They put 8 natural spike proteins on a well-known backbone, WIV-1. SARS-CoV-2 is not made up of any known viral backbone. It's an entirely novel virus, which differs from all previously known viruses throughout its entire genome. This is very much not what you would get from these sorts of infectivity studies.
There's nothing in that list that argues against SARS-CoV-2—and its spike protein and furin cleavage site in particular—being produced by serial passage through any of a variety of cell lines expressing human ACE-2.
It does seem unlikely that the SARS-CoV-2 genome, or spike protein, or even just a small segment including the furin cleavage site, was synthesized. Although without knowing what protein folding modeling capabilities and synthesis capabilities the WIV had, who knows for sure?
The problem with this whole article is that we know of no suitable backbone virus to use, and we know of no suitable spike-protein sequence to form a chimera which results in SARS-CoV-2.
The experiments done on the SARS-CoV-1 or WIV1 backbone don't remotely get you close to SARS-CoV-2 and you're dealing with centuries of evolutionary difference there.
The RaTG13 virus backbone is also several decades of evolution away from SARS-CoV-2.
Learning how to replicate a virus in the lab is also not simple so they're not going to be doing this with every virus they find. We know they managed to do it with SARS-CoV-1 and WIV-1, but they'd need a reason to undertake it with any other virus.
So you have to assume that WIV has a virus which they found which is similar to RaTG13 which they have never published, and for some reason they jumped straight to making that virus replicate in the lab and creating chimeras, and they also had a previously and still unpublished spike protein which was similar to the Pangolin spike which they used. Then for some reason they didn't do this in petri dishes, but used animals and/or somehow managed to aerosolize enough of it that researchers at WIV got sick from it. This is with a virus that we now know doesn't stick to surfaces very well at all, so the actual accident remains unexplained (they had a party and someone chopped up some chimera and railed it like a line of coke? that'd do it).
While you're pondering all that keep in mind that the person who "broke" the story in the WSJ about the sick workers at the Wuhan lab was Michael R. Gordon. He's also notable for having co-authored with Judith Miller in 2002 the NYT story on Hussein's nuclear program and WMDs that arguably helped propel us into the Iraq War.
It is also worthwhile to read Shi Zhengli's rebuttal to the lab leak theory:
Every published backbone used for genetic experimentation was at some point unpublished. The WIV had the biggest program in the world to sample novel SARS-like coronaviruses from nature, plus the ability to engineer them in the lab. In the words of David Relman:
> This argument [that SARS-CoV-2 must be natural since it doesn't use a known backbone] fails to acknowledge the possibility that two or more as yet undisclosed ancestors (i.e., more proximal ancestors than RaTG13 and RmYN02) had already been discovered and were being studied in a laboratory—for example, one with the SARS-CoV-2 backbone and spike protein receptor-binding domain, and the other with the SARS-CoV-2 polybasic furin cleavage site. It would have been a logical next step to wonder about the properties of a recombinant virus and then create it in the laboratory.
Note also that the WIV's public database of viral genomes went offline in Sept 2019, and hasn't come back.
As to the binding, Andersen looked at the binding of SARS-CoV-2's RBD to human ACE2 in silico, and found that it was suboptimal. But that proves only that the RBD wasn't designed in silico using his software workflow. Among unnatural origins, it's far more likely that the RBD either evolved naturally (as Relman proposed above) in a different virus, or evolved quasi-naturally in the lab during culture in human cells or in humanized mice. Andersen's argument doesn't address these more likely possibilities.
SARS-CoV-2 isn't based on a SARS-CoV-1 backbone or spike or any known backbone or spike that would have been used in a lab.
The closest known viral backbone is a few decades of random mutations away from SARS-CoV-2 and there's no evidence that WIV even tried to work with RaTG13 and did anything beyond sequencing it.
And you have the usual Schroedingers-Information problem that plagues conspiracy theories. You have to assume that on the one had all that information you just cited would be available to you, while a fairly massive project involving forming a chimera from an unknown spike protein and unknown backbone would have been going on in perfect secrecy in 2019 before there was any reason to keep that information secret. In 2019 if they had sequences of those viruses they would have just published them, they certainly would have published them before going through the effort to create chimeras from them. They would have used those sequences to get justification to get grants to do studies. The idea that all of that happened in perfect secrecy, before there was a need for perfect secrecy is the idea that is fucking laughable.
And nature creates "chimeras" and does "gain of function experiments" all the time on a massive scale using many billions of animals in the "lab". That is what recombination and serial passage does -- particularly as viruses burn through bioreactors in animal farms in close proximity to humans.
And when it comes to the FCS, the PRRAR sequence is unlike any other known FCS. If humans engineered it they would have picked another one that they already knew worked. That sequence absolutely screams that it was zoonotic in origin. It was novel and never previously seen before. Nobody would have added that in a lab.
But at the end of the day you have zero evidence of any of that actually happened. The backbone doesn't exist, the spike doesn't exist, the effort necessary to culture that completely unknown virus in the lab isn't documented anywhere. And the grant proposal very specifically is concerned with using the WIV1 and SHC014 backbones, nothing related to SARS-CoV-2. And going from sequence to live culturable virus that you can work with is _difficult_. They aren't out collecting bats in the morning and whipping up live novel virus backbones in the evening. And if they actually carried out the research in this grant proposal you don't get from there to SARS-CoV-2, those are all SARS-1-like.
It is research that "sounds like" what happened with the SARS-CoV-2 zoonotic spillover, but that isn't a strange coincidence. They were researching the thing they were worried about happening, and then it happened. Their research proposals naturally rhyme with what actually occurred because they had studied and understood the problem enough to guess more or less accurately what the process would be. There are still massive gaps in between this proposal and SARS-CoV-2 that you could fly a plane through.
> “We will conduct in vitro pseudovirus binding assays, using established techniques2, and live virus binding assays (at WIV to prevent delays and unnecessary dissemination of viral cultures) for isolated strains.” (D1, p.12)
> “We will validate results from chimeric viruses by re-characterizing full-length genome versions, testing whether backbone genome sequence alters full length SARSr-CoV spillover potential. QS for full-genome characterization will be selected to reflect strain differences in antigenicity, receptor usage, growth in human cells and pathogenesis.”(D1, p.13)
> “We will test growth in primary HAE cultures and in vivo in hACE2 transgenic mice. We anticipate recovering ~3-5 full length genome viruses/year.”(D1, p.13)
> “We will analyze all SARSr-CoV S gene sequences for appropriately conserved proteolytic cleavage sites in S2 and for the presence of potential Furin cleavage sites74,75.
SARSr-CoV S with mismatches in proteolytic cleavage sites can be activated by exogenous Trypsin or Cathepsin L.
Where clear mismatches occur, we will introduce appropriate human-specific cleavage sites and evaluate growth potential in Vero cells and HAE cultures.”
> “We will also review deep sequence data for low abundant high risk SARSr-CoV that encode functional proteolytic cleavage sites, and if so, introduce these changes into the appropriate high abundant, low risk parental strain.” (D1, p.13)
The problem for this speculation is that given the types of experiments the WIV is known to have done, it is impossible to produce anything that looks remotely like SARS-CoV-2. The reverse genetics system used by WIV researchers is well known, and SARS-CoV-2 is simply not a product of it.
IIRC, this is still true if you exclude the spike protein and use a higher similarity threshold.
Why would one do that? Well, two reasons. First, the spike more variable as it is subject to greater evolutionary pressure as the major component of the viral surface. Second, in coronavirus reverse genetics typically the virus is segmented into multiple pieces, most of which compose the non-spike backbone and a subset which compose the spike protein. This is intentional to enable the swapping of spike proteins. So, if SARS-CoV-2 is spike-swap or spike variant assembly, a RaTG13-like virus could be the "backbone" of SARS-CoV-2.
Moreover, a hypothetical SARS-CoV-2 backbone could exist in the viral sequences list the WIV took down in Sept. 2019. They sequenced RaTG13 a few years prior. The lab's raison d'etre is collecting and sequencing coronaviruses poised for spillover. And, with modern DNA synthesis technology, it's not difficult to print out arbitrary backbone contigs for a viral assembly.
The spike protein is the biggest difference between RaTG13 and SARS-CoV-2. To produce SARS-CoV-2 from it that would imply that WIV had unpublished sequences from the Pangolin-CoV spike protein that they used to combine with an RaTG13 backbone. You then do not get SARS-CoV-2 out of passing that through mice, you get a mouse virus. You'd need to pass it serially through something with a human-like ACE2 like minks. Then you need to do that enough to accumulate a thousand mutations which takes decades in nature and would take millions of animals.
That likely did happen, but Charles Darwin was the geneticist that executed the gain of function experiment via serial passage through that many animals.
> Have you read the fine article? It cites more than a few papers.
Yes, i read it. The ability to construct bibliographic references is also a fairly widely-held and unimpressive skill.
You don't get SARS-CoV-2 by combining an RaTG13 backbone with a pangolin spike in a lab -- it is still decades of evolution away form SARS-CoV-2 which you don't get via passing it through a dozen generations of mice. There's no evidence WIV was ever doing GOF research (although they did collaborate with GOF research that happened on US Soil), it is entirely circular logic. The idea that WIV employees were treated for SARS-CoV-2 is entirely evidence free, nobody knows the names of those employees, China has claimed those were 3 samples submitted in Jan from community collection which is rejected out of hand because it comes from China. The whole lab leak theory is that its a coincidence that the pandemic started in the city that had the lab, and the theory that coincidences never happen.
In the Washington Post an American virologist finally published a detailed analysis of the "spike protein research" theory:
Some people have wondered whether these types of experiments could have produced SARS-CoV-2. The answer is, in this case, not really. In theory, if you had the right viruses in your catalogue, sure. But there are no indications that anyone had ever seen this virus nor any viruses similar enough to serve as its genetic building blocks before SARS-CoV-2 emerged in the population. The Wuhan institute’s most recent chimeric virus used a very different coronavirus as its genetic backbone. Looking at the body of research produced there, it’s clear that scientists were laser-focused on the bat viruses related to SARS-CoV, which spurred research on coronaviruses worldwide after it emerged in 2003 because of its pandemic potential. There’s just no trace of SARS-CoV-2 in the lab, and if the SARS-CoV-2 progenitor or its building blocks weren’t in the lab before the pandemic, the pandemic could not have started there — even accidentally.
RaTG13 is a thousand mutations and several decades of evolution away from SARS-CoV-2, you don't get from having RaTG13 in a lab to SARS-CoV-2. There's no evidence that WIV recovered whole virus of RaTG13 or cultured it. SARS-CoV-2 is not a chimera of a RaTG13 backbone and an ACE2-attaching spike, there's a lot more mutations involved. You also don't get there from serial passage experiments in a lab, you need serial passage through decades and many millions of infections in nature, we can't operate at that scale.
They found that the spike protein, a receptor-binding domain (RBD) that hooks onto host cells, had evolved to target ACE2, an enzyme founded on the outer surface of human cells that helps to regulate blood pressure. The team say the COVID-19 spike protein is so efficient at binding to human cells that it could only be a result of natural selection, not artificial engineering. Another tell-tale sign of natural origins is the molecular structure of COVID-19, which is substantially different from other known viruses. Rather than mimicking other viruses known to cause severe illness in humans, COVID-19 more closely resembles strains of coronavirus found in bats and pangolins.
"These two features of the virus, the mutations in the RBD portion of the spike protein and its distinct backbone, rules out laboratory manipulation as a potential origin for SARS-CoV-2" says Andersen.
Here's the Cliff Notes version of the argument in this paper:
1. SARS-CoV-2 has a number of unique and unusual genetic features, when compared to close relatives, many of which explain its high virulence and infectivity among humans.
2. A series of research papers published by a group of virologists, dating back a little over a decade, demonstrate (1) a progressively increasing understanding of viral features which make coronaviruses more infectious and virulent in humans, and (2) laboratory capabilities for successfully creating chimeric viruses (e.g. moving one specific protein sequence from a bat SARS-like virus to human SARS virus) to test their hypotheses.
3. Each of the unique and unusual features of SARS-CoV-2 appears somewhere in this line of research.
4. Researchers from the Wuhan Institute of Virology, located in the city where the outbreak began, were intimately involved this line of research.
Taken together, the publicly-available evidence indicates that a select group of virologists had the domain knowledge and laboratory capabilities to create chimeric viruses which possess each of the unusual features of SARS-CoV-2, and that select group of virologists was concentrated at the Wuhan Institute of Virology located at ground zero for the pandemic.
The authors feel that, in light of this preponderance of circumstantial evidence, the hypothesis that the biogenesis of SARS-CoV-2 involved human intervention should be seen as the leading (i.e. most likely) explanation.
They do not make any statement about how the virus first infected a live human and spread into a pandemic, but conditioned on their biogenesis hypothesis being true, one would then assume an accidental lab release from WIV as the most likely explanation.
Of course that says little about SARS-CoV-2 relative to all the other viruses we don't know about, either sitting in a Chinese government lab, or in a bat cave somewhere.
I guess I don't find the argument "we can't figure out how to reconstruct SARS-COV-2 from known viruses" very convincing on either side.
But lots of aspects and features of SARS-CoV2 point to it being a natural virus with a human specific furin cleavage site inserted into it. In fact it looks almost exactly what you would expect from the type of experiments outlines in the DEFUSE Proposal https://www.documentcloud.org/documents/21066966-defuse-prop...
The fact that the location happens to be in the exact location proposed in experiments and commonly used in virology, and the fact that SARS-CoV2 binds to Human ACE2 more efficiently than any other species really stands out:
> Spike protein exhibited the highest binding to human (h)ACE2 of all the species tested. . .
> These findings show that the earliest known SARS-CoV-2 isolates were surprisingly well adapted to bind strongly to human ACE2, helping explain its efficient human to human respiratory transmission
> Our observations suggest that by the time SARS-CoV-2 was first detected in late 2019, it was already pre-adapted to human transmission to an extent similar to late epidemic SARS-CoV. However, no precursors or branches of evolution stemming from a less human-adapted SARS-CoV-2-like virus have been detected
Not to mention that it's absurd to think that such an infectious virus would have been circulating in Raccoon Dogs or Civets and just simply disappear after the first human was infected with zero traces to be found. Like when humans passed covid to white tailed deer that did not stop the virus from circulating in humans.
Are we supposed to just accept SARS-CoV2 spillover was the result of an "Immaculate Infection">?
If SARS-CoV-2 was a spike spliced onto a backbone it wouldn't look like they evolved from each other (similar to a photoshopped picture with different shadows and noise).
It also didn't arise from serial passage since the distance is large enough that the 1,000 base pair difference would take passage through many, many millions of animals, not something that could be accomplished in a lab. 30-50 years of evolution is an awful lot of serial passage, and only nature can accomplish that large of a serial passage experiment.
It is also very unlikely that the lab found SARS-CoV-2 or the immediate ancestor and cultured the live virus without publishing the sequence. They did culture WIV-1 and used the WIV-1 backbone, but they also published the sequence years before they did that and did it all in the open. That's the reason why people know about that. Before the pandemic there would be no reason to keep a SARS-CoV-2 sequence secret, and they earned their living by sequencing sarbecoviruses and publishing them. And still its unclear how a lab leak would happen with this virus, since you need to both culture the live virus and somehow aerosolize it and snort it in -- as we've learned it doesn't transmit by surfaces and restaurants doing deep cleaning after COVID issues are just engaging in sanitation theater.
The actual bioreactors where it formed are all sitting right out in the open. All the bat caves across China, all the factory farms which have tightly packed intermediate animal hosts. All the humans interacting with those animals through factory farming or collecting bat guano for fertilizer. All the mixing that occurs by those animals being transported across china. There's a million times more serial passage and animal-animal or animal-human contact happening right out in the open.
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