently hidden. Although most scientists support the natural origin idea the other cannot yet be dismissed. Evidence for each hypothesis is presented. If the first theory is correct then it is a powerful warning, from nature, that our species is running a great risk. If the second theory is proven then it should be considered an equally powerful, indeed frightening, signal that we are in danger, from hubris as much as from ignorance. More pandemics are inevitable, but their severity can be reduced by greater transparency, international cooperation , and retreat from planetary boundaries.
Full-text available
The legal and illegal trade in wildlife for food, medicine and other products is a globally significant threat to biodiversity that is also responsible for the emergence of pathogens that threaten human and livestock health and our global economy. Trade in wildlife likely played a role in the origin of COVID-19, and viruses closely related to SARS-CoV-2 have been identified in bats and pangolins, both traded widely. To investigate the possible role of pangolins as a source of potential zoonoses, we collected throat and rectal swabs from 334 Sunda pangolins ( Manis javanica ) confiscated in Peninsular Malaysia and Sabah between August 2009 and March 2019. Total nucleic acid was extracted for viral molecular screening using conventional PCR protocols used to routinely identify known and novel viruses in extensive prior sampling (> 50,000 mammals). No sample yielded a positive PCR result for any of the targeted viral families—Coronaviridae, Filoviridae, Flaviviridae, Orthomyxoviridae and Paramyxoviridae. In the light of recent reports of coronaviruses including a SARS-CoV-2-related virus in Sunda pangolins in China, the lack of any coronavirus detection in our ‘upstream’ market chain samples suggests that these detections in ‘downstream’ animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. While confirmatory serologic studies are needed, it is likely that Sunda pangolins are incidental hosts of coronaviruses. Our findings further support the importance of ending the trade in wildlife globally.
Full-text available
English translation of a French manuscript to be published in the August-Sept 2020 issue of Médecine/Sciences.
Full-text available
Severe acute respiratory syndrome-coronavirus (SARS-CoV)-2′s origin is still controversial. Genomic analyses show SARS-CoV-2 likely to be chimeric, most of its sequence closest to bat CoV RaTG13, whereas its receptor binding domain (RBD) is almost identical to that of a pangolin CoV. Chimeric viruses can arise via natural recombination or human intervention. The furin cleavage site in the spike protein of SARS-CoV-2 confers to the virus the ability to cross species and tissue barriers, but was previously unseen in other SARS-like CoVs. Might genetic manipulations have been performed in order to evaluate pangolins as possible intermediate hosts for bat-derived CoVs that were originally unable to bind to human receptors? Both cleavage site and specific RBD could result from site-directed mutagenesis, a procedure that does not leave a trace. Considering the devastating impact of SARS-CoV-2 and importance of preventing future pandemics , researchers have a responsibility to carry out a thorough analysis of all possible SARS-CoV-2 origins.
Full-text available
With the COVID-19 pandemic reaching its worse heights, everyone is genuinely interested in the origin of SARS-CoV-2. In our quest, we started with two important questions: First, were there any similar atypical pneumonia outbreaks, even on a smaller level, reported in between SARS (2004) and COVID-19 (2019) from China? Secondly, where did the beta-coronavirus most closely related to date with SARS-CoV-2 at the genome sequence level, strain RaTG13 (CoV4991) sampled from a horseshoe bat in Yunnan province, exactly come from? It was found that RaTG13/CoV4991 was collected from Tongguan mineshaft in Mojiang, Yunnan, China, in 2013. Surprisingly, the same mineshaft was also associated with a severe pneumonia-like illness in miners in 2012 killing three of the six miners. A Master’s thesis (in the Chinese language) was found on the website which described in detail the severe illness in miners. The thesis concluded that a SARS-like CoV originating from Chinese horseshoe bats (Rhinolophus) was the predicted causative agent. The cases were remotely monitored by a prominent pulmonologist in China. The retrospective analysis of the pneumonia cases shows striking similarities with COVID-19. We propose that the Mojiang mineshaft and the miners' illness cases could provide important clues to the investigation of the origin of SARS-CoV-2. The cases should be studied by various academicians, researchers, and medical professionals. Many important questions are raised in this context. Fr
Full-text available
There is a consensus that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) originated naturally from Bat coronaviruses (CoVs), in particular RaTG13. However, the SARS‐CoV‐2 host tropism/adaptation pattern has significant discrepancies compared to other CoVs, raising questions concerning the proximal origin of SARS‐CoV‐2. This article is protected by copyright. All rights reserved.
Full-text available
The COVID-19 outbreak has sickened over six million people across the world. The origin of COVID-19 coronavirus (CoV) remains unknown although pangolins have been suggested as potential hosts. We investigated two pangolins seized in Guangdong Province, China. Molecular screening revealed CoV in one pangolin (“Dahu”), while another (“Meidong”) was infected by Ehrlichia ruminantium. Dahu exhibited difficulty breathing, and infections of lung, intestines and nostrils, as revealed by CT imaging and necropsy. Phylogenetic analysis showed bat coronavirus RaTG13 (96% genome identity) is closer to COVID-19 CoV compared to pangolin coronavirus (91%). Over twenty caregivers have had close physical contact with CoV-positive Dahu, but none became infected with CoV. Our data suggest that pangolins are unlikely the natural reservoir or secondary hosts of COVID-19 CoV. Pangolins seems to be victims infected by CoV carried by a not yet unidentified natural reservoir host species, perhaps due to their weakened immune system.
Despite claims from prominent scientists that SARS‐CoV‐2 indubitably emerged naturally, the etiology of this novel coronavirus remains a pressing and open question: Without knowing the true nature of a disease, it is impossible for clinicians to appropriately shape their care, for policy‐makers to correctly gauge the nature and extent of the threat, and for the public to appropriately modify their behavior. Unless the intermediate host necessary for completing a natural zoonotic jump is identified, the dual‐use gain‐of‐function research practice of viral serial passage should be considered a viable route by which the novel coronavirus arose. The practice of serial passage mimics a natural zoonotic jump, and offers explanations for SARS‐CoV‐2's distinctive spike‐protein region and its unexpectedly high affinity for angiotensin converting enzyme (ACE2), as well as the notable polybasic furin cleavage site within it. Additional molecular clues raise further questions, all of which warrant full investigation into the novel coronavirus's origins and a re‐examination of the risks and rewards of dual‐use gain‐of‐function research.
The emergence of COVID-19 has triggered many works aiming at identifying the animal intermediate potentially involved in the transmission of SARS-CoV-2 to humans. The presence of SARS-CoV-2-related viruses in Malayan pangolins, in silico analysis of the ACE2 receptor polymorphism and sequence similarities between the Receptor Binding Domain (RBD) of the spike proteins of pangolin and human Sarbecoviruses led to the proposal of pangolin as intermediary. However, the binding affinity of the pangolin ACE2 receptor for SARS-CoV-2 RBD was later on reported to be low. Here, we provide evidence that the pangolin is not the intermediate animal at the origin of the human pandemic. Moreover, data available do not fit with the spillover model currently proposed for zoonotic emergence which is thus unlikely to account for this outbreak. We propose a different model to explain how SARS-CoV-2 related coronaviruses could have circulated in different species, including humans, before the emergence of COVID-19.