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SARS-CoV-2 coronavirus origins alternative theories – do they hold up against science? Part 2

SARS-CoV-2 coronavirus origins alternative theories – do they hold up against science? Part 2

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This is the second post of a two part series dedicated to analyzing the conspiracy theories regarding the SARS-CoV-2 origins that are different from the widely accepted “natural origin”. In the first part we started analyzing very controversial claims from a lead scientist who defected from China, along with some of her colleagues, who proposed that SARS-CoV-2 was engineered. The first part was dedicated to claims about why the natural origins theory does not work well, and we went in detail through her analysis, and provided our criticism, basing it on some the widely available reported scientific information. At the end of first part we noted, the authors of those controversial claims (we will refer to them as such for the remainder of the post, and any other authors will be referred to by name to make a distinction) claimed that for SARS-CoV-2 to have occurred naturally, it would have required a recent recombination event between two independent coronaviruses to take place - an unlikely event - not in the least that it would require the same cells to be host to these viruses. We highly recommend reading part 1 before proceeding with this second installment.

We will pick up from there and offer a contradictory, equally controversial viewpoint, and review the authors’ “smoking gun” evidence of why the SARS-CoV-2 was engineered.


An unusual theory of how SARS-CoV-2 became adapted to humans

Earlier in the summer an unusual online report came out outlining a completely new theory of how SARS-CoV-2 might have come into existence penned by Drs. Jonathan Latham and Allison Wilson. We bring it up here as an answer to the last point made by the authors of the controversial report on the synthetic origins of SARS-CoV-2 proclaiming that the natural path of independent viruses residing in the same cells for a recombination to be unlikely. And because we are already on a tangent of unusual origin theories, the one proposed by Drs. Latham and Wilson also belongs in that category. In Drs. Latham and Wilson’s eyes, it is a theory of everything, and they sure documented it well, so they do deserve some credit for creating a compelling story from incredibly obscure pieces of evidence.

They relay a documented account of three individuals who fell ill with a mysterious pneumonia in 2012 and subsequently died. These individuals worked in an abandoned mine in Mojiang Hani Autonomous County in the Yunnan Province of China. This same cave was subsequently heavily investigated for viruses in resident bats, first scientifically reported in 2014 (this is how these death reports have been committed to published scientific accounts), and later on in 2016, get this, by Dr. Zhengli Shi of the Wuhan Institute of Virology! More about her later. The 2016 report recounts the isolation of a fragment of novel coronavirus termed BtCoV/4991, which is supposedly… a fragment of Bat-CoV RaTG13 virus (see previous blog post for detailed background, the virus that is most closely related to SARS-CoV-2)! Yes, you read that right. The Database of Bat-Associated Viruses compiled by the Institute of Pathogen Biology in Beijing that Drs. Latham and Wilson point to still lists this virus under both names, pointing to both the BtCoV/4991 reference from 2016 and the Bat-CoV RaTG13 reference from 2020 (which also detailed one of the first SARS-CoV-2 genomes). Not to point this out in the 2020 publication that these two different names refer to the same virus is certainly very unscientific behaviour. Here is a screenshot of this entry.

Merogenomics Blog Figure showing a screenshot from the Database of Bat-Associated Viruses

Besides the Chinese database of viruses two additional sources confirmed it. Drs. Latham and Wilson uncovered email correspondence with the curator of that database, Dr. Jian Yang who confirmed it with the principal author of the RaTG13 genome that it is the same. In addition, the Sunday Times of UK has confirmed with Dr. Peter Daszak the bat coronavirus origins and that it is one and the same virus. Since then, under the heat, the leading author of the RaTG13 genome also finally publicly verified it that RaTG13 and BtCoV/4991 are one and the same. This seriously should not have been so hard to establish, and this is no doubt bizarre that this is not getting more attention and scrutiny to figure out if there is a link between these miners and the closest bat virus relative to SARS-CoV-2.

The account of these three individuals who died, and three more who also fell ill but survived, has been described in a 2013 thesis written by a doctor who was supervising their treatment. The abstract to that thesis states that SARS-CoV-like virus was isolated from the feces of bats in the Mojiang cave. This document was considered so significant that the entire thesis was translated and is available in the top link of this section. Most tellingly, apparently the thesis also stated that some of these affected individuals with severe pneumonia like symptoms were likely infected with an unknown virus that was suspected to be a SARS-CoV-like virus from bats, and their blood samples were also sent to the Wuhan Institute of Virology for further analysis (which confirmed antibody exposure to viruses). If it was not for this thesis, this obscure link between a mysterious pneumonia-like disease caused by unknown coronavirus in 2013 and the Wuhan Institute of Virology would never have come to light, as this information has never been officially published by their researchers.

What Drs. Latham and Wilson then proposed is that at least one of the workers of the Mojiang cave who became affected by this mysterious pneumonia in 2012 was actually infected by the Bat-CoV RaTG13 (or a closely related virus), and their body (or lungs to be exact, the CT scans being provided in the thesis for all six patients) was the site of evolution of a virus that would then become SARS-CoV-2! In essence the patient 0 of the COVID-19 pandemic! They then propose that it was this new SARS-CoV-2 virus now highly adapted to infect humans and which was sent to the Wuhan Institute of Virology that eventually likely leaked out to start the pandemic in 2019. Why the long gap in years? Because Wuhan did not get its high security level 4 biohazard laboratory ready till 2018 (required to test the most dangerous pathogens)!

They argue that the lungs of these individuals working in the bat cave allowed for massive quantities of virus to be present, thus allowing for its rapid evolution, which is further supported by the 2013 thesis statement of a weakened immune system in these patients. Their infections also lasted a very long time, more than 100 days in two instances. And finally, due to the nature of lungs, it would allow different viral development in different areas of the lung which could then recombine together upon a chance encounter therein. The 2016 publication on BtCoV/4991 even mentioned their observation of co-infections of the same bats by different coronaviruses, to which these patients could have been exposed.

Further support for their theory also comes from the fact that the one of the early publications identifying the molecular details of the structural binding between SARS-CoV-2 virus and the human ACE2 receptor, also demonstrated that the Bat-CoV RaTG13 virus can also interact with human ACE2 receptor and was able to enter cells using this receptor! This is significant because this could explain why a bat virus could actually directly infect a human without the need of an intermediate species!

However, they note there is no recorded precedent of such event ever occurring. But according to them no human laboratory engineering of the virus had to take place, but rather accidental adaptation right inside a human host’s lungs. It is a mere hypothesis with no proof currently available. They also noted that normally in nature the virus would not have had the chance to adapt because it would have killed the host but the miners were kept alive for 100 days in the hospital and also the square cms of their lungs were exponentially larger than were this adaptation normally happens in the upper respiratory tract.

Nevertheless, that is definitely not the story that our first authors are promoting, as they claimed to offer evidence of SARS-CoV-2 genetic manipulation!


Creating new deadly viruses, the smoking gun

This now brings us to the most condemning part of the original focus paper. It is the fact that China, and especially the Wuhan Institute of Virology, have been engineering novel versions of infectious coronaviruses from non-human origins, and publishing all of that evidence! These types of experiments are referred to as gain-of-function, and have been condemned in the past by certain members of scientific community precisely due to potential risk of an accidental pandemic. Looking back right now, they probably wish they never published that data because it sure adds fuel to the fire behind conspiracy theories that SARS-CoV-2 was also such a gain-of-function experiment that escaped the lab. On top of that the, "Wuhan Institute of Virology has engaged in decades-long coronavirus surveillance studies and therefore owns the world’s largest collection of coronaviruses", in theory allowing them to create any number of new human-infecting coronaviruses at will. This of course is not a proof of anything, but it certainly paints a bad image, and there is no easy way of escaping it.

Image of Merogenomics article quote on Wuhan Institute of Virology past genetic work

And probably the best part of this report, that frankly should have been already discussed by others ...

The authors point to two unique restriction sites at either end of the spike protein receptor binding motif (RBM, a fragment of receptor binding domain, the region of the spike protein that is used to bind to human receptors) of the SARS-CoV-2 genome! Restriction sites are short sequence of genetic information that are recognized by specific proteins, allowing them to bind to the genetic material and cut it. These proteins are referred to as restriction enzymes and are a hallmark of molecular genetic manipulation. Ever since their discovery in the 1960s, it has allowed scientists to manipulate genetic information at will. Apart from being extremely important in helping understand the function of genomes, it has allowed scientists to create novel genetic entities, such as all those deeply unpopular GMOs.

The two restriction sites found are for the EcoRI and BstEII restriction enzymes, which would allow placement of any type of RBM within the spike gene you want, and check for resulting virus behavior. On top of that, this is not seen in any other coronaviruses of the beta family (see our past post for explanation) according to the authors, making their presence in SARS-CoV-2 extremely suspicious. This is by far the strongest hint of human manipulation of the virus we have seen presented thus far, and the fact that this has gone unnoticed for so long is frankly embarrassing. You can see the sequence below.

Merogenomics Blog Figure of SARS-CoV-2 genome sequence fragment

Adapted from Yan L-M et al. 2020. DOI: 10.5281/zenodo.4028830

The authors continue: "It is noteworthy that introduction of the EcoRI site here would change the corresponding amino acids from -WNT- to -WNS- (Figure [... above]). As far as we know, all SARS and SARS-like bat coronaviruses exclusively carry a T (threonine) residue at this location. SARS-CoV-2 is the only exception in that this T has mutated to an S (serine), save the suspicious RaTG13 and pangolin coronaviruses published after the outbreak” (in part 1 of the series we mentioned how the authors think that RaTG13 and pangolin coronaviruses are fake). Yikes!

Then the authors continue with their crucifixion: "the feasibility of this RBM-swap strategy has been proven. In 2008, Dr. Zhengli Shi’s group [of the Wuhan Institute of Virology, and the same principal investigator behind the publication of Bat-CoV RaTG13 virus!] swapped a SARS RBM into the Spike proteins of several SARS-like bat coronaviruses after introducing a restriction site into a codon-optimized spike gene (Figure [... below labeled as Ren, W et al. 2008, color residues denoting the substituted RBM]). They then validated the binding of the resulted chimeric Spike proteins with hACE2. Furthermore, in a recent publication, the RBM of SARS-CoV-2 was swapped into the receptor-binding domain (RBD [slightly larger area than RBM and which encompasses RBM]) of the SARS-CoV, resulting in a chimeric RBD fully functional in binding hACE2 (Figure [... below labeled as Shang, J et al. 2020]). Strikingly, in both cases, the manipulated RBM segments resemble almost exactly the RBM defined by the positions of the EcoRI and BstEII sites (Figure [... below labeled as SARS-CoV-2_RBM_EcoRI/BstEII]). [...] It is noteworthy that the corresponding author of this recent publication, Dr. Fang Li, has been an active collaborator of Dr. Zhengli Shi since 2010. Dr. Li was the first person in the world to have structurally elucidated the binding between SARS-CoV RBD and hACE2 and has been the leading expert in the structural understanding of Spike-ACE2 interactions."

Merogenomics Blog Figure of viruses genome sequence gain of function

Adapted from Yan L-M et al. 2020. DOI: 10.5281/zenodo.4028830

The only problem is, why would Dr. Li carry out this experiment and potentially bring attention to the synthetic nature of SARS-CoV-2? Unless they could not resist getting another publication. It is always good on your resume. ;)

The authors thus boldly conclude (literally, plus underlining the following statement to really make sure you do not miss it): "it is the smoking gun proving that the RBM/Spike of SARS-CoV-2 is a product of genetic manipulation."

We do not agree. The smoking gun would be laboratory books from the lab stating that this is exactly what took place (by the way, these have never been made publicly available to attempt to dispel the arguments that the Wuhan Institute of Virology was behind anything shady related to SARS-CoV-2 but that is also not proof of any wrong doing). We still cannot discount that these restriction sites are a mere coincidence of random mutagenesis. But we agree, this is by far most damning type of evidence that anyone has yet dared to publish on this topic.

Image of Merogenomics article quote on coronavirus design


Manipulated cleavage for optimum effect

That brings us to a third segment of structural analysis done by authors: the unusual furin-cleavage site present in the spike protein of SARS-CoV-2 which we also discussed in detail previously in our past posts. As we mentioned previously, this furin-cleavage site is located at the junction of S1 and S2 domains of spike protein, and is recognized and cleaved by the ubiquitously abundant furin protease. Cleavage of the spike protein in this area promotes its fusion with host cells membrane, and therefore promotes the infectivity of a SARS-CoV-2 virus.

There is only one way this site can suddenly show up like that in SARS-CoV-2: yet another recombination event (see part 1 for explanation). "Specifically, an ancestor β [beta] coronavirus containing no furin-cleavage site would have to recombine with a closely related coronavirus that does contain a furin-cleavage site."

The authors continue: "However, two facts disfavor this possibility. First, although some coronaviruses from other groups or lineages do contain polybasic furin-cleavage sites, none of them contains the exact polybasic sequence present in SARS-CoV-2 (-PRRAR/SVA-) ["/" denotes the cleavage site within the amino acid sequence. Second, between SARS-CoV-2 and any coronavirus containing a legitimate furin-cleavage site, the sequence identity on the spike gene is no more than 40%. Such a low level of sequence identity rules out the possibility of a successful homologous recombination ever occurring between the ancestors of these viruses. Therefore, the furin-cleavage site within the SARS-CoV-2 Spike protein is unlikely to be of natural origin and instead should be a result of laboratory modification."

Now you may wonder, how likely is it that so many coincidences could start to align naturally together?

Because here comes another one: the unusual furin-cleavage site introduces another restriction site! This time for a FauI restriction enzyme. The authors propose that this was done on purpose in order to easily monitor if the furin-cleavage site as it was successfully introduced into the viral genome, and apparently prone to deletions. To support this suggestion, the genetic sequence in the virus genome to produce this FauI restriction cleavage site and a corresponding amino acid sequence for furin-cleavage site, required a rare use of codons CGGCGG.

A codon is a genetic sequence that defines what amino acid is to be placed in a sequence when a protein is being produced. This is how genomes are a book of life and how they code for building cells and organisms, through coding information to build proteins (or tiny molecular robots that perform most of the work inside your cells), and how their production should be regulated (which allows the same genome to produce fantastic variety of different cells). This is how a genome encodes information for protein synthesis: a series of codons tell specific robots which free flowing amino acids to string together, and this string of amino acids can fold like origami to produce three-dimensional proteins, or other robots.

What the authors note is that the CGG codon is the least often used codon in the SARS-CoV-2 virus genome (it encodes the Arginine amino acid, designated as letter R in the above mentioned furin-cleavage site), and its presence two times in a row is the only such instance in the SARS-CoV-2 virus genome. In other words, such rare event that conveniently resulted in both the desired furin-cleavage site in the protein, and a restriction site in a genome (marked below in a figure with arrows) that would allow monitoring if the SARS-CoV-2 virus retained its furin-cleavage site within its genome (this would be achieved by isolating some of the viruses, sacrificing them by destroying them to get their genomes and inspecting the genome by cutting it in half).

Merogenomics Blog Figure of SARS-CoV-2 genome fragment 2

Adapted from Yan L-M et al. 2020. DOI: 10.5281/zenodo.4028830

Because this genetic section is so small, it could be introduced into the virus genome without the need of restriction sites and without leaving any trace behind in the sequence.

Here is the big issue with this last claim though. Within a week of our original post on the SARS-CoV-2 origin (even prior to COVID-19 being pronounced a pandemic by the WHO ), another bat coronavirus was discovered and reported termed RmYN02, which not only was the second closest relative to SARS-CoV-2 after Bat-CoV RaTG13 with 93.3% identity, but more importantly, it showed a presence of a degenerate furin-cleavage site! Its RBD was closely matching that of RaTG13.

Below is the image of the amino acid sequence of the different coronaviruses around the controversial furin-cleavage site.

Merogenomics Blog Figure comparing coronaviruses sequences around furin cleavage site

Adapted from Yan L-M et al. 2020. DOI: 10.5281/zenodo.4028830

So why did the authors not mention this important publication that contradicts their thesis? Would this also be another fake virus then according to them? After all, this was also reported in China (and yes, the Wuhan Institute of Virology was involved in this publication as well). If this were to be another fake publication, this level of coordination between different institutes with such precision of understanding of sequences would be quite genius we might add! That would be equivalent to faking a moon landing! And yes, the authors did briefly mention they believe this virus to also be fake! It will be interesting to see their follow up report on all of this fakery (which just came out, so we will be digging into that one)!

Here is another great figure from that same publication showing phylogenetic tree indicating closeness of relationship between different coronaviruses either for entire virus genomes, or their segments. The closer the distance along the lines of the tree, the closer the evolutionary relationship. Basically SARS-CoV-2 got its body from RmYN02, spike protein from RaTG13 and its RBD (including RBM) from pangolin coronavirus. Either naturally through infecting humans directly, or some yet undiscovered intermediary host species, or by being synthesized. Or perhaps a combination of a human infection followed by manipulation. Take your pick. We do not see a smoking gun for synthetic origin yet. But it sure is weirdly complicated.

Merogenomics Blog Figure of coronaviruses evolutionary tree

Adapted from Zhou H et al. 2020. Curr Biol 30(11):2196-2203.e3.

Oh, and guess where the RmYN02 was uncovered? Mengla County in the Yunnan Province, not too far from the Mojiang Hani Autonomous County of the mysterious 2012 mine workers infection!

Another issue is that these accusations of virus engineering and corresponding scientific fraud were not voiced at all by the recent report released by the US House Foreign Affairs Committee on China’s irresponsible mishandling of the COVID-19 pandemic. This report is designed to find as much wrong-doing as possible that could be pinned on China and it is extremely detailed. The Wuhan Institute of Virology and its dangerous gain-of-function viral research is discussed in detail. But none of the information presented by the authors have made it into this scathing report, even though it did not omit the suggestion of the virus being leaked from a laboratory. Believe us, if they could find any garbage to be heaped on China, it would be there! Perhaps they still will, since that is one of the proposed mandates of the international investigation which is to include an inquiry into potential scientific fraud. They probably will love reading the reports coming from these authors. But the burden of proof will have to be insanely high as such an investigation should not become a political witch-hunt (probably too late for that?).

The authors own final conclusion obviously speaks for itself though: "the possibility that SARS-CoV-2 could have been created through gain-of-function manipulations at the WIV [Wuhan Institute of Virology] is significant and should be investigated thoroughly and independently." We totally agree with this although do not see it as likely to occur. Not that pinning the blame on the synthesis of the virus would serve any benefit now, apart from the fact to point out how dangerous gain-of-function viral experiments can be, and bringing the collective global community to agree to place a moratorium on such research.

In the face of how destructive the COVID-19 pandemic turned out to be, both in terms of lives lost and the impact on the global economy, we hope that such moratorium will take place irrespective of what the true origins of SARS-CoV-2 virus are.

In the meantime, conspiracy theories around SARS-CoV-2 will remain just that.


This article has been produced by Merogenomics Inc. and edited by Jason Chouinard, B.Sc. Reproduction and reuse of any portion of this content requires Merogenomics Inc. permission and source acknowledgment. It is your responsibility to obtain additional permissions from the third party owners that might be cited by Merogenomics Inc. Merogenomics Inc. disclaims any responsibility for any use you make of content owned by third parties without their permission.


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