Origins of Covid

angrysoba said:

... So, the evidence that the particular virus we are talking about has escaped should be in the genome somewhere.

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It might be but right as the pandemic started the Chinese government took access to a lot of work on coronaviruses offline and has denied access to it. The link in is the thread somewhere. I'll look for it.

angrysoba said:

... For the most part they are pretty engrossed in the nitty gritty details and then they do a little aside, beginning somewhere around 20 or 25 minutes in which they talk about how there are some lab leak theories and how the stuff they are talking about makes this really unlikely.

The whole thing is quite long and I am listening to it now, but maybe you might be interested in it...

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Re the lab leak hypothesis This should be of interest (don't know if it was posted before):
MIT Tech Review: Did the coronavirus leak from a lab? These scientists say we shouldn’t rule it out.

Perhaps no one played a greater role in galvanizing scientific opinions in support of natural origins than Peter Daszak,...

Daszak is purported to have written a first draft of the Lancet statement condemning hypotheses other than natural origins as conspiracy theories. ...

Relman agrees that in the absence of conclusive evidence, the message on origins should be “We don’t know.” After the Lancet statement, and then a subsequent paper on SARS-CoV-2’s origins written by scientists who concluded that “we do not believe any type of laboratory-based scenario is plausible,” he found himself increasingly disheartened by those who he claimed had seized on a spillover scenario, despite “an amazing absence of data.” Relman says he felt he had to push back.

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Motive:

Relman proposes that among those trying to suppress the lab-release hypothesis, there might have been “far too much protection of one’s self and one’s peers before allowing a really important question to receive a hearing.” And scientists collaborating with researchers in China “might worry about their working relationship if they say anything other than ‘This threat comes from nature.’”

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RecoveringYuppy said:

That is not an accurate description of what you and Sherkeu have been claiming.

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No offense but this is silly. From your second link:

We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province.

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Sherkeu and I have been discussing how the biological clock was used to estimate when and where the first case(s) occurred.

Skeptic Ginger said:

No offense but this is silly. From your second link:

Sherkeu and I have been discussing how the biological clock was used to estimate when and where the first case(s) occurred.

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Yeah, right. Are you walking back all the lab leak claims??

RecoveringYuppy said:

Yeah, right. Are you walking back all the lab leak claims??

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Of course not!

WTF???

I give up. You have some misconception somewhere that is beyond my ability to understand what you are even talking about.

Maybe if you spelled your issue out in more detail than these little quips I might understand so I could reply.

Sometimes it's easier to search for the link again than to find it in the thread. This is from 11 months ago.

China clamping down on coronavirus research, deleted pages suggest

Two websites for leading Chinese universities appear to have recently published and then removed pages that reference a new policy requiring academic papers dealing with Covid-19 to undergo extra vetting before they are submitted for publication.

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But then I always find new stuff I missed earlier. There are caches of these papers somewhere.

I posted this earlier but there is no way to see the article other than the bullets.
Chinese laboratory that first shared coronavirus genome with world ordered to close for ‘rectification’, hindering its Covid-19 research

And there is this which oddly cites Sept 2019 for the removal databases.

An investigation into the WIV databases that were taken offline On the 12th Sep 2019, the main database of samples and viral sequences of the Wuhan Institute of Virology went offline. Eventually every single of the 16 virus databases managed by the WIV was taken offline. Here we show how these databases may provide essential clues at to the origins of SARS-CoV-2 and review the circumstances in which they were taken offline. I'm going to see what's on that site about the specific COVID 19 precursor viruses.

...

Skeptic Ginger said:

It might be but right as the pandemic started the Chinese government took access to a lot of work on coronaviruses offline and has denied access to it. The link in is the thread somewhere. I'll look for it.

Re the lab leak hypothesis This should be of interest (don't know if it was posted before):
MIT Tech Review: Did the coronavirus leak from a lab? These scientists say we shouldn’t rule it out.

Perhaps no one played a greater role in galvanizing scientific opinions in support of natural origins than Peter Daszak,...

Daszak is purported to have written a first draft of the Lancet statement condemning hypotheses other than natural origins as conspiracy theories. ...

Relman agrees that in the absence of conclusive evidence, the message on origins should be “We don’t know.” After the Lancet statement, and then a subsequent paper on SARS-CoV-2’s origins written by scientists who concluded that “we do not believe any type of laboratory-based scenario is plausible,” he found himself increasingly disheartened by those who he claimed had seized on a spillover scenario, despite “an amazing absence of data.” Relman says he felt he had to push back.

Click to expand...

Motive:

Relman proposes that among those trying to suppress the lab-release hypothesis, there might have been “far too much protection of one’s self and one’s peers before allowing a really important question to receive a hearing.” And scientists collaborating with researchers in China “might worry about their working relationship if they say anything other than ‘This threat comes from nature.’”

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I am puzzled by the sides of this argument of 'lab' vs 'natural'.
Why are 'naturally occurring" viruses in the wild and the 'naturally occurring' viruses the lab was collecting in the wild mutually exclusive to determining origin?

There are many different scenarios where it comes from nature (or is otherwise natural as in a mutation happening from live specimens) but connected to work the lab was doing.

Sure, viruses of all kinds are likely to cross species much more in nature, millions of interactions. And there are far far more farmers and traders working with animals than researchers. However, the work in Southern China was not a random sample among these interactions. It was in a high-risk, very small, targeted area of caves where SARS viruses that can infect human cells were found, where the closest known relation of SARS-Cov-2 was found, and where test results showed spillover of some unknown bat SARS virus in nearby villagers.

eta: removes specific cave number since RaTG13 was collected in an abandoned mine and not one of the 2 'tourist' caves near the villages. looking for proximity....

Daszak did a PBS interview Aug 2016. (At this point he would have had at least the initial results of the testing on villagers from Oct 2015 near the Yanzi and Shitou caves))

Why southern China is a hotbed for disease development
https://www.pbs.org/newshour/show/southern-china-hotbed-disease-development

Daszak: This is a big tourist cave. Shall we go?

Sreenivasan: Daszak is concerned about a bat cave that is a popular tourist destination.
The bats here in this cave are the same bats that carry SARS virus.

Daszak:Bats live in the cave all day long, because they're nocturnal. And when they're up there, they urinate and defecate, right on top of the tourists that are walking through.

And all you have got to do is be that one person to breathe in at the wrong time, and suddenly you have been infected with a virus that is not only potentially lethal to people. It could cause a future pandemic.

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He doesn't say specifically if tourists could catch a SARS virus direct from bats but that seem to be the implication.

Sherkeu said:

...

I am puzzled by the sides of this argument of 'lab' vs 'natural'.
Why are 'naturally occurring" viruses in the wild and the 'naturally occurring' viruses the lab was collecting in the wild mutually exclusive to determining origin?

There are many different scenarios where it comes from nature (or is otherwise natural as in a mutation happening from live specimens) but connected to work the lab was doing.

Sure, viruses of all kinds are likely to cross species much more in nature, millions of interactions. And there are far far more farmers and traders working with animals than researchers. However, the work in Southern China was not a random sample among these interactions. It was in a high-risk, very small, targeted area of caves where SARS viruses that can infect human cells were found, where the closest known relation of SARS-Cov-2 was found, and where test results showed spillover of some unknown bat SARS virus in nearby villagers.

eta: removes specific cave number since RaTG13 was collected in an abandoned mine and not one of the 2 'tourist' caves near the villages. looking for proximity....

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It's called framing the argument with a nice straw man distraction.

Claim there is no evidence the virus was developed as a bioweapon or "made in a lab" and cite the fact one would expect to see evidence in the genome if it had been. Let the news media, sometimes with a bit of a nudge here and there, conflate that with any virus coming from a lab leak.

I know people on this forum love to discount anything that might be a CT. So when Dasvak started suggesting well ahead of the WHO investigation that any suggestion of an origin in the WIV was a conspiracy theory, not only did a lot of people here buy it, but so did other investigators that have been cited here.

Take this Twitter feed angrysoba linked to from K G Anderson who asserts the lab leak story isn't supported by any evidence.

After one year of political bluster and pure speculation, still nothing.

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The Twitter thread seems to be somewhat dead and it appears that Mr Andersen neither addressed any of the evidence posted in the thread, nor did he respond to posts in the thread that the animal jump had just as much evidence.

I've seen other researchers and scientists making the same kind of statements, the lab leak is so unlikely..... look over here at the animal 'spillover' hypothesis.

And as I cited a source above, Daszak made sure that 'couldn't have been the lab' narrative got out there well ahead of anyone suggesting the lab remains a viable hypothesis. The narrative makes it look like if you dare to look at the lab, you are a CTer.

A lot of scientists have pushed back and continue to do so.

Sherkeu said:

Daszak did a PBS interview Aug 2016. (At this point he would have had at least the initial results of the testing on villagers from Oct 2015 near the Yanzi and Shitou caves))

Why southern China is a hotbed for disease development
https://www.pbs.org/newshour/show/southern-china-hotbed-disease-development

He doesn't say specifically if tourists could catch a SARS virus direct from bats but that seem to be the implication.

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I had to poke around a bit to find the video since it is older. It's less than 7 minutes. Much better with the pics.

It won't play directly here, but you can watch it on YT

https://www.youtube.com/watch?v=vb4oDJ4T1kE

Skeptic Ginger said:

I had to poke around a bit to find the video since it is older. It's less than 7 minutes. Much better with the pics.

It won't play directly here, but you can watch it on YT

https://www.youtube.com/watch?v=vb4oDJ4T1kE

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Thanks! Yes, better with video.

Digging further into what caves had which viruses, the virus that killed 3 of 6 hospitalized guano-cleaners in 2012 was about 100mi SW (as the crow flies) along the same highway. That cave (an abandoned copper mine) is not for tourists (or journalists). The RaTG13 sample came from this location.

A summary here:
Lethal Pneumonia Cases in Mojiang Miners (2012) and the Mineshaft Could Provide Important Clues to the Origin of SARS-CoV-2
https://www.frontiersin.org/articles/10.3389/fpubh.2020.581569/full

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 cnki.net 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. Retrospective analysis of the pneumonia cases shows striking similarities with COVID-19. Bilateral pneumonia, vascular complications like pulmonary thromboembolism, and secondary infections are the main similarities. The treatment regimes were similar to the current treatments for COVID-19.

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The translation of the paper referred to above can be found here:

MS Thesis 2013 (medical case documentation/"glassy" xrays here! one patient was in hospital for 109 days before succumbing)
https://drive.google.com/file/d/1d6GdDYtVrstULLSZmmqcu3NlLsYol2OA/view

Phd Thesis 2015 (partial translation)
https://drive.google.com/file/d/1OdWCjEJEqEyxbujWwvkf0hknxDoRTCAw/view

This one follows the first with the addition of bat/rat samples and antibody blood testing.

...blood test results of 4 cases showed that: 4 people carried SARS virus lgG antibodies, of which 2 were discharged with higher antibody levels and 2 were hospitalized with lower antibody levels (Wuhan, Chinese Academy of Sciences) Virology Institute).

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Sherkeu said:

...



I am puzzled by the sides of this argument of 'lab' vs 'natural'. Why are 'naturally occurring" viruses in the wild and the 'naturally occurring' viruses the lab was collecting in the wild mutually exclusive to determining origin?
There are many different scenarios where it comes from nature (or is otherwise natural as in a mutation happening from live specimens) but connected to work the lab was doing.

Sure, viruses of all kinds are likely to cross species much more in nature, millions of interactions. And there are far far more farmers and traders working with animals than researchers. However, the work in Southern China was not a random sample among these interactions. It was in a high-risk, very small, targeted area of caves where SARS viruses that can infect human cells were found, where the closest known relation of SARS-Cov-2 was found, and where test results showed spillover of some unknown bat SARS virus in nearby villagers.

eta: removes specific cave number since RaTG13 was collected in an abandoned mine and not one of the 2 'tourist' caves near the villages. looking for proximity....

Click to expand...

Skeptic Ginger said:

It's called framing the argument with a nice straw man distraction.

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No, it is NOT framing with a strawman.

I have asked, and not been told, what the theory that you are proposing is.

On the one hand we have claims of gain of function creating a virus that is highly adaptive to humans, right?


So we have:

1.) Lab leak of manipulated virus.

How does someone address this claim? Well, maybe by seeing if there is evidence of a manipulated virus.

But then you argue that that is a "strawman"???!?!? Okay, so what role does GoF have in this thing? If you want us to dispense with this claim then we have...

2.) Lab leak of virus that just so happens to be well adapted to humans.

Okay, how does someone address this? Well, we just look and see if there is evidence of it. Apparently, no evidence that it just got out through someone being sickened by it. Or is there? But also no evidence that the specific virus was even there in the lab to begin with.

So then, I presume you are arguing that maybe it was there, and the WIV sequenced it and put it in its database but then hid the evidence by taking down the database.

Okay, then the answer is in the database?

Yes, or maybe no.

If not, then what?

Then, maybe there was a bat that had the virus in the WIV but nobody realized it. Or maybe it was on some guano or something else.......


Ummmm...okay, but what exactly is being covered up here if they just happened to have the virus but didn't know about it.

Sorry, I am asking you to tell me what your theory is. You can't complain about a strawman if you don't clearly explain the theory.

Sherkeu said:

Thanks! Yes, better with video.

Digging further into what caves had which viruses, the virus that killed 3 of 6 hospitalized guano-cleaners in 2012 was about 100mi SW (as the crow flies) along the same highway. That cave (an abandoned copper mine) is not for tourists (or journalists). The RaTG13 sample came from this location.

A summary here:
Lethal Pneumonia Cases in Mojiang Miners (2012) and the Mineshaft Could Provide Important Clues to the Origin of SARS-CoV-2
https://www.frontiersin.org/articles/10.3389/fpubh.2020.581569/full



The translation of the paper referred to above can be found here:

MS Thesis 2013 (medical case documentation/"glassy" xrays here! one patient was in hospital for 109 days before succumbing)
https://drive.google.com/file/d/1d6GdDYtVrstULLSZmmqcu3NlLsYol2OA/view

Phd Thesis 2015 (partial translation)
https://drive.google.com/file/d/1OdWCjEJEqEyxbujWwvkf0hknxDoRTCAw/view

This one follows the first with the addition of bat/rat samples and antibody blood testing.

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What claim are you making about RaTG13?

What is its significance?

angrysoba said:

What claim are you making about RaTG13?

What is its significance?

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I'm simply adding some pieces to the puzzle.

2012- cleaners at a mine hospitalized with symptoms strikingly similar to Covid.
2013- sample RaTG13 taken from a bat at same location
2014- samples of 2012 patients are positive for SARS antibodies
2020- RaTG13 is closest known relation to SARS-Cov-2

What I take from it is that 2019 is not the first lethal SARS coronavirus from bats since the original SARS outbreak (2002-3). I would strongly suspect that the area around this location held the bat with a SARS virus that started the 2019 outbreak, whether it happened there or followed some other chain to humans.

What do you think? Related novel virus? or coincidence? or other?

Sherkeu said:

I'm simply adding some pieces to the puzzle.

2012- cleaners at a mine hospitalized with symptoms strikingly similar to Covid.
2013- sample RaTG13 taken from a bat at same location
2014- samples of 2012 patients are positive for SARS antibodies
2020- RaTG13 is closest known relation to SARS-Cov-2

What I take from it is that 2019 is not the first lethal SARS coronavirus from bats since the original SARS outbreak (2002-3). I would strongly suspect that the area around this location held the bat with a SARS virus that started the 2019 outbreak, whether it happened there or followed some other chain to humans.

What do you think? Related novel virus? or coincidence? or other?

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Sure, related, but research by Linfa Wang and others show that these types of related viruses have a wide range over which they are found in bats.

I'm going to answer this without repeating all the sources which can be found in this thread. Cited sources for all this are in the thread.

angrysoba said:

No, it is NOT framing with a strawman.

I have asked, and not been told, what the theory that you are proposing is.

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I don't understand how you don't know what my lab-leak hypothesis is. I have spelled it out including recently summarizing the evidence supporting it and stating what evidence still needs to be found.

As for the second viable hypothesis: a species jump to humans in the wild, I'm not ruling that out. It could be proven if the animal harboring the intermediate virus could be found. With SARS they did just that. They found infected civet cats in the wet market where the first infections were found. That is not the case with COVID 19.

IMO the lab leak is supported by more evidence than the natural jump (spillover) hypothesis.

angrysoba said:

On the one hand we have claims of gain of function creating a virus that is highly adaptive to humans, right?

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It's high up on the likely hypothesis list. It is not, however, what the assertion being made that 'one could tell' claims. By straw man I mean describing a virus originating in the lab in only one way, thereby making it easy to argue that didn't happen or we would see it. The harder arguments against a lab leak are ignored. Thus it is a straw man.

angrysoba said:

So we have:

1.) Lab leak of manipulated virus.

How does someone address this claim? Well, maybe by seeing if there is evidence of a manipulated virus.

But then you argue that that is a "strawman"???!?!? Okay, so what role does GoF have in this thing? If you want us to dispense with this claim then we have...

Click to expand...

If by "manipulated" you mean one built in a lab by taking a piece of virus here and a piece of virus there, that is the virus which the narrative uses to dismiss any and all lab-leaked virus as if anything touched by a researcher would show these same manipulated patterns. The GoF research is much different from a built-in-the-lab or bioengineered type virus.

angrysoba said:

2.) Lab leak of virus that just so happens to be well adapted to humans.

Okay, how does someone address this? Well, we just look and see if there is evidence of it. Apparently, no evidence that it just got out through someone being sickened by it. Or is there? But also no evidence that the specific virus was even there in the lab to begin with.

So then, I presume you are arguing that maybe it was there, and the WIV sequenced it and put it in its database but then hid the evidence by taking down the database.

Okay, then the answer is in the database?

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You have a mixed bag of issues here. As for "just so happened to be ready to go", there is some evidence that is possible. There is evidence that all the parts are there in the wild in horseshoe bats in a cave in Yunnan. All those parts found in one bat that matches COVID 19 has not been found.

There is evidence the pangolin coronaviruses could have been passed back and forth between bat and pangolin and back.

In addition, a generalist bat coronavirus has been found that can infect humans directly. In fact, several cases of a coronavirus pneumonia occurred in miners who worked in one of the bat caves in Yunnan.

No one has said yet that those infections were with a virus that contained the pangolin genome segment. (Only a segment of the pangolin coronavirus matches COVID 19, BTW. As a whole genome, the bat coronaviruses are much closer genetically.)

Recombinant viruses are occurring: Mutation = drift; recombination = shift.

angrysoba said:

Yes, or maybe no.

If not, then what?

Then, maybe there was a bat that had the virus in the WIV but nobody realized it. Or maybe it was on some guano or something else.......

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Oh they realized it. The Chinese government removed the evidence from where it had been available online.
I found additional evidence this was done in Sept 2019. DRASTIC via ResearchGate: An investigation into the WIV databases that were taken offline

Abstract
On the 12th Sep 2019, the main database of samples and viral sequences of the Wuhan Institute of Virology went offline. Eventually every single of the 16 virus databases managed by the WIV was taken offline. Here we show how these databases may provide essential clues at to the origins of SARS-CoV-2 and review the circumstances in which they were taken offline.

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It's quite technical, not like research write-up would be structured. It's copy protected anyway so I can't quote anything from it. But I can repeat this:

Objectives

List all the DBs that were taken offline
Explain their significance
Back it up with screenshots and proofs of deletion​

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It's extensive.

I'm going to come back to the Sept date of action in a follow up post.

angrysoba said:

Ummmm...okay, but what exactly is being covered up here if they just happened to have the virus but didn't know about it.

Sorry, I am asking you to tell me what your theory is. You can't complain about a strawman if you don't clearly explain the theory.

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The straw man is what Daszak and other government officials have done claiming any manipulated virus in the lab would have an easily spotted genetic pattern. Try to argue: yes but what about possible lab cultures that were coaxed but not artificially created and they shift back to distracting people with the implication anything that comes from the lab would have a signature.

angrysoba said:

Sure, related, but research by Linfa Wang and others show that these types of related viruses have a wide range over which they are found in bats.

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Types of related, sure but these isolated viruses were very closely related to COVID 19.

This is one of the caves the researchers from the WIV collected specimens and were working with them.

This is very much narrowed down and has little to do with the fact bat coronaviruses are found over a wide range.

Skeptic Ginger said:

Oh they realized it. The Chinese government removed the evidence from where it had been available online.

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You are talking about the database, right? But do we know what was in it or not?

If not, we can't say what was in it?

If we do, we can see if they had SARS CoV2.

Now, Peter Daszak says they do know what was in the database. Obviously you don't trust him.

Obviously we can argue for greater transparency, but I am still not clear on whether or not you are saying:

a) the database has the smoking gun virus!

or

b) I think it should be investigated.

Maybe I am misreading you, but sometimes you are saying things that look far more defininitive than we know to be true.

Now, from what I can see, gain of function involves "any selection process involving an alteration of genotypes and their resulting phenotypes is considered a type of Gain-of-Function (GoF) research"

https://www.ncbi.nlm.nih.gov/books/NBK285579/

The alteration is what I am talking about as being something that the virologists on the TWiV episode seem to be disputing.

One thing, from what I understand, is that they say, "Sure, you can alter the genome to see how it will behave in vitro, in cell cultures, but the idea that you can then make it viable in animals is another vastly more complicated step, that we don't know anyone who is able to do that...." etc...

Maybe you might want to watch that latest TWiV called "Weiss hath no furin like a virus scorned". It seems that some of the lab leak theorists are interested in the "furin cleavage site", and there is loads of discussion about it on Twitter.

Skeptic Ginger said:

Types of related, sure but these isolated viruses were very closely related to COVID 19.
This is one of the caves the researchers from the WIV collected specimens and were working with them.

This is very much narrowed down and has little to do with the fact bat coronaviruses are found over a wide range.

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Which viruses are we talking about?

RaTG13 is 96% similar to SARS CoV2

According to Wikipedia:

It was discovered in 2013 in bat droppings from a mining cave near the town of Tongguan in Mojiang county in Yunnan, China. As of 2020, it is the closest known relative of SARS-CoV-2, the virus that causes COVID-19

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Skeptic Ginger said:

I've been reading a bit about the genetics of COVID 19, I'll post the inks and specifics later. But there is a general principle here that needs addressing.

There is a bat strain that is about 97ish% a match for COVID. And either all or just the spike protein of the pangolins is about the same, 97%.
Given the genetics and assuming a recombinant event, it does not get you to COVID-19. It's not close enough. I brought this up earlier, chimpanzee DNA is ~99% match for human DNA. And look how different we are.
...
With the bat COVID relative being ~97% different from COVID-19, you can't just take the pangolin COVID relative and end up with a virus capable of infecting human cells no matter how you recombine the viruses.

...

97% might sound like a very close match, but as far as genomes go, it's not close. Chimpanzees are not like Neanderthals, they are not close enough to breed with humans (think in vitro). 98.8% is not close enough...

As for it being a natural event, the evidence is clear that it was. But such recombinant events can be coaxed in the lab and that is what there is at least some question the researchers were working with coronaviruses where such a 'natural' event could have taken place.

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So...forgive my confusion, but when I talked about related viruses, you yourself ahile back said that they are not related. Now, you say they are.

And it looks to me as though you were claiming some kind of genetic alterations being done in the lab.

This is why I am confused.

I want to carry on this discussion with you, angrysoba, and I will . But you need to follow the discussion.

Yes, I did say that. Yes it's not a problem. If you'd been following you might understand we've been gathering evidence and posting it throughout the thread. My position, and I believe Sherkeu's as well have been developing. You expect the case to be established from the beginning of the thread but that is not the case.

For example, I'm correcting the molecular time frame yet again BECAUSE I HAVE NEW EVIDENCE.

More than one researcher tracked the timing of the first case back using the molecular clock. One said the end of Oct. One said the middle of Oct. But I now find one researcher who believes the clock shows the first case in Wuhan was in early Sept based on the molecular clock. These people are using good science. There is a discrepancy in the timeline but they are all essentially on the same page.

Now there is corroborating evidence the Sept date for the first case is right. The Chinese government moved at that time to start removing any evidence that might exist implicating the WIV.
They may not have known at that time the virus had been beyond stopping. And the scenario sounds just like a movie.

An accident occurs at the level 4 bio-safety lab. Someone got infected. No one is absolutely sure the exposed worker (or student) didn't pass it on. But this person took the mass transit line 2. Posted upthread:

COVID-19 Origin and Spread Linked to PLA Hospital and Wuhan Metro System Line 2 by Physician-Scientist Dr. Steven Quay

The researchers know an accident occurred. They probably knew it because at least one person developed symptoms. The government acted right away covering up any research with a dangerous coronavirus they know had infected human cells in vitro.

Is there any other explanation for the removal of all the files in Sept that might contain this research? Come on, any explanation?
I'm not sure this was widely known in the WIV. Daszak knows what he was working on. Did he know about the lab accident at the time it happened?

Someone needs to ask Daszak why he thinks the Chinese government purged (or tried to given it was discovered and the database viewed) the data bases of the WIV's genomic work with dangerous coronaviruses.
It's very likely the government was unaware the infection had gone from an accident to an outbreak until the cluster of pneumonia cases related to the seafood market emerged in early Dec. It was too late at that time to stop it. I don't believe the government would have been able to contact trace everyone who the initial accident person had contact with.

So coverup, yes. Incompetence to stop it before it spread around and out of Wuhan, no, I don't think so. The US would not have been able to do any better. You are trying to contain a contagious disease but it's already potentially spread within a large city.

This is my hypothesis to date.

Give me more evidence and I might revise that position. But I do believe the pieces are coming together.
There still needs to be that initial viral culture in the WIV that matches COVID 19. And it may have been effectively purged.

Look at the alternative hypothesis that it was a jump (spillover) from a pangolin or even a horseshoe bat and there is no growing body of evidence to support that hypothesis.

Skeptic Ginger said:

I want to carry on this discussion with you, angrysoba, and I will . But you need to follow the discussion.

Yes, I did say that. Yes it's not a problem. If you'd been following you might understand we've been gathering evidence and posting it throughout the thread. My position, and I believe Sherkeu's as well have been developing. You expect the case to be established from the beginning of the thread but that is not the case.

For example, I'm correcting the molecular time frame yet again BECAUSE I HAVE NEW EVIDENCE.

More than one researcher tracked the timing of the first case back using the molecular clock. One said the end of Oct. One said the middle of Oct. But I now find one researcher who believes the clock shows the first case in Wuhan was in early Sept based on the molecular clock. These people are using good science. There is a discrepancy in the timeline but they are all essentially on the same page.

Now there is corroborating evidence the Sept date for the first case is right. The Chinese government moved at that time to start removing any evidence that might exist implicating the WIV.
They may not have known at that time the virus had been beyond stopping. And the scenario sounds just like a movie.

An accident occurs at the level 4 bio-safety lab. Someone got infected. No one is absolutely sure the exposed worker (or student) didn't pass it on. But this person took the mass transit line 2. Posted upthread:

COVID-19 Origin and Spread Linked to PLA Hospital and Wuhan Metro System Line 2 by Physician-Scientist Dr. Steven Quay

The researchers know an accident occurred. They probably knew it because at least one person developed symptoms. The government acted right away covering up any research with a dangerous coronavirus they know had infected human cells in vitro.

Is there any other explanation for the removal of all the files in Sept that might contain this research? Come on, any explanation?
I'm not sure this was widely known in the WIV. Daszak knows what he was working on. Did he know about the lab accident at the time it happened?

Someone needs to ask Daszak why he thinks the Chinese government purged (or tried to given it was discovered and the database viewed) the data bases of the WIV's genomic work with dangerous coronaviruses.
It's very likely the government was unaware the infection had gone from an accident to an outbreak until the cluster of pneumonia cases related to the seafood market emerged in early Dec. It was too late at that time to stop it. I don't believe the government would have been able to contact trace everyone who the initial accident person had contact with.

So coverup, yes. Incompetence to stop it before it spread around and out of Wuhan, no, I don't think so. The US would not have been able to do any better. You are trying to contain a contagious disease but it's already potentially spread within a large city.

This is my hypothesis to date.

Give me more evidence and I might revise that position. But I do believe the pieces are coming together.
There still needs to be that initial viral culture in the WIV that matches COVID 19. And it may have been effectively purged.

Look at the alternative hypothesis that it was a jump (spillover) from a pangolin or even a horseshoe bat and there is no growing body of evidence to support that hypothesis.

Click to expand...

Okay, but just for the benefit of anyone reading this, the red stuff and what follows from it are complete speculation.

The blue stuff is also conjecture.

angrysoba said:

Okay, but just for the benefit of anyone reading this, the red stuff and what follows from it are complete speculation.

The blue stuff is also conjecture.

Click to expand...

And what changes something from speculation to an evidence based hypothesis?

Also answer these two questions:

Is there any other explanation for the government removing access to a lot of genome databases from the WIV in Sept?

And upon what evidence are you speculating about the 'spillover' hypothesis?

Go on, support your position with evidence, not conjecture.

Skeptic Ginger said:

And what changes something from speculation to an evidence based hypothesis?

Also answer these two questions:

Is there any other explanation for the government removing access to a lot of genome databases from the WIV in Sept?

Click to expand...

Well, an explanation has been given, whether you believe it or not...

In January this year, Prof Shi Zhengli became one of the first people in the world to sequence Sars-Cov-2, which was already spreading rapidly through the streets and homes of her city.

She then compared the long string of letters representing the virus's unique genetic code with the extensive library of other viruses collected and stored over the years.

And she discovered that her database contained the closest known relative of Sars-Cov-2.

RaTG13 is a virus whose name has been derived from the bat it was extracted from (Rhinolophus affinis, Ra), the place it was found (Tongguan, TG), and the year it was identified, 2013.

...

In what has become the definitive paper ruling out the possibility of a lab leak, RaTG13 has a starring role.

Published in March in the magazine Nature Medicine, it suggests that if there had been a leak, Prof Shi Zhengli would have found a much closer match in her database than RaTG13.

While RaTG13 is the closest known relative - at 96.2% similarity - it is still too distant to have been manipulated and changed into Sars-Cov-2.

...

Prof Shi has also faced questions about why the WIV's online public database of viruses was suddenly taken offline.

She told the BBC that the WIV's website and the staff's work emails and personal emails had been attacked, and the database taken offline for security reasons. "All our research results are published in English journals in the form of papers," she said. "Virus sequences are saved in the [US-run] GenBank database too. It's completely transparent. We have nothing to hide."
After a decade of sampling and experimenting on viruses collected from bats, we now know that back in 2013 the closest known ancestor was discovered of a future threat that would claim well over a million lives and devastate the global economy.

Yet the WIV, according to the published information, did nothing with it, except sequence it and enter it into a database.

Click to expand...

Link

Skeptic Ginger said:

And upon what evidence are you speculating about the 'spillover' hypothesis?

Go on, support your position with evidence, not conjecture.

Click to expand...

Why do I think spillover is more likely than lab leak?

Well, if the virus was not in the lab, then where else would it be, except in nature?

Have you actually found any actual lies that Zhengli Shi or Peter Daszak have said?

Do you have any reason to think that the rest of the world's virologists are just covering for them?

angrysoba said:

Sure, related, but research by Linfa Wang and others show that these types of related viruses have a wide range over which they are found in bats.

Click to expand...

I tried looking for this research but did not find anything. Of course bats all over the world carry viruses with a chance of adapting to infect humans, many of them coronaviruses, many SARS related. Transferring these to humans is still a rare event.

The point of those teams collecting bat samples (besides hunting down the origin of the first SARS) was to find hotspots where a virus is most likely to jump to humans. They did, and they reported it. It's in Yunnan. They spent years taking samples from bats there to Wuhan for study (as was their job to do)

As far as I know, before the current pandemic emerged, only areas in Yunnan showed strong evidence of SARS-CoV bat viruses that had the ability to efficiently infect and replicate in human cells.

The original SARS was traced to a cave in Yunnan (by Shi), the workers in the mine sick and dead with Covid-like symptoms and SARS-antibody positive tests were in Yunnan, and the closest related virus to the current pandemic is also in Yunnan.

Could other far-away bats also be the source? Anything is possible. A similarly capable virus would need to arise and cause spillover elsewhere, independently. Before 2002, SARS-CoV viruses were unknown to infect humans.
Could we be so unlucky?

*One could argue (not saying you would) that maybe the first SARS outbreak circulated (and mutated) among other mammals or back into different bats in a different area, and then infected human populations years later. Also possible. However, all the elements of human SARS, past and present, are right there in Yunnan where researchers had warned was high risk for another emergence.

disclaimer: This is all stated as my opinion citing the available evidence and is not 100% a claim for anything. It is meant to add to collaborative discussions about the origin of SARS-CoV-2 as well as can be deduced by laypersons on a forum. I reserve the right to be wrong, correct errors, and to change my mind at any time with or without compelling new information.

Sherkeu said:

I tried looking for this research but did not find anything. Of course bats all over the world carry viruses with a chance of adapting to infect humans, many of them coronaviruses, many SARS related. Transferring these to humans is still a rare event.

Click to expand...

The research is here and was conducted in Thailand.

These are not just viruses, but pretty similar (if RatG13 is similar) to SARS CoV2:

Phylogenetic analysis of the SC2r-CoV RacCS203
When screened by a published pan-CoV PCR method targeting a 328-bp region in the RdRp gene19, 13 of the 100 rectal swabs were positive (Supplementary Table 1). Sequencing of PCR amplicons from all positive samples revealed an identical sequence which has the highest sequence identity of 96.21% to bat CoV-RaTG13 (NCBI accession no. MN996532.1), 95.86% to human SARS-CoV-2 (NCBI accession no. MT631834.1), and 94.48% to CoV-RmYN02 (GISAID no. EPI_ISL_412977). Five samples with high levels of viral RNA were chosen for further analysis by next-generation sequencing (NGS). The whole-genome sequence with the best assembly quality, named RacCS203, was used as a reference genome for subsequent analysis. The sequences from the other four genomes were almost identical to RacCS203 (Supplementary Fig. 1), indicating this to be the most dominant CoV circulating in this bat colony at the time of sampling.

Click to expand...

Sherkeu said:

The point of those teams collecting bat samples (besides hunting down the origin of the first SARS) was to find hotspots where a virus is most likely to jump to humans. They did, and they reported it. It's in Yunnan. They spent years taking samples from bats there to Wuhan for study (as was their job to do)

As far as I know, before the current pandemic emerged, only areas in Yunnan showed strong evidence of SARS-CoV bat viruses that had the ability to efficiently infect and replicate in human cells.

The original SARS was traced to a cave in Yunnan (by Shi), the workers in the mine sick and dead with Covid-like symptoms and SARS-antibody positive tests were in Yunnan, and the closest related virus to the current pandemic is also in Yunnan.

Could other far-away bats also be the source? Anything is possible. A similarly capable virus would need to arise and cause spillover elsewhere, independently. Before 2002, SARS-CoV viruses were unknown to infect humans.
Could we be so unlucky?

*One could argue (not saying you would) that maybe the first SARS outbreak circulated (and mutated) among other mammals or back into different bats in a different area, and then infected human populations years later. Also possible. However, all the elements of human SARS, past and present, are right there in Yunnan where researchers had warned was high risk for another emergence.

disclaimer: This is all stated as my opinion citing the available evidence and is not 100% a claim for anything. It is meant to add to collaborative discussions about the origin of SARS-CoV-2 as well as can be deduced by laypersons on a forum. I reserve the right to be wrong, correct errors, and to change my mind at any time with or without compelling new information.

Click to expand...

Well, the authors of the piece I quoted said...

Although the origin of the virus remains unresolved, our study extended the geographic distribution of genetically diverse SC2r-CoVs from Japan and China to Thailand over a 4800-km range. Cross-border surveillance is urgently needed to find the immediate progenitor virus of SARS-CoV-2.

Click to expand...

Sherkeu said:

Before 2002, SARS-CoV viruses were unknown to infect humans.
Could we be so unlucky?

Click to expand...

Well, wait a second here.

Before 2002, we had nothing named SARS at all. SARS is just the name given initialy to the syndrome caused by the disease, hence Severe Acute Respiratory Syndrome.

SARS is itself a type of coronavirus, and within that family is the betacoronavirus and then there are four lineages a, b, c, and d. The common cold is often caused by a betacoronavirus from lineage a, whereas lineage b is known as a sarbecovirus, within which there are:

SARS-Cov1
SARS-Cov2

and...

MERS! But wait, MERS comes to humans presumably from bats via camels, and yet that one emerged not that long after SARS. How can we be that unlucky?

angrysoba said:

Well, wait a second here.


MERS! But wait, MERS comes to humans presumably from bats via camels, and yet that one emerged not that long after SARS. How can we be that unlucky?

Click to expand...

Yes, MERS is a coronavirus originally from bats. It had (has?) a different mechanism of infection (something other than ACE2). I know it has been in camels for a long time. Don't know much more about MERS evolution or where those bats came from as it just isn't discussed in depth in the SARS papers.

Is it relevant to sources for either SARS? Or were you kindly pointing out another bat-derived coronavirus that infected humans?
It did, and I failed to include it in my post.

China has pragmatically and correctly deleted the evidence.
Putin would do so but ramshackle America would fail
China has control financially and geopollitically.

Sherkeu said:

Yes, MERS is a coronavirus originally from bats. It had (has?) a different mechanism of infection (something other than ACE2). I know it has been in camels for a long time. Don't know much more about MERS evolution or where those bats came from as it just isn't discussed in depth in the SARS papers.

Is it relevant to sources for either SARS? Or were you kindly pointing out another bat-derived coronavirus that infected humans?
It did, and I failed to include it in my post.

Click to expand...

I think it is relevant in the sense that the WHO among others have been warning about the increased emergence of coronaviruses that can be deadly to humans. I think many of them simply don't think this will be the last SARS or deadly coronavirus and I think that many of the virologists working on this think that more zoonotic spillovers are likely in the future because of bad ecological policies.

ETA: And I have just seen this...

UN’s Kunming biodiversity summit delayed a second time

...
Cop15 will be the first time China has led the world in a major international agreement on the environment.

Links between the destruction of the natural world and the emergence of zoonotic diseases have been amplified during the coronavirus pandemic, with increased awareness about humanity’s destruction of nature. But parties to the CBD have not been able to carry out scientific and preparatory work before Cop15, with some states objecting to online negotiations. The UN said it was working with regional representatives to find a solution so the meetings could take place before the Kunming summit.

Click to expand...

Kunming is of course in Yunnan Province.

Samson said:

China has pragmatically and correctly deleted the evidence.Putin would do so but ramshackle America would fail
China has control financially and geopollitically.

Click to expand...

Okay, so the theory here is that they found SARS CoV2 and had it on their database.

Then, when the outbreak occurred (and the theory is now pushing it back to September 2019) they just deleted the whole database.

Oops! And no one had duplicate information anywhere - except Zheng-li Shi said a copy of it is at GenBank:

GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms. The database started in 1982 by Walter Goad and Los Alamos National Laboratory. GenBank has become an important database for research in biological fields and has grown in recent years at an exponential rate by doubling roughly every 18 months.

Click to expand...

Apparently this is GenBank.

How would that work? Does anyone know if they can access it at GenBank?

It seems to me if Zheng-li Shi is lying it would be pretty easy to discover right now. And why delete the whole thing?

Why didn't they just decide to remove the incriminating ones?

This attempt at trying to force everything to fit a completely made-up narrative looks full of holes to me.

angrysoba said:

Have you actually found any actual lies that Zhengli Shi or Peter Daszak have said?

Click to expand...

Why does it have to be a lie?

angrysoba said:

Do you have any reason to think that the rest of the world's virologists are just covering for them?

Click to expand...

Here you go again repeating this falsehood. You know there are many virologists questioning the WHO's conclusion. I've cited many of them. And there is an even larger number of virologists who have not weighed in.

your cite said:

She then compared the long string of letters representing the virus's unique genetic code with the extensive library of other viruses collected and stored over the years.

Click to expand...

And some of the viruses studied at the WIV were not entered into the the data base. Plus she compared COVID 19 in Jan after the data was scrubbed by the Chinese government in Sept.

This is from my DRASTIC link of all the data bases taken off line (I opened it in pdf and now I can copy-paste from it).

WIV: Bat and rodent borne viral pathogens - batvirus.whiov.ac.cn

Part of batvirus.whiov.ac.cn data was always confidential ...

The aim of the projects funded by the NIH includes pathogenicity enhancement studies using unpublished viruses...

External access to Batvirus.whiov.ac.cn ended on 12th Sep 2019...

Batvirus.whiov.ac.cn holds essential information on SARS-CoV-2 origins

Questions as to the unavailability of batvirus.whiov.ac.cn are not being properly answered

Click to expand...

The author of 'I looked and it wasn't there' is

The administrator of the database is Shi Zhengli herself.

Click to expand...

Does she say she included her access to the confidential parts of the data base?

And more importantly:

Batvirus.whiov.ac.cn holds a password protected section for data that was not to be freely shared. That private data includes:
■ (1) Sampling data of viruses not yet sequenced and (2) sequences of viruses that have not yet been the object of publication.
● Note: The idea is very likely to get the WIV and its associates the privilege of writing the first papers on the viruses sampled by the WIV.
■ (3) sampling data from sites that the WIV prefers not to make public

Click to expand...

The rest of the password protected parts of the data base are for the usual research reasons, holding one's research close to the vest in order to be first to be published.

So we have Daszik (see my next post) and the Chinese keeper of the data base all telling us "nothing to see here".

Skeptic Ginger said:

Why does it have to be a lie?

Daszak has refused to acknowledge he has a conflict of interest.
He stated the lab leak was unlikely before the WHO team went to Wuhan.
He came back saying they had completely discounted the lab leak based on interviews but not based on any objective evidence which they were denied access to.
We don't know if he was the only person working with live cultures at the WIV or elsewhere​

Here you go again repeating this falsehood. You know there are many virologists questioning the WHO's conclusion. I've cited many of them. And there is an even larger number of virologists who have not weighed in.

And some of the viruses studied at the WIV were not entered into the the data base. Plus she compared COVID 19 in Jan after the data was scrubbed by the Chinese government in Sept.

Click to expand...

That doesn’t help your theory then if it was taken down in response to a virus on the database being the cause of Covid 19 because if it wasn’t on the database why take it down?

If it WAS on the database then it would be accessible through GenBank.

If it was in the confidential part of the database why not take that portion down and leave the rest up so as not to appear too obvious?

You are using the takedown of the database as a clue but also trying to have it both ways by saying maybe it wasn’t on the database. Huh?

So have the DRASTIC people been looking through the database on GenBank if Big Virology haven’t done so?

angrysoba said:

That doesn’t help your theory then if it was taken down in response to a virus on the database being the cause of Covid 19 because if it wasn’t on the database why take it down?

If it WAS on the database then it would be accessible through GenBank.

If it was in the confidential part of the database why not take that portion down and leave the rest up so as not to appear too obvious?

You are using the takedown of the database as a clue but also trying to have it both ways by saying maybe it wasn’t on the database. Huh?

Click to expand...

I have more, it's just very long and I'm trimming. If you want extra credit homework, start at page 5 of the DRASTIC record and go from there.

But as to them not knowing what the COVID sequence was, it explains the shotgun approach: take down everything.

angrysoba said:

So have the DRASTIC people been looking through the database on GenBank if Big Virology haven’t done so?

Click to expand...

Why GenBank when the data was not entered in that DB?

Page 8:

They are likely the same as the 8 from the 7896 clade published as part of a batch of 630 viruses of Latinne et al without further details . On that occasion only the RdRp portions were uploaded to GenBank on the 13 Aug 2019 (around 360 bases, not the full sequences of the viruses). ■ That clade is very close to RaTG13 (the closest relative of SARS-CoV-2), so should offer some very important clues as to but is not discussed in the literature.
■ Questions as to why no more attention is being paid to that essential clade are not being answered.

Click to expand...

COVID 19 has almost 30,000 bases.

angrysoba said:

Okay, so the theory here is that they found SARS CoV2 and had it on their database.

Then, when the outbreak occurred (and the theory is now pushing it back to September 2019) they just deleted the whole database.

Click to expand...

No, that is not the hypothesis. The hypothesis is people working on one specific project discovered a lab leak, be it someone got infected or they found and corrected the breach. But they either knew it had already gone beyond the lab down that metro line, or they weren't sure, but they decided to be proactive about removing the incriminating evidence. And another case for removing a whole database is that someone from the lab turned up seriously ill with a coronavirus of unknown type.

Or maybe just the suspicious ground glass chest X-ray was seen at one of the hospitals and they knew what that X-ray meant. It's a reason to remove lots of files.

And another possibility is removing a large amount of data supported the cover-up story that it was to prevent hacking the data while removing specific files would be incriminating.

We have here another improbable coincidence: They just happened to remove these files just before the outbreak which just happened to be very near the WIV where research on these particular pathogens was taking place and it just coincidentally included live (in vivo) studies with human adapted cells, which also was denied at first. The first story was no live virus was being studied, just the genomes.

I answered the rest of your post already.

Supporting the significance of missing data and the less than convincing denials to come.

Skeptic Ginger said:

No, that is not the hypothesis. The hypothesis is people working on one specific project discovered a lab leak, be it someone got infected or they found and corrected the breach. But they either knew it had already gone beyond the lab down that metro line, or they weren't sure, but they decided to be proactive about removing the incriminating evidence. And another case for removing a whole database is that someone from the lab turned up seriously ill with a coronavirus of unknown type.

Or maybe just the suspicious ground glass chest X-ray was seen at one of the hospitals and they knew what that X-ray meant. It's a reason to remove lots of files.

And another possibility is removing a large amount of data supported the cover-up story that it was to prevent hacking the data while removing specific files would be incriminating.

We have here another improbable coincidence: They just happened to remove these files just before the outbreak which just happened to be very near the WIV where research on these particular pathogens was taking place and it just coincidentally included live (in vivo) studies with human adapted cells, which also was denied at first. The first story was no live virus was being studied, just the genomes.

I answered the rest of your post already.

Supporting the significance of missing data and the less than convincing denials to come.

Click to expand...

Okay, thanks. I’ll look at this information more carefully. It’s interesting.

Looks like two new articles suggesting the lab leak is at least a plausible hypothesis.

First, one in USA Today gives an account of a litany of previous lab leaks and the lamentable state of biosecurity in labs around the world.

Then there is one in Washington Post although this is paywalled so I can't read it.

Skeptic Ginger said:

I'm correcting the molecular time frame yet again BECAUSE I HAVE NEW EVIDENCE.

More than one researcher tracked the timing of the first case back using the molecular clock. One said the end of Oct. One said the middle of Oct. But I now find one researcher who believes the clock shows the first case in Wuhan was in early Sept based on the molecular clock. These people are using good science. There is a discrepancy in the timeline but they are all essentially on the same page.

Now there is corroborating evidence the Sept date for the first case is right. The Chinese government moved at that time to start removing any evidence that might exist implicating the WIV.

Click to expand...

May I ask about this claim of Covid-19 cases stretching back as far as September.

You say you have found one researcher saying this. Do they have a paper or some evidence?