Lab Leak: The conspiracy theory is shaping up to look like real possibility

[Juvenal]

Without the evidence Juvenal gave, I could easily see many scenarios in which the virus could have been leaked from the lab in a way that makes it more substantially deadly than the wild type virus that aren't "circular reasoning".

Juvenal provided info that makes the virus leaking from a lab look less likely.

Whoa, thanks, but Andersen et al. provided that info. I'm just reporting it as best as I can.

I've got an undergrad in bioengineering, but I'm not any kind of biologist. This is hard.

I hit these papers, dig in for a bit, and then bounce. And then I hit them again, get a little deeper, and bounce again. We're into double-digits, and weeks now, on my attempts to make sense of this one paper. I've finally made it all the way through, but there's big gaps in what I'm understanding. I've been wicked busy this entire time, too, especially last week, finals week, which is always crazy, even without the extra-special load from doing it all remote. I went three days without sleeping last week. I've been doing this for the last decade. I pull all-nighters pretty regularly, but no, not that, never.

So here's the big picture, Figure 1 from Andersen.

Andersen 1.jpg

SARS-CoV-2 is RNA-based, 29,903 bases long, or about ten thousand amino acids.

From Zheng-Li Shi, head of the bat lab at WIV, its closest match at 96.2 percent is RaTG13, captured in 2013 for WIV in Pu'er, Yunnan Province about 1200 miles from Wuhan.

Simplot analysis showed that 2019-nCoV was highly similar throughout the genome to RaTG13 (Fig. 1c), with an overall genome sequence identity of 96.2%.

RaTG13 was published to the gene bank in late January. From Susanna K.P. Lau out of Hong Kong, it's at 96.1 percent similarity to SARS-CoV-2 with another close match at 89.7 percent, Pangolin-SARSr-CoV/Guangdong/1/2019, captured in 2019 in Guangzhou, Guangdong Province about 600 miles from Wuhan.

SARSr-Ra-BatCoV-RaTG13 (96.1% genome identity with SARS-CoV-2) ... captured in Pu’er, China, during 2013 ... Pangolin-SARSr-CoV/Guangdong/1/2019 (... 89.7% ...) ... in smuggled pangolins captured in ... Guangzhou, China, during 2019.

Wuhan Yunnan Guangdong.jpg

The difference between SARS-CoV-2 and RaTG13 is just under four percent, 1200 bases, or 400 amino acids.

In news reporting posted earlier in-thread, it was estimated that difference would require 20 to 50 years to evolve in the wild. WIV has had RaTG13 for seven years. In the same article a researcher speculated that because most of the differences from RaTG13 are in the receptor binding domain and show selection for the human-ACE2 receptor, the gap might have been bridged by growing it in human lung cell cultures. That's called a "gain of function" experiment. The goal is to discover mutations which could occur in nature and negatively impact human health.

Yes, that's as dangerous as it sounds.

More controversial was the Wuhan institute’s 2015 research into creating a chimera, the hybrid virus that combined elements from two bat-borne coronaviruses, including one that causes SARS. The mutated virus that resulted was more easily able to infect human cells, making it more useful for lab experiments. Such “gain of function” experiments — which enhance a pathogen’s natural traits — have been a source of controversy in the West because of the potential for harm if an altered strain escapes the confinement of the lab, experts say.

So let's look at the receptor binding domain.

Andersen, Figure 1a.

Andersen 1a.jpg

The spike region codes for 1285 amino acids. The receptor binding domain spans 59 amino acids. Six target human-ACE2. One is found in RaTG13. All are found in a consensus pangolin coronavirus.

The pangolin coronavirus sequences are a consensus generated from SRR10168377 and SRR10168378 (NCBI BioProject PRJNA573298).

The pangolin differs in the RBD by only one amino acid, but it takes a consensus of two viruses to get there. RaTG13 is off by eleven. Eleven is nowhere close to the entire difference, but still, that's nearly 20 percent off here vs 4 percent off overall. If SARS-CoV-2 came from RaTG13, that points to selection pressure.

Now, about those O-linked glycans.

Figure 1b.

Andersen 1b.jpg

That's a blow-out of 27 amino acids between the S1 and S2 subunits. There is no difference between RaTG13 and SARS-CoV-2 outside the cleavage site. There are two differences between them and the consensus pangolin. All three match at the O-linked glycan residues, which obviates an important issue:

Finally, the generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system.

If SARS-CoV-2 came from RaTG13, that leaves only the polybasic cleavage site unaccounted for.

[Juvenal]

ok - Sparko, Juvenal, looks like it was I that misunderstood Juvenal's point, which I apparently unconsciously assumed matched the conclusion of the paper itself (one of those unconscious biases we talked about in another thread)

Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.

That conclusion is strongly confirmed and I strongly agree with it.

So - to clarify - Juvenal - do you believe the virus evolved naturally (in the wild) but after being sent to the lab for analysis it leaked out of the lab, or do you believe the virus evolved from other virus being worked with in the lab and then leaked out?

There's a meaningful difference between what I think and what I know.

I think it came from the lab, and specifically, from RaTG13. Because it's the closest match, and at least one researcher has offered a plausible scenario outside a gain of function experiment. I know it's not a laboratory construct, and that it did not arise from purposeful manipulation. It didn't arise through artificial recombination. That leaves marks. There are no marks.

I'm drawn back to statements from Zheng-Li, that she swears on her life that it did not escape from the lab, specifically because she trusts proper containment procedures were followed. I'm not convinced that's the same as saying gain of function experiments weren't undertaken on RaTG13. That remains the most likely scenario given the available data.

But it's not conclusive, there are still issues to be resolved.

[shunyadragon]

Whoa, thanks, but Andersen et al. provided that info. I'm just reporting it as best as I can.

I've got an undergrad in bioengineering, but I'm not any kind of biologist. This is hard.

I hit these papers, dig in for a bit, and then bounce. And then I hit them again, get a little deeper, and bounce again. We're into double-digits, and weeks now, on my attempts to make sense of this one paper. I've finally made it all the way through, but there's big gaps in what I'm understanding. I've been wicked busy this entire time, too, especially last week, finals week, which is always crazy, even without the extra-special load from doing it all remote. I went three days without sleeping last week. I've been doing this for the last decade. I pull all-nighters pretty regularly, but no, not that, never.

So here's the big picture, Figure 1 from Andersen.

[ATTACH=CONFIG]44436[/ATTACH]

SARS-CoV-2 is RNA-based, 29,903 bases long, or about ten thousand amino acids.

From Zheng-Li Shi, head of the bat lab at WIV, its closest match at 96.2 percent is RaTG13, captured in 2013 for WIV in Pu'er, Yunnan Province about 1200 miles from Wuhan.

Simplot analysis showed that 2019-nCoV was highly similar throughout the genome to RaTG13 (Fig. 1c), with an overall genome sequence identity of 96.2%.

RaTG13 was published to the gene bank in late January. From Susanna K.P. Lau out of Hong Kong, it's at 96.1 percent similarity to SARS-CoV-2 with another close match at 89.7 percent, Pangolin-SARSr-CoV/Guangdong/1/2019, captured in 2019 in Guangzhou, Guangdong Province about 600 miles from Wuhan.

SARSr-Ra-BatCoV-RaTG13 (96.1% genome identity with SARS-CoV-2) ... captured in Pu’er, China, during 2013 ... Pangolin-SARSr-CoV/Guangdong/1/2019 (... 89.7% ...) ... in smuggled pangolins captured in ... Guangzhou, China, during 2019.

[ATTACH=CONFIG]44437[/ATTACH]

The difference between SARS-CoV-2 and RaTG13 is just under four percent, 1200 bases, or 400 amino acids.

In news reporting posted earlier in-thread, it was estimated that difference would require 20 to 50 years to evolve in the wild. WIV has had RaTG13 for seven years. In the same article a researcher speculated that because most of the differences from RaTG13 are in the receptor binding domain and show selection for the human-ACE2 receptor, the gap might have been bridged by growing it in human lung cell cultures. That's called a "gain of function" experiment. The goal is to discover mutations which could occur in nature and negatively impact human health.

Yes, that's as dangerous as it sounds.

More controversial was the Wuhan institute’s 2015 research into creating a chimera, the hybrid virus that combined elements from two bat-borne coronaviruses, including one that causes SARS. The mutated virus that resulted was more easily able to infect human cells, making it more useful for lab experiments. Such “gain of function” experiments — which enhance a pathogen’s natural traits — have been a source of controversy in the West because of the potential for harm if an altered strain escapes the confinement of the lab, experts say.

So let's look at the receptor binding domain.

Andersen, Figure 1a.

[ATTACH=CONFIG]44438[/ATTACH]

The spike region codes for 1285 amino acids. The receptor binding domain spans 59 amino acids. Six target human-ACE2. One is found in RaTG13. All are found in a consensus pangolin coronavirus.

The pangolin coronavirus sequences are a consensus generated from SRR10168377 and SRR10168378 (NCBI BioProject PRJNA573298).

The pangolin differs in the RBD by only one amino acid, but it takes a consensus of two viruses to get there. RaTG13 is off by eleven. Eleven is nowhere close to the entire difference, but still, that's nearly 20 percent off here vs 4 percent off overall. If SARS-CoV-2 came from RaTG13, that points to selection pressure.

Now, about those O-linked glycans.

Figure 1b.

[ATTACH=CONFIG]44439[/ATTACH]

That's a blow-out of 27 amino acids between the S1 and S2 subunits. There is no difference between RaTG13 and SARS-CoV-2 outside the cleavage site. There are two differences between them and the consensus pangolin. All three match at the O-linked glycan residues, which obviates an important issue:

Finally, the generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system.

If SARS-CoV-2 came from RaTG13, that leaves only the polybasic cleavage site unaccounted for.

Why is the time factor an issue? The viruses are constantly evolving in the wild. This of course a possibility, bu so far the epidemiologists and biologists do not support the lab scenario. You have not cited any support for your scenario elsewhere.

I believe this is a problem origination from the lab:

"That's a blow-out of 27 amino acids between the S1 and S2 subunits. There is no difference between RaTG13 and SARS-CoV-2 outside the cleavage site. There are two differences between them and the consensus pangolin. All three match at the O-linked glycan residues, which obviates an important issue:

Finally, the generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system.

If SARS-CoV-2 came from RaTG13, that leaves only the polybasic cleavage site unaccounted for."

[Cerebrum123]

Whoa, thanks, but Andersen et al. provided that info. I'm just reporting it as best as I can.
snip

I didn't mean you were the one who did the research, just that you were the one who provided the information in this thread. You presented it here, and thus get credit for bringing it to my attention.

Edit. Just asking this for clarification. You are saying you think it was the RaTG13 that was being kept in a lab, and while there mutated into the current strain of Covid 19? That has been my thought on the subject based on what I've seen. The actions of China are way too suspicious to me if it was just something from the wet market.

[Sparko]

Well I am going to do some checking, but nonetheless the other question remains unanswered.

"Pompuse Pompeo said there was a great deal of evidence that the virus came from the lab.Where is the evidence?"

You cited one question and answer. Do you have a reference for the whole interview verbatuum.

Do you???

[Sparko]

Actually I think you are citing the wrong interview (?). I believe his interview with NAtional Geographic cites his view more accurately.

Source: https://www.nationalgeographic.com/science/2020/05/anthony-fauci-no-scientific-evidence-the-coronavirus-was-made-in-a-chinese-lab-cvd/

ANTHONY “TONY” FAUCI has become the scientific face of America’s COVID-19 response, and he says the best evidence shows the virus behind the pandemic was not made in a lab in China.

Fauci, the director of the U.S. National Institute of Allergy and Infectious Diseases, shot down the discussion that has been raging among politicians and pundits, calling it “a circular argument” in a conversation Monday with National Geographic.

“If you look at the evolution of the virus in bats and what's out there now, [the scientific evidence] is very, very strongly leaning toward this could not have been artificially or deliberately manipulated … Everything about the stepwise evolution over time strongly indicates that [this virus] evolved in nature and then jumped species,” Fauci says. Based on the scientific evidence, he also doesn’t entertain an alternate theory—that someone found the coronavirus in the wild, brought it to a lab, and then it accidentally escaped.

Fauci is most concerned that the United States will be put to the test this fall and winter by a second wave of COVID-19 if the country does not blunt the infection rate by the summer.

“Shame on us if we don't have enough tests by the time this so-called return might occur in the fall and winter,” he says, advising that the U.S. needs to make sure we not only have an adequate supply of tests available before a second wave hits, but also a system for getting those tests to the people who most need them.

“I don't think there's a chance that this virus is just going to disappear,” he says. “It's going to be around, and if given the opportunity, it will resurge.” As such, Fauci says the U.S. should also focus this summer on properly reinforcing the nation’s health care system, ensuring the availability of hospital beds, ventilators, and personal protective equipment for health care workers.

He also stressed the importance of continuing to social distance everywhere until the case counts start to fall in cities and states. The U.S. witnessed about 20,000 to 30,000 new cases every day in the month of April, suggesting the country is stuck in its peak.

© Copyright Original Source

"Pompuse Pompeo said there was a great deal of evidence that the virus came from the lab. Where is the evidence?"

Can you cite any scientists or better yet epidemiologist that advocates you position that a natural COVID 19 escaped from the lab. If it was taken from nature. What would prevent it from jumping hosts and infecting humans in the Natural world?

There is no paper trail that identifies the COVID 19 virus was ever in the lab.

The evidence is through security agencies, Shuny. spies. And reports of unsafe practices at the lab in the past going back to 2015. Read the OP and following posts. This is stuff Fauci probably is not aware of. He didn't say it couldn't have escaped from the lab, he indicated he didn't believe it did. Basically he is guessing.

here is part of the trail:

https://www.nationalreview.com/2020/...to-wuhan-labs/

As far as Pompeo goes, he hasn't released his evidence. That doesn't mean it doesn't exist. It is probably classified while they investigate further.

[Juvenal]

I didn't mean you were the one who did the research, just that you were the one who provided the information in this thread. You presented it here, and thus get credit for bringing it to my attention.

It's just that after looking over the yeoman's work done by the professionals, my best efforts look like mud pies. Glad you appreciated it.

Edit. Just asking this for clarification. You are saying you think it was the RaTG13 that was being kept in a lab, and while there mutated into the current strain of Covid 19? That has been my thought on the subject based on what I've seen. The actions of China are way too suspicious to me if it was just something from the wet market.

^of the virus responsible for Covid 19.

The market showed up in Zheng-Li's paper, and nowhere since. I'm not seeing any evidence scientists are still taking it seriously. In any case, China's since wiped out any chance to investigate it. But make no mistake, "if it was just something from the wet market," China would still lose face, and they'd still cover up.

They're China.

If I was being more guarded, I'd describe a lab leak of RaTG13 as a working hypothesis, but that's the gist. SARS-CoV-2 is a kissing cousin of RaTG13, and an alternative "has not been observed" in the literature.

The literature now includes Andersen, and what has been described includes Figure 1b.

Andersen1b insertion.jpg

Unpacked, here are the principle objections to a lab leak provided by Andersen et al.

In theory, it is possible that SARS-CoV-2 acquired RBD mutations (Fig. 1a) during adaptation to passage in cell culture, as has been observed in studies of SARS-CoV.

I've inserted a link to the provided reference.

Note this was a gain of function experiment on SARS-CoV-1 from 2007. The lead author was Timothy Sheahan, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.

The finding of SARS-CoV-like coronaviruses from pangolins with nearly identical RBDs, however, provides a much stronger and more parsimonious explanation of how SARS-CoV-2 acquired these via recombination or mutation.

The point is these things can happen outside a lab, and with no description of gain of function experiments undertaken on RaTG13, that's "more parsimonious."

The acquisition of both the polybasic cleavage site and predicted O-linked glycans also argues against culture-based scenarios.

The O-linked glycans are there. The 12-base, four-amino-acid insertion, PRRA, is not.

New polybasic cleavage sites have been observed only after prolonged passage of low-pathogenicity avian influenza virus in vitro or in vivo.

"After 24 consecutive passages by air sac inoculation, followed by five passages in chicken brain, the avirulent virus became highly pathogenic in chickens, producing a 100% mortality rate." The cleavage site was responsible. "By contrast, avirulent-virus HAs do not possess a series of basic amino acids at the cleavage site ... so that the viruses only produce localized infections, resulting in mild or asymptomatic infections."

As a side note, that 2001 study was also a gain of function experiment, this time from Japanese researchers. The lead author was Toshihiro Ito, Department of Veterinary Public Health, Faculty of Agriculture, Tottori University, Tottori 680-8553.

Furthermore, a hypothetical generation of SARS-CoV-2 by cell culture or animal passage would have required prior isolation of a progenitor virus with very high genetic similarity, which has not been described.

That's the biggest hurdle. At a four percent difference, RaTG13 is close, but it's not close enough.

Subsequent generation of a polybasic cleavage site would have then required repeated passage in cell culture or animals with ACE2 receptors similar to those of humans, but such work has also not previously been described.

It's not enough that the passages were performed in tissue. To achieve the selection shown in positions 455, 486, 493, 494, 501, 505 of the spike domain, the passages had to have been in tissue with human-ACE2 receptors or a close homolog.

Finally, the generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system.

The O-linked glycans are there. That objection is gone.

Again, by far the biggest hurdle is pushing 20 to 50 years of random mutation and selection into the time frame between its collection in 2013 and the appearance of SARS-CoV-2 in 2019.

[Juvenal]

As far as Pompeo goes, he hasn't released his evidence. That doesn't mean it doesn't exist. It is probably classified while they investigate further.

Have you seen SeanD's sig?

[shunyadragon]

The evidence is through security agencies, Shuny. spies. And reports of unsafe practices at the lab in the past going back to 2015. Read the OP and following posts. This is stuff Fauci probably is not aware of. He didn't say it couldn't have escaped from the lab, he indicated he didn't believe it did. Basically he is guessing.

here is part of the trail:

https://www.nationalreview.com/2020/...to-wuhan-labs/

As far as Pompeo goes, he hasn't released his evidence. That doesn't mean it doesn't exist. It is probably classified while they investigate further.

Arguing for a stubborn, 'arguing from ignorance' based on a personal Trumpian agenda. Fauci is completely clear on the status of the evidence, and his conclusions stand.

Even Juvenal's citation of the scientific evidence refutes Trump, Pompeo and you. It has been several days since Pompeo stuck his foot in his mouth, and he has not taken it out yet.

All you can say is the fact the there is no known evidence for a release from the lab, well ah . . . maybe evidence exists.

Still waiting for a coherent response with documented evidence.

[Sparko]

I'm not Juvenal, but I quite like the lab theory, in the sense that there was a lab that was trying to study animal diseases in order to protect humans from them, and in the course of this work they had gathered a bunch of diseased animals from around China and had them in cages like a zoo would, and they were trying to assess how likely/unlikely the diseases they had were to pose a threat to human health (since previously things like SARS, HIV etc have transferred to humans from animals)... and perhaps in the course of that work a human working with an infected animal caught the infection off them.

In that scenario, the virus is not man-made, and the lab would be doing little different to the average zoo in terms of humans interacting with animals. In this scenario, at no stage would there have been any human intervention to alter the virus.

Fauci's view seems to be that if the virus is natural, it doesn't matter where the virus happened to transfer to a human (be it a wet-market, a lab, a zoo, a child playing in a tree, a person eating infected meat, etc). However, I'd say there is an important difference going forward in order to prevent a repeat of this, because one political policy result could be a tightening of quality standards used in labs, and a different political policy result could be shutting down wet-markets.

That pretty much summarizes my view too.

[Sparko]

Arguing for a stubborn, 'arguing from ignorance' based on a personal Trumpian agenda. Fauci is completely clear on the status of the evidence, and his conclusions stand.

Even Juvenal's citation of the scientific evidence refutes Trump, Pompeo and you. It has been several days since Pompeo stuck his foot in his mouth, and he has not taken it out yet.

All you can say is the fact the there is no known evidence for a release from the lab, well ah . . . maybe evidence exists.

Still waiting for a coherent response with documented evidence.

Are you daft? Juvenal's data supports a lab escape.

In fact, it is the evidence you have been asking for.

[oxmixmudd]

Are you daft? Juvenal's data supports a lab escape.

In fact, it is the evidence you have been asking for.

Sparko, he is not draft. Clearly there is debate among scientists that know the topic well, that is not something to dismiss. Second, many here (not juvenal) are partial to the lab escape theory only because it supports their ideological need to cast blame away from Trump, and so calling people names because they are not convinced by juvenal's take on the data is not based on any superior understanding of the science and is not justifiable.

A lab escapee might be due to lax protocols, and it might not. But there are a large number of labs doing research where one small mistake could let loose something very bad. That is a good reason to work as charitably as possible and focus on maintaining a global high standard in all of these labs by working together with the various governments involved rather that stoking fear and casting blame.

[shunyadragon]

Are you daft? Juvenal's data supports a lab escape.

In fact, it is the evidence you have been asking for.

No this did not answer my questions. So far absolutely nothing has been presented from an epidemiologist supporting specifically an escape from the lab.

No it did not. You need a lesson in English. From his source:

"That's a blow-out of 27 amino acids between the S1 and S2 subunits. There is no difference between RaTG13 and SARS-CoV-2 outside the cleavage site. There are two differences between them and the consensus pangolin. All three match at the O-linked glycan residues, which obviates an important issue:

Finally, the generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system.

If SARS-CoV-2 came from RaTG13, that leaves only the polybasic cleavage site unaccounted for.

No one, including Luvenal have presented a scientific reference to support specifically the escape from the lab over infection naturally from animals in Wuhan Market. Not counting Trump and Pompeo. I have asked Juvenal several times to provide a source that specifically supports his position and he has failed to do so . Still waiting . . .

I cited Fauci specifically support the source of COVID 19 as being a natural source in Wuhan Market, and NOT the lab in the NAtional Geographic interview. You cited one question and answer without citing the source, nor the complete interview.Again . . . Source please with complete interview.


"Pompuse Pompeo said there was a great deal of evidence that the virus came from the lab.Where is the evidence?"

[Sparko]

Sparko, he is not draft. Clearly there is debate among scientists that know the topic well, that is not something to dismiss. Second, many here (not juvenal) are partial to the lab escape theory only because it supports their ideological need to cast blame away from Trump, and so calling people names because they are not convinced by juvenal's take on the data is not based on any superior understanding of the science and is not justifiable.

A lab escapee might be due to lax protocols, and it might not. But there are a large number of labs doing research where one small mistake could let loose something very bad. That is a good reason to work as charitably as possible and focus on maintaining a global high standard in all of these labs by working together with the various governments involved rather that stoking fear and casting blame.

How would it be Trump's fault if it didn't escape from a lab?

And I never said it WAS a lab escape, but that it is starting to look likely. Truthfully, barring China admitting it, or some smoking gun being found, I don't think we will ever know for sure. But it does fit all of the known facts, such as China's coverup, disappearing scientists, etc.

And Shuny continually has misread Juvenal's posts, claiming he was trying to say it didn't escape from a lab (as did you but you apologized) and still hasn't realized his error. And I know Juv's posts and data doesn't PROVE anything, but it sure seems to indicate the virus being in a lab, where humans, bats, and pangolins were all in close proximity.

[Sparko]

No this did not answer my questions. So far absolutely nothing has been presented from an epidemiologist supporting specifically an escape from the lab.

No it did not. You need a lesson in English. From his source:

"That's a blow-out of 27 amino acids between the S1 and S2 subunits. There is no difference between RaTG13 and SARS-CoV-2 outside the cleavage site. There are two differences between them and the consensus pangolin. All three match at the O-linked glycan residues, which obviates an important issue:

Finally, [I]the generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system."

Once it infected a live animal or human, it would have the markers showing involvement with an immune system.