About the origin of SARS-CoV-2

Face, meet palm. :man_facepalming:

Thanks for the reference. However, as far as I could see, it doesn’t mention neither Wuhan nor some other cities in the Hubei province as hotspots of viral outbreaks. I’ve done some googling to see if I could find some evidence supporting this idea but unsuccessfully until know. So I’m not sure that your firemen analogy works here and for this reason, I still think that the fact that the pandemic broke out precisely in Wuhan, the very city in China where gain of function experiments on bat coronaviruses were ongoing, is a genuine surprise.

The virus in the Wuhan lab that is most closely related to SARS- CoV2 is only 96% similar.

There is no way this could be modified to SARS- CoV2 using current technology.

Unless the lab has secretly hired the same “intelligent designer” who invented the bacterial flagellum?

Wrong

Wrong. It would be more correct to say that according to the Wuhan lab officials, the virus in this lab that is most closely related to SARS2 is only 96% similar.

Oh? Give a detailed description of how that would be done, then.

So you are saying they are lying, and fooled the WHO officials who inspected the lab and issued the report below (p. 118)?

What evidence have you for this?

I think both of you are wrong.

@Faizal_Ali, it was possible to generate SARS-CoV-2 in the laboratory using current technology prior to the outbreak. This could have been done using existing reverse genetic systems.

@Giltil, for SARS-CoV-2 to have been created via manipulation in some lab, an existing reverse genetic system would have been used and that would have shown in the genetic data. Unfortunately for the lab manipulation hypothesis, there is no evidence of any previously used virus backbone in SARS-CoV-2’s genome, thus refuting this hypothesis.

Its true that the most closely related bat coronavirus in the Wuhan Institute of Virology (WIV), which was RaTG13, is 96% similar to SARS-CoV-2 (SARS2) but you are ignoring that there are other SARS2-related bat coronaviruses discovered in other countries, years before the pandemic began. For example, some bat coronaviruses sampled in Cambodia as far back as 2010 were 92.6% similar to SARS2. This raises the likelihood of a natural emergence by far and suggests that SARS2 may have been circulating unnoticed in the wild for more than a decade before it made the jump to humans.

Furthermore, this findings are disturbing. They indicate another coronavirus disease outbreak might just be around the corner. There is need for extensive sampling of wildlife known to harbor coronaviruses so that we won’t be taken by surprise. By “we” I mean the public in general, not virologists and other public health researchers whose warnings of potential zoonotic events leading to disastrous pandemics have been largely ignored. Of course, if we are take the fight to the viruses, the experts have to try as much as possible to prevent lab leaks of collected samples and I know that even now there are pretty solid containment measures in labs working with viruses.

This is quite wrong. The earliest cluster of cases where the virus was first identified were detected in Wuhan, but according to the WHO report, there is some evidence suggesting that SARS2 was already circulating in other places before the first case was detected in Wuhan. For now, no one knows where the pandemic really began.

I suggest you read the WHO report for more details:

Phase I WHO Report on Covid-19 Origins.pdf (2.3 MB)

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Hey if the Chinese can just make up and synthesize new SARS-Cov2 genomes I have to wonder why they haven’t just concocted a sequence for the ancestor and claim to have found it in wild animals already?

I think if proponents of the lab-escape hypothesis consider anything output by the Chinese so suspect as to be effectively worthless as evidence, then how is this not a pseudoscientific conspiracy theory? Every time the Chinese might give new evidence it can be automatically dismissed as fake or untrustworthy.

In it’s most extreme form (and it will go there eventually for many as they become more and more wedded to defending the initial position they took) it’s sort of like the flat-Earthers who insist satellite photos of the Earth are all being photoshopped somewhere by artists hiding away in secret NASA bunkers. At some point we’re going to come up against the rationalization that everyone have been bought, everything is made up, and nobody can be trusted because the communists have infiltrated every organization on Earth.

I’m not saying this to advocate blind trust or obedience in everything said by China, but we have to spend some time thinking about how far his has to go. Is there anything the Chinese could say, or data they could find and make public, that would convince conspiracy-thinkers? Or are we already at the level where everything needs to be vetted and independently confirmed by some 3rd party?

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No. What I am saying is that they may have lied. This is why even Fauci now agrees that the issue of the origin of Covid-19 should be investigated further.
Now, are you denying than humans are lying sometimes? And that lies are not uncommon under a communist dictatorship?

I believe Faizal was referring to the fact that the SARS-CoV-2 genome contains substitutions all over the genome that amount to that 4% difference (that also match a natural mutation spectrum, btw), and the only feasible way to achieve that is through many years of passaging, too many to have been performed in the lab between the collection of RaTG13 and the start of the pandemic.

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^This. I mean, I suppose you could engineer all of those substitutions, but that’s utterly insane. For the lab-leak theory to be true, the Wuhan lab had to be working with the immediate precursor of SARS-CoV-2 (with or without gain-of-function work) and not have mentioned it to anyone. And of course they’d have to be lying about it now. That’s all possible but not particularly plausible. Why would they hide one coronavirus?

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This nuance wasn’t present in Faizal’s comment, hence my response. I agree with you though.

Cool point, any papers on the “natural mutation spectrum”?

In addition, according to a study cited in the WHO report the divergence at neutral sites was 17% (higher than the human-chimp difference), while in protein coding regions it was 0.8% between SARS2 and RaTG13. Genome-wide differences amounted to that 4%. This is the paper:

Whispers in Steve’s ears

Reptoids have infiltrated the Chinese government and set up labs to engineer coronaviruses that will help fulfill their goals of global human domination. In case you don’t know, SARS2 was made on the moon and transported here via intergalactic waves so that our satellites won’t pick it up in transit. The plan failed to an extent and now the reptoids are trying to get rid of any incriminating data. US reptoids like Bill Gates are sulking at the failure of their Chinese counterparts and chugging down more adenochrome than usual, planning for the next global assault

Steve looks at me, mortified. I just came up with the most outlandish conspiracy theory in human history studded with sciencey words. I grin in satisfaction and walk out the door smiling devilishly

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Figure 1 from this paper:

https://onlinelibrary.wiley.com/doi/10.1002/bies.202000325

we observe similar relative frequencies of single nucleotide substitutions distinguishing SARS-CoV-2 and SARS-CoV from their bat relatives RaTG13 and Rs4231, respectively

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This is a bit of a chicken or egg consideration, given that the virology lab was situated in Wuhan because that location is proximate to caves harboring viral reservoir bats, and a concerning local epidemiological history. While the virology institute is at ground zero of the pandemic, it would not be surprising if the virus emerged from that region independently.

I agree, but note it is possible the “lab leak”, if indeed that turns out to be the origin of SARS-CoV-2, took the form of exposure in the course of field work, crawling over guano and handling bats. That exactly such surveillance sampling might have been the source of COVID may be as credible a scenario as laboratory manipulation.

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Yes in fact, why not just claim to have found the animal host source of the virus now?

If they in fact already have the immediate ancestor of SARS-Cov2 at the WIV, and know where it originally came from, but have been secretly studying it for a while, what is stopping them from just making up a new lie claiming they’ve just now found the source?

Many high profiles scientists that are not conspiracy theorists disagree with you, including David Baltimore and Robert Redfield, former president of the CDC.

Given the devastating consequences for the Chinese regime if it were found to be responsible for a pandemic that caused such devastation around the world, it is not hard to see that if the regime were indeed responsible, it would have a vested interest in doing everything possible to hide it.

Okay, I see. You opine that anyone who think that the lab escape theory is a live possibility that should be investigated further is a conspiracy theorist! So David Baltimore (Virologist and Nobel laureate) Robert Redfield (virologist and former CDC director), Anthony Fauci (director of the U.S. National Institute of Allergy and Infectious Diseases and the chief medical advisor to the president), Tedros Ghebreyesus (WHO director-general) Joe Biden (president of the United States of America) and the guys that signed the letter below are all conspiracy theorists, aren’t they?
https://science.sciencemag.org/content/372/6543/694.1.full

That’s an excellent paper. Thanks for the share.

I agree with you, but we wouldn’t call it a leak anymore. It would be simply called direct zoonosis.

Not ‘why are they hiding it now?’ Why were they hiding it before it escaped? If they were doing gain-of-function research on a virus, it would be one they’d sequenced and characterized earlier. This lab has made public other viruses they’ve worked on – why not this one, if they were doing a lot of work on it?

That doesn’t make a lab leak impossible, but it makes it less likely, just as the presence of the lab in Wuhan makes it more likely.

Its strange you couldn’t tell I was being sarcastic. This is also a strawman because I have never excluded the possibility of a lab leak, neither have I opined that anyone who holds to that possibility is a conspiracy theorist.

Knock down your strawman. Like these guys, I recognize the possibility of a lab leak, but like Anthony Fauci I realize its an unlikely one.

In addition, the letter penned and signed by those scientists was wholly unnecessary. The recently concluded WHO investigation was just the first phase and this is clearly stated in their report. Investigations have not come to a halt.

Finally, keep track of the data not the opinions of experts. In science, rigorous data trumps expert opinion.