About the origin of SARS-CoV-2

[Art (Arthur Hunt)]

@Giltil

If it is the case that US agencies have funded gain of function studies at the WIV,

From here:

Aim 3. In vitro and in vivo characterization of SARSr-CoV spillover risk, coupled with spatial and phylogenetic analyses to identify the regions and viruses of public health concern. We will use S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments and analysis of receptor binding to test the hypothesis that % divergence thresholds in S protein sequences predict spillover potential.

It seems to me that someone could settle this issue by making available the section of the proposal that describes Aim 3.

[swamidass (S. Joshua Swamidass)]

@Art

Aim 3. In vitro and in vivo characterization of SARSr-CoV spillover risk, coupled with spatial and phylogenetic analyses to identify the regions and viruses of public health concern. We will use S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments and analysis of receptor binding to test the hypothesis that % divergence thresholds in S protein sequences predict spillover potential.

It seems to me that someone could settle this issue by making available the section of the proposal that describes Aim 3.

Very true.

The problem is that no one is authorized to do so except the researchers who submitted the proposal. I’m sure that NIH officers have reviewed the grant, we are stuck with taking their word for it, at least for now.

What the scientists involved could do is voluntarily make their proposal public. Usually that is not required, but this is not a normal situation.

If there really was GoF work done, they might make their lab books public too (assuming that’s possible and confidentiality of individuals can be protected).

If there is nothing implicating here, the transparency would put a lot of questions to rest. If there was implicating information here, making it transparent now would build trust. Even if they are implicated, it clearly was not intentional and does not mean they necessarily did something wrong or should be punished.

[davecarlson]

@swamidass

If there is nothing implicating here, the transparency would put a lot of questions to rest. If there was implicating information here, making it transparent now would build trust.

Given the many utterly unhinged responses to Fauci’s emails, I’m not sure that this is true. Doesn’t mean it shouldn’t be done anyway, of course.

[swamidass (S. Joshua Swamidass)]

The issue there was another failure of public communication based on false equivalency. Transparency about this a year ago, would have faired a better chance of maintaining trust than what we are seeing now.

[BrianLopez]

@Faizal_Ali : I’d like to add the clarification that a conspiracy theory (flat earth, area-51, majestic 12 documents, Qanon, Bill Gates vaccines and depopulation etc.) is normally used in the context of world elites (deep state, illuminati, NASA, Gov., etc.) intentionally covering up global-impacting manipulative efforts to hide the truth from the public for world control, or the sort.

Conspiracy theories are normally not actual, unintentional accidents that can then be potentially covered up because of some fear of blame, prison-time, shutting down a business, etc.

Therefore, if it turns out that SARS-CoV-2 did escape WIV and it was covered up (and there was some GoF research), this is not automatically a conspiracy theory in the sense that it is normally used in all the conspiracy theories that have surfaced for the past decades. If there is a nuance with one example, it must be clarified, but this does not signify that a lab-leak in the sense that were are discussing here would make it a conspiracy theory if it was covered up or someone lied somewhere.

[glipsnort (Steve Schaffner)]

@BrianLopez

Therefore, if it turns out that SARS-CoV-2 did escape WIV and it was covered up (and there was some GoF research), this is not automatically a conspiracy theory in the sense that it is normally used in all the conspiracy theories that have surfaced for the past decades. If there is a nuance with one example, it must be clarified, but this does not signify that a lab-leak in the sense that were are discussing here would make it a conspiracy theory if it was covered up or someone lied somewhere.

Yeah, I’d just call that a plain old conspiracy, which is a thing that happens sometimes.

[Michael_Okoko]

@Rumraket

The best evidence for a lab-leak hypothesis is the circumstantial evidence surrounding the location of the origin of the pandemic (Wuhan specifically, though also rather weak considering it’s regional role as a animal trading hub), and a number of strange inconsistencies in the statements made by Chinese officials and scientists concerning when, where, and how their bat-virus database close to the start of the pandemic was taken offline. From my perspective it is these circumstantial pieces of evidence that most merits the lab-leak hypothesis, and forms the basis for any call for a more in-depth, independent investigation.

I wouldn’t call this the best evidence for a lab leak because China could just be doing what it usually does in situations like this when foreign countries and groups try to poke into its national business.

During the SARS outbreak the Chinese government greatly hindered international efforts to uncover its cause and depth of spread. They refused to inform the WHO about the outbreak early on and also delayed the WHO team’s entry into China for weeks. When the WHO team was eventually allowed to enter China, there were still constraints on the extent of investigations they could conduct. All these actions are exactly what they recapitulated in the current pandemic.

If a virology lab working on coronaviruses operated in Guangdong, where the earliest cases of the SARS outbreak were recorded, coupled with the suspicious actions of the Chinese government, then its most likely a lab leak hypothesis would have been brought up to explain the origins of SARS-CoV in 2002-2003. Of course, 15 years later, Chinese scientists were able to hunt down the bat that sparked the SARS outbreak.

The bottom line is that China has acted suspiciously with regards to disease outbreaks in the past, so its not surprising (at least to me) that they are reenacting the same behavior now. They might know something incriminating we don’t, or they could just be acting like they usually do, either way this is not strong evidence for a lab leak in the absence of further evidence.

http://www.umass.edu/sts/ethics/online/cases/SARS/case.html

[Rumraket (Mikkel R.)]

@Giltil

In this regard, the video below is interesting.

It starts out with the host making some misleadingly simplistic statements, such as the claim that “extremely dangerous viruses” that “never existed before” were created at the WIV.

And that sure does sound scary, but of course basically any deliberate alteration to an “extremely dangerous” natural virus would qualify for that. Even if it was intentionally made less lethal. It would then still be work done on an extremely dangerous virus resulting in one that never existed before.

And then we realize the rhetorical trick that was just played on us. If we take a step back and try to think rationally about it, we also see that any new “extremely dangerous” virus that evolves in nature is then a new extremely dangerous virus that never existed before in nature until now, and that this is basically how every other pandemic in history began.

She then goes on to state that “gain of function research involves experiments that can increase transmissibility or the virulence of pathogens, and that’s what was going on in the Wuhan labs”.

And it’s true that those are among the kinds of things gain of function research can involve. But what evidence is presented that they actually did specifically those kinds of experiments - to “increase transmissibility or the virulence” of pathogens - at WIV? None.

Then she goes on to state that “even when this worrying research was banned in the US back in 2014, US money was still continuing to flow through to china to fund the same research” (but she’s not been specific about what actual experiments they did at the WIV) or whether it really corresponds to the examples with “increased transmissibility or virulence” she gave immediately before.

So I ask again, what evidence is there that researchers at the WIV were deliberately experimenting on viruses to “increase transmissibility or the virulence”?

The whole things is really fantastically misleading. The way Fauci is clipped, what is stated leading up to the clips, the ridiculous oversimplifications and equivocations, misleading implications and so on.

It’s a load of crap. Like @Glipsnort I couldn’t finish it.

Take one look at the comments on that video to see the effects of that egregiously dishonest trash. This one in particular stands out:

Jude Blanch

[3 hours ago]

Fauci’s home should be raided like Giulanies Apt + Roger Stones home, this will get his attention.

Sounds like hatred motivated by a political vendetta concerning Fauci’s lack of compliance with the previous administration’s party line. Election bitterness, politics, and ridiculous fear of communist conspiracies is driving so much of this nonsense.

[Giltil (Gilbert Thill)]

@Rumraket

So I ask again, what evidence is there that researchers at the WIV were deliberately experimenting on viruses to “increase transmissibility or the virulence”?

If the information reported in the paragraph titled Inside the Wuhan Institute of Virology of Wade’s article below are correct, then there remains few doubt that dangerous gain of function experiments have been carried out at the WIV.

The origin of COVID: Did people or nature open Pandora’s box at Wuhan?

[cwhenderson (Curtis Henderson)]

@Giltil

If the information reported in the paragraph titled Inside the Wuhan Institute of Virology of Wade’s article below are correct, then there remains few doubt that dangerous gain of function experiments have been carried out at the WIV.

Wade’s argument leans heavily on exactly what a “pseudovirus” is. Obviously, I have not seen all of Shi’s related data, but the pseudovirus term implies a testing method that involves virus portions (in this case, the S protein), and not the whole virus. The most logical conclusion from the quotes Wade provided would be completely safe with no chance of altering infectious virus.

[Art (Arthur Hunt)]

@Giltil

If the information reported in the paragraph titled Inside the Wuhan Institute of Virology of Wade’s article below are correct, then there remains few doubt that dangerous gain of function experiments have been carried out at the WIV.

The question is - how much is Wade making up, and how much is informed by knowledge of the specific aims of the proposal (NOT the grant abstract, which seems to be all Wade is working from).

[Faizal_Ali]

@Giltil

If the information reported in the paragraph titled Inside the Wuhan Institute of Virology of Wade’s article below are correct, then there remains few doubt that dangerous gain of function experiments have been carried out at the WIV.

Yes.

But, since his information is completely incorrect, there is every reason to doubt, and very little to believe, that claim.

Debunking Nicholas Wade's Origin of COVID Conspiracy Theory - Medika Life

[Dan_Eastwood]

^^^ A very well explained analysis, thus my highlight.

[Rumraket (Mikkel R.)]

@Giltil

If the information reported in the paragraph titled Inside the Wuhan Institute of Virology of Wade’s article below are correct, then there remains few doubt that dangerous gain of function experiments have been carried out at the WIV.

Sorry but I find that section rather misleading. Yes it’s dangerous research, no doubt about that. Which is why it’s carried out in a BSL-4 facility.

But first of all, they’re using pseudoviruses. Viruses deliberately created to be incapable of replicating. Giving a pseudovirus a new spike protein to see if this facilitates infection doesn’t appear to be to constitute the creation of “novel coronaviruses with the highest possible infectivity for human cells”.

This appears to refer to similar work as that in the articles that @Michael_Okoko referenced earlier in this thread, where proteins were taken from a bat virus known to infect bats, replace those on a virus known to infect humans, to see if these proteins really did facilitate infection of human cells.

Can you explain to me what, if anything, was rendered more dangerous than it already was? Is the bat virus the protein came from more dangerous because someone copied it’s spike protein gene and inserted in another virus? No.

Is the virus already infecting human cells more dangerous (does it have increased “transmissibility and virulence”) when given the bat spike protein in replacement of the one it already had, which it already used to infect human cells? No. As a pseudovirus, is it lethal? No. It possibly isn’t even dangerous at all.

Wade quotes this from the proposal:

“We will use S protein sequence data, infectious clone technology, in vitro and in vivo infection experiments and analysis of receptor binding to test the hypothesis that % divergence thresholds in S protein sequences predict spillover potential.”

They are testing a hypothesis that % divergence in protein sequence predicts spillover potential. Which seems completely rational to do to try to predict and prevent new pandemics, and likely sources of potentially dangerous new pandemics.

If they are successful in identifying what those thresholds are, and where specifically in the proteins to look for mutants that facilitate transmission to human hosts, then they’re also much more likely to be able to identify potentially dangerous new viruses before they emerge naturally. It would be stupid to NOT do this kind of research.

There is a reasonable discussion to be had about safety levels (when is it safe enough?), but it seems irrational to try to ban this kind of research when nature generally isn’t in the business of abiding by human political conventions.

Thou shalt not swap genes with thy neighbor might make for a nice 11th commandment, but viruses don’t read books.

I find this statement misleading:

What this means, in non-technical language, is that Shi set out to create novel coronaviruses with the highest possible infectivity for human cells.

Is the virus already infecting human cells more dangerous when given the bat spike protein in replacement of the one it already had, which it already used to infect human cells? No.

Would using a pseudovirus to fin out where the threshold of % similarity lies that facilitates infection of human cells constitute creating a “novel coronavirus with the highest possible infectivity of human cells”? No. That’s wrong. Misleading and wrong.

Is it made as infectious as possible? No.

It seems to me this research likely really does tell us that there is a good chance the wild bat virus with it’s spike protein potentially is capable of transmitting to humans, and that therefore this is eminently rational research to be doing so that one can actually prepare for that possibility. That’s the whole damn point of this research. With this knowledge in hand, you can continously monitor wild populations of viruses and start developing vaccines before the inevitable actually occurs.

I think you would have a case if some replication-capable virus that was not previously capable of infecting humans was deliberately made not only capable of infecting humans, but also synthetically more lethal than any natural variant. But I have seen no evidence to indicate this was being done.

[Michael_Okoko]

I agree. It reiterates some points we have made here and adds new ones too. Its an excellent takedown of Wade’s misuse of the science of virology.

[Faizal_Ali]

A good example of the kind of junk science underlying much of the lab leak theory, courtesy of an interview by that esteemed journal The Daily Mail with two gentlemen named Angus Dalgleish and Birger Sørensen regarding an article they were about to publish:

Dalgleish and Sørensen claim that scientists working on Gain of Function projects took a natural coronavirus ‘backbone’ found in Chinese cave bats and spliced onto it a new ‘spike’, turning it into the deadly and highly transmissible SARS-Cov-2.

One tell-tale sign of alleged manipulation the two men highlighted was a row of four amino acids they found on the SARS-Cov-2 spike.

In an exclusive interview with DailyMail.com, Sørensen said the amino acids all have a positive charge, which cause the virus to tightly cling to the negatively charged parts of human cells like a magnet, and so become more infectious.

But because, like magnets, the positively charged amino acids repel each other, it is rare to find even three in a row in naturally occurring organisms, while four in a row is ‘extremely unlikely,’ the scientist said.

‘The laws of physics mean that you cannot have four positively charged amino acids in a row. The only way you can get this is if you artificially manufacture it,’ Dalgleish told DailyMail.com.

Their new paper says these features of SARS-Cov-2 are ‘unique fingerprints’ which are ‘indicative of purposive manipulation’, and that ‘the likelihood of it being the result of natural processes is very small.’

[Michael_Okoko]

@Rumraket

This appears to refer to similar work as that in the articles that @Michael_Okoko referenced earlier in this thread, where proteins were taken from a bat virus known to infect bats, replace those on a virus known to infect humans, to see if these proteins really did facilitate infection of human cells.

Wade claimed they enhanced the ability of a bat coronavirus to infect human cells and cited a paper wherein Zheng Li (“Bat Lady”) and Baric were among the authors as proof they did this. I looked at the article and found they did no such thing. This is the article in question:

https://www.nature.com/articles/nm.3985

Its a blatant false claim in Wade’s article. The authors used SARS-CoV (a coronavirus that already had the ability to infect human cells) as the backbone for the spike protein of a bat coronavirus (SCH014-CoV) and to their surprise, found that the bat spike protein allowed SARS-CoV infect human cells. They went on to use the actual bat coronavirus to infect human cells and not surprisingly, it couldn’t. Thus, the researchers concluded the bat coronavirus evaluated in the study had the potential to cross over into human populations (since its spike protein could aid the entry of SARS-CoV into human cells) but could not at the moment because it needed adaptations (akin to or different from those present in the SARS-CoV backbone it’s spike protein was inserted into) to make that jump. The paper never described a gain-of-function experiment, neither did the study “enhance the ability” of the bat coronavirus to attack human cells.

[Michael_Okoko]

@Faizal_Ali

‘The laws of physics mean that you cannot have four positively charged amino acids in a row. The only way you can get this is if you artificially manufacture it,’ Dalgleish told DailyMail.com.

Their new paper says these features of SARS-Cov-2 are ‘unique fingerprints’ which are ‘indicative of purposive manipulation’, and that ‘the likelihood of it being the result of natural processes is very small.’

This gave me a good laugh. It appears the authors are ignorant of protein and amino acid biochemistry.

It seems they think the arginine and proline residues are entirely positively charged, when in fact, it’s just their side-chains that are. They also ignore that these side-chains can adopt different rotations in space that prevent steric clashes, allowing proteins assume and maintain their folds.

If you search through the sequences of putative human proteins you would find many examples of positively charged amino acid residues in series. I wonder who designed us in a lab?

Addendum: I checked to see if the serially arranged positive amino acid residues (PRR, where “P” is proline and “R” is arginine) in the furin cleavage site of SARS-CoV-2 are also present in human proteins using BLAST and unsurprisingly its rife.

Here is a screenshot of some of the hits on BLASTp:

Screenshot of some of the alignments (“Query 1” is for SARS-CoV-2, while “sbjct” is for any hit, in this case a human being):

Again, we must Dalgleish which lab we were made in and by whom?

[Faizal_Ali]

@Michael_Okoko

If you search through the sequences of putative human proteins you would find many examples of positively charged amino acid residues in series. I wonder who designed us in a lab?

It’s also very impressive that the Chinese have figured out how to break the laws of physics.

[Michael_Okoko]

They deserve a Turbo Nobel Prize for that, because it vastly outshines their recent technological stride of maintaining artificial fusion for nearly two minutes.