Origins of Covid

[Sherkeu]

Originally Posted by angrysoba

Don't her actions and her concerns and the fact that she voiced them not sound completely reasonable to you?

Totally reasonable. Being so certain after only looking at limited data is not. This should have had a very detailed in-depth investigation.

Quote:

I don't understand how they are at odds. Presumably the virus in the second case can be isolated from the lab rats themselves.

I think we have already seen an argument for why the virus did not come from the lab in this case which is that the viruses they had sequenced were not similar enough.

They don't sequence every sample, and not every virus arising in every lab animal could be sampled- as was the case with the rats. They did not even know that 50% of one set of rats had Hanta antibodies before testing.

Further, animals are regularly disposed. They may be long dead before you have a chance to test them. Especially for SARS CoV-2 which can fly under the radar for a period of time.

Quote:

I think lab escapes have sometimes been noticed in other ways such as sending the wrong vials to people, or when a researcher accidentally stabs themselves with a syringe.

It should be pointed out as well that some viruses just appear in unexpected places. This has happened, for example, with Ebola.

Fair enough. I was focusing more on infections but mishandling of these bio-hazards is also an area of concern.

[Sherkeu]

Originally Posted by Skeptic Ginger

Yes it was Sept 2019, about the time of the first case as calculated by the genetic history clock.

This is an interesting date as it is the same month that predict PREDICT program was shutting down after 10 years of USAID funding. Could changes in the lab at that time have led to a mistake? (yeah...I'm in speculation mode!)

Areas of research and education in PREDICT were rolled into other programs- including a new one called Spillover. But no new funding would be given to seeking out dangerous viruses and manipulating them in the lab to see how dangerous they could be to humans.
They had til March 2020 to wrap things up. Some disbanded before that.

2019 News:

SCNL-USAID PREDICT-2 Ebola Host Project Ends in Liberia
(Oct 14, 2019)

Quote:

PREDICT-2 Liberia research project has been focused on the sampling of animals’ specimen for scientific purposes, mainly with the aim to understand the spillover of viruses from animal to animal and from animal to human.

Over 5,000 bats and 300 rodents in total were sampled during the research process with one of the bats showing positive for the Zaire strain of the Ebola Virus.

According to PREDICT-2 Liberia Project Country Coordinator Jim Desmond, he was pleased with the level of research and data generated during the research process and encouraged all those that worked with the project to make maximum use of the knowledge and skills acquired from the various experts.

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Cameroon Charge d’Affaires’ Speech- Closeout Ceremony of the USAID PREDICT Project Sept 24, 2019

Quote:

The PREDICT project has benefitted from some of the most advanced and prestigious institutions in the American scientific and medical communities. It was implemented by a consortium led by the University of California at Davis that included EcoHealth Alliance, Metabiota Inc., the Smithsonian Institution, and Wildlife Conservation Society, with support from Columbia and Harvard universities. Working with partners in 30 countries, PREDICT has built virus surveillance platforms that identify and monitor zoonotic pathogens or those that can be shared between animals and people.

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Pandemic prevention program ending after 10 years -USAID Predict led virus discovery, health training, risk education Jan 2, 2020

Quote:

The Predict project is winding down after 10 years of work that identified 1,100 unique viruses, provided aid to 60 disease detection laboratories, and trained 6,200 people in 30 countries. The project, led by the UC-Davis One Health Institute, is part of the USAID Emerging Pandemic Threats program.

David Wolking (senior manager for the One Health Institute at UC-Davis and global operations manager for Predict) said Predict’s second five-year term ended Sept. 30, 2019, although USAID provided a six-month extension for studies that use the project’s accumulated evidence to learn about virus spillover, spread, and countermeasures. He knows USAID officials want to continue the type of work conducted by Predict: reducing pandemic threats, increasing laboratory capacity, and learning what dangerous viruses threaten people, especially those circulating in wildlife.

Dr. William Karesh is executive vice president for health and policy at EcoHealth Alliance, one of the founding organizations in Predict. He said Predict’s 10-year run was a success, and it makes sense to move on.

The local partners from Predict are staying in their home countries, where they can teach others and build defenses against emerging disease, Dr. Karesh said.

“At some point, when we do foreign aid and when we do development projects, they’re supposed to become self-sustaining or sustainable,” he said. “That’ll never happen if you continue projects for hundreds of years.”

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Scientists Were Hunting for the Next Ebola. Now the U.S. Has Cut Off Their Funding. NYT, Oct 25, 2019

Quote:

Dennis Carroll, the former director of USAID’s emerging threats division who helped design Predict, oversaw it for a decade and retired when it was shut down. The surveillance project is closing because of “the ascension of risk-averse bureaucrats,” he said. Because USAID’s chief mission is economic aid, he added, some federal officials felt uncomfortable funding cutting-edge science like tracking exotic pathogens.

The end of the program “is definitely a loss,” said Peter Daszak, president of the EcoHealth Alliance, a nonprofit global health organization that received funding from the program. “Predict was an approach to heading off pandemics, instead of sitting there waiting for them to emerge and then mobilizing. That’s expensive."

“The United States spent $5 billion fighting Ebola in West Africa,” he added. “This costs far less.”

Of course September 30 was just the official end date- they would have known for some time prior that the program was about to end. I'm not sure how the WIV would have been affected though. They continued to receive funding from the NIH, which is referenced in their scientific papers.

I am left wondering if the end of PREDICT may have affected the research or staffing decisions of Shi's team at the WIV.

[Puppycow]

I was recently alerted to this very good piece, which I found well worth the time it took to read:

Origin of Covid — Following the Clues

I'll refrain from quoting excerpts, unless requested, because I think it is best read from beginning to end. It is somewhat lengthy as it discusses many details, but it is definitely readable.

[The Atheist]

Originally Posted by Puppycow

I was recently alerted to this very good piece, which I found well worth the time it took to read:

Origin of Covid — Following the Clues

I'll refrain from quoting excerpts, unless requested, because I think it is best read from beginning to end. It is somewhat lengthy as it discusses many details, but it is definitely readable.

Thanks, an excellent piece and food for thought.

I don't know enough genetic science to know, but I'm sending Capsid a PM to ask for his opinion. The furin cleavage seems particularly damning.

[Capsid]

Yes, interesting read. My understanding from TWIV was that the proline in the furin cleavage site would have been removed if the virus was engineered. It’s not intuitive to keep it there. Not a strong argument IMO.


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[Lplus]

Originally Posted by Capsid

Yes, interesting read. My understanding from TWIV was that the proline in the furin cleavage site would have been removed if the virus was engineered. It’s not intuitive to keep it there. Not a strong argument IMO.


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Would removing it have been a further stage in development? Could the virus have still been a work in progress?

[Capsid]

Originally Posted by Lplus

Would removing it have been a further stage in development? Could the virus have still been a work in progress?

Maybe. But if the focus is on that site to improve binding to the receptor, I would expect some thought into what amino acid residues would be used and including a proline that introduces a kink would normally be avoided.


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[angrysoba]

Originally Posted by Capsid

Yes, interesting read. My understanding from TWIV was that the proline in the furin cleavage site would have been removed if the virus was engineered. It’s not intuitive to keep it there. Not a strong argument IMO.


Sent from my iPhone using Tapatalk

Interesting that you say that. My own view here is based partly on the fact that TWiV has been absolutely adamant that there is no way that this came from a lab.

I know that Vincent Raccanielo is a big proponent of GoF research (judging by his comments on the podcast and elsewhere), but I have no real understanding of the complexities of this.

May I ask you as someone who I gather knows a lot about viruses what your ideas are about where this comes from?

Specifically,

1.) Do you think this is more likely to be a naturally created or lab-created virus?
2.) If it is simply a natural virus, then do you think it more or less likely that it emerged in the wild, or that somehow it is a natural virus that leaked from the WiV?
3.) How much do you find the actions of Zhengli Shi, Peter Daszak, and their associates (Linfa Wang, Angela Rasmussen, Eddie Holmes, Kristian Andersen, etc...) to be reasonable/suspicious?

[Capsid]

Originally Posted by angrysoba

Interesting that you say that. My own view here is based partly on the fact that TWiV has been absolutely adamant that there is no way that this came from a lab.

I know that Vincent Raccanielo is a big proponent of GoF research (judging by his comments on the podcast and elsewhere), but I have no real understanding of the complexities of this.

May I ask you as someone who I gather knows a lot about viruses what your ideas are about where this comes from?

Specifically,

1.) Do you think this is more likely to be a naturally created or lab-created virus?
2.) If it is simply a natural virus, then do you think it more or less likely that it emerged in the wild, or that somehow it is a natural virus that leaked from the WiV?
3.) How much do you find the actions of Zhengli Shi, Peter Daszak, and their associates (Linfa Wang, Angela Rasmussen, Eddie Holmes, Kristian Andersen, etc...) to be reasonable/suspicious?

As a scientist, I don’t think anything. I need more evidence to answer your questions.


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[Skeptic Ginger]

Originally Posted by Puppycow

I was recently alerted to this very good piece, which I found well worth the time it took to read:

Origin of Covid — Following the Clues

I'll refrain from quoting excerpts, unless requested, because I think it is best read from beginning to end. It is somewhat lengthy as it discusses many details, but it is definitely readable.

Some worthwhile points:

Quote:

From early on, public and media perceptions were shaped in favor of the natural emergence scenario by strong statements from two scientific groups. These statements were not at first examined as critically as they should have been. ...

By this criterion, the signatories of the Lancet letter were behaving as poor scientists: they were assuring the public of facts they could not know for sure were true.

They note Daszak's undisclosed (at the time of the letter) conflict of interest.


And there's been a lot of denial this was going on:

Quote:

Virologists like Dr. Daszak had much at stake in the assigning of blame for the pandemic. For 20 years, mostly beneath the public’s attention, they had been playing a dangerous game. In their laboratories they routinely created viruses more dangerous than those that exist in nature.

More unfounded assertions followed that a lab accident was so unlikely as to be a certain: didn't happen. Many people in this discussion have adopted that underlying premise, Some of whom I think left the discussion believing the lab leak hypothesis belonged in the CT forum.


Again it was proposed it would be possible to see lab markers had the virus been genetically manipulated in the lab.

Quote:

The Andersen paper’s speculation about designing a viral spike protein through calculation has no bearing on whether or not the virus was manipulated by one of the other two methods.

They note another piece of evidence it couldn't have been manmade ...

Quote:

And this conclusion, grounded in nothing but two inconclusive speculations, convinced the world’s press that SARS2 could not have escaped from a lab.

Serious thought on the matter interrupted by a bit of humor:

Quote:

In 2000 Dutch researchers, for instance, earned the gratitude of rodents everywhere by genetically engineering the spike protein of a mouse coronavirus so that it would attack only cats.

Human hubris:

Quote:

That statement was made in 2015. From the hindsight of 2021, one can say that the value of gain-of-function studies in preventing the SARS2 epidemic was zero. The risk was catastrophic, if indeed the SARS2 virus was generated in a gain-of-function experiment.

The denials this kind of thing went on at the WIV are disgusting:

Quote:

Dr. Shi returned to her lab at the Wuhan Institute of Virology and resumed the work she had started on genetically engineering coronaviruses to attack human cells.

Further:

Quote:

The approach could have generated SARS2-like viruses, and indeed may have created the SARS2 virus itself with the right combination of virus backbone and spike protein.

It cannot yet be stated that Dr. Shi did or did not generate SARS2 in her lab because her records have been sealed, but it seems she was certainly on the right track to have done so. “It is clear that the Wuhan Institute of Virology was systematically constructing novel chimeric coronaviruses and was assessing their ability to infect human cells and human-ACE2-expressing mice,” says Richard H. Ebright, a molecular biologist at Rutgers University and leading expert on biosafety.

Re Daszak, we posted a link to this upthread:

Quote:

On 9 December 2019, before the outbreak of the pandemic became generally known, Dr. Daszak gave an interview in which he talked in glowing terms of how researchers at the Wuhan Institute of Virology had been reprogramming the spike protein and generating chimeric coronaviruses capable of infecting humanized mice.

And we posted about this as well re the new WIV level 4 biosafety lab:

Quote:

“The new lab has a serious shortage of appropriately trained technicians and investigators needed to safely operate this high-containment laboratory,” the inspectors wrote in a cable of 19 January 2018.

But all this talk of the WIV's level 4 lab implies they were being super careful with their experiments. Turns out no one likes all those level 4 conditions.

Quote:

Before 2020, the rules followed by virologists in China and elsewhere required that experiments with the SARS1 and MERS viruses be conducted in BSL3 conditions. But all other bat coronaviruses could be studied in BSL2, the next level down. BSL2 requires taking fairly minimal safety precautions, such as wearing lab coats and gloves, not sucking up liquids in a pipette, and putting up biohazard warning signs. Yet a gain-of-function experiment conducted in BSL2 might produce an agent more infectious than either SARS1 or MERS. And if it did, then lab workers would stand a high chance of infection, especially if unvaccinated.

This is the thing mentioned up thread but which was dismissed by some posters here because it couldn't be verified:

Quote:

According to a fact sheet issued by the State Department on January 15,2021, “ The U.S. government has reason to believe that several researchers inside the WIV became sick in autumn 2019, before the first identified case of the outbreak, with symptoms consistent with both COVID-19 and common seasonal illnesses.”

I think this strengthened the finding:

Quote:

Three people working at a BSL3 lab at the institute fell sick within a week of each other with severe symptoms that required hospitalization. This was “the first known cluster that we’re aware of, of victims of what we believe to be COVID-19.” Influenza could not completely be ruled out but seemed unlikely in the circumstances, he said.

Circumstantial evidence is how close to the WIV the pandemic started. The article suggests the first cases occurred in Sept. That's important because that's when the Chinese authorities restricted access to a ton of genetic information being studied in Wuhan.

I mentioned this argument:

Quote:

The infected person (or animal) carrying this highly transmissible virus must have traveled to Wuhan without infecting anyone else. No one in his or her family got sick. If the person jumped on a train to Wuhan, no fellow passengers fell ill.

There's a discussion about the lack of a natural trail such as was documented in SARS 1.

Quote:

... Even those who think lab origin unlikely agree that SARS2 genomes are remarkably uniform. Dr. Baric writes that “early strains identified in Wuhan, China, showed limited genetic diversity, which suggests that the virus may have been introduced from a single source.”

A single source would of course be compatible with lab escape, less so with the massive variation and selection which is evolution’s hallmark way of doing business....

The uniform structure of SARS2 genomes gives no hint of any passage through an intermediate animal host, and no such host has been identified in nature.

TBC...

[The Atheist]

Originally Posted by Capsid

Yes, interesting read. My understanding from TWIV was that the proline in the furin cleavage site would have been removed if the virus was engineered. It’s not intuitive to keep it there. Not a strong argument IMO.

Thanks!

Originally Posted by Capsid

As a scientist, I don’t think anything. I need more evidence to answer your questions.

And double thanks for that.

That's why I asked you - you deal in evidence of the kind necessary to make sense of the claims and counter-claims.

Originally Posted by Skeptic Ginger

Some worthwhile points:They note Daszak's undisclosed (at the time of the letter) conflict of interest...

He's pretty heavy on that point, yet I notice that Nicholas Wade himself is not above making scientific claims without evidence that have been refuted by actual scientists.

I do however, trust Capsid implicitly and his points leave things at the same situation we had before it - more evidence needed, so it's still all speculation.

[Skeptic Ginger]

Continued:

Quote:

So it’s hard to explain how the SARS2 virus picked up its furin cleavage site naturally, whether by mutation or recombination.

That leaves a gain-of-function experiment.

And we have Dr Quay also cited above and IIRC dismissed by some:

Quote:

“Since 1992 the virology community has known that the one sure way to make a virus deadlier is to give it a furin cleavage site at the S1/S2 junction in the laboratory,” writes Dr. Steven Quay, a biotech entrepreneur interested in the origins of SARS2. “At least eleven gain-of-function experiments, adding a furin site to make a virus more infective, are published in the open literature, including [by] Dr. Zhengli Shi, head of coronavirus research at the Wuhan Institute of Virology.”

We're running out of smoking guns:

Quote:

So how did SARS2 acquire a pair of arginine codons that are favored by human cells but not by coronaviruses?

But a natural event is still on the table:

Quote:

“Yes, but your wording makes this sound unlikely — viruses are specialists at unusual events,” is the riposte of David L. Robertson, a virologist at the University of Glasgow who regards lab escape as a conspiracy theory. “Recombination is naturally very, very frequent in these viruses, there are recombination breakpoints in the spike protein and these codons appear unusual exactly because we’ve not sampled enough.”

Egads Batman is that possible?

Quote:

A long chain with several improbable steps is unlikely to ever be completed.

We've posted upthread about the generalist hypothesis.

Quote:

One problem with this idea, though, is that if SARS2 jumped from bats to people in a single leap and hasn’t changed much since, it should still be good at infecting bats. And it seems it isn’t.

Why is this?

Quote:

... Dr. Shi reports she collected at the same time but has not yet published despite their great relevance to the ancestry of SARS2.

This certainly doesn't let the WIV off the hook:

Quote:

Researchers could have gotten infected during their collecting trips, or while working with the new viruses at the Wuhan Institute of Virology. The virus that escaped from the lab would have been a natural virus, not one cooked up by gain of function.

There were images of these guys collecting their specimens from the caves and it hardly looked like any precautions were taken. The article notes why this is still an unlikely scenario.


Of course we can't rule anything out yet until something (ie the genetic trail) is ruled in. But:

Quote:

That said, the available evidence leans more strongly in one direction than the other. Readers will form their own opinion. But it seems to me that proponents of lab escape can explain all the available facts about SARS2 considerably more easily than can those who favor natural emergence.

A summary of all the evidence for lab leak includes the following smoking gun that has been rationalized in this thread in any number of ways as well has been by DasZak along with the Chinese authorities who came up with the farmed wild animal hypothesis.

Quote:

In all of China, the pandemic broke out on the doorstep of the Wuhan institute.

I thought the arguments for a natural spillover would contain just that. Instead the article rebuts every argument for spillover.


Blame is assigned to multiple entities by the article. I'm glad they included this about Daszak:

Quote:

Anyone who rocks the boat by raising awkward political issues runs the risk that their grant will not be renewed and their research career will be ended. Maybe good behavior is rewarded with the many perks that slosh around the distribution system. And if you thought that Dr. Andersen and Dr. Daszak might have blotted their reputation for scientific objectivity after their partisan attacks on the lab escape scenario, look at the 2nd and 3rd names on this list of recipients of an $82 million grant announced by the National Institute of Allergy and Infectious Diseases in August 2020.

Just because Eco is a non-profit organization doesn't mean there was no profit motive to assert the narrative we should all rule out a lab leak as a CT.


As I noted upthread, here's one more harm done by Dump:

Quote:

Because President Trump said the virus had escaped from a Wuhan lab, editors gave the idea little credence.

I'm going to go back over the discounting of Dr Quay was in this thread.

Quote:

Steven Quay, a physician-researcher, has applied statistical and bioinformatic tools to ingenious explorations of the virus’s origin, showing for instance how the hospitals receiving the early patients are clustered along the Wuhan №2 subway line which connects the Institute of Virology at one end with the international airport at the other, the perfect conveyor belt for distributing the virus from lab to globe.

Told ya so.

[Skeptic Ginger]

Originally Posted by The Atheist

He's pretty heavy on that point, yet I notice that Nicholas Wade himself is not above making scientific claims without evidence that have been refuted by actual scientists.

Which claim(s) is that?

Originally Posted by The Atheist

I do however, trust Capsid implicitly and his points leave things at the same situation we had before it - more evidence needed, so it's still all speculation.

I'm pretty sure we all respect Capsid's POV.

I'm pretty sure I've not said anything close to "there is proof". If you think I have, please quote me so I can clear that up.

That said, I have said and continue to believe that the evidence by far favors a lab leak. This thorough presentation of the evidence, much of which we have posted corroborating sources for up thread, makes an excellent case why 'prove it was a natural event' falls upon the people making that claim.

We have very good evidence COVID came from a lab, almost certainly from the WIV. That evidence has grown stronger not weaker with time.

And the implications are stunning!

[The Atheist]

Originally Posted by Skeptic Ginger

Which claim(s) is that?

https://cehg.stanford.edu/letter-fro...on-geneticists

Originally Posted by Skeptic Ginger

I'm pretty sure I've not said anything close to "there is proof". If you think I have, please quote me so I can clear that up.

The lady doth protest too much, methinks. What does that have to do with my post?

[Skeptic Ginger]

Originally Posted by The Atheist

https://cehg.stanford.edu/letter-fro...on-geneticists

That's about a different paper by Wade.

Quote:

To the Editor:

As scientists dedicated to studying genetic variation, we thank David Dobbs for his review of Nicholas Wade’s “A Troublesome Inheritance: Genes, Race and Human History” (July 13), and for his description of Wade’s misappropriation of research from our field to support arguments about differences among human societies.

As discussed by Dobbs and many others, Wade juxtaposes an incomplete and inaccurate account of our research on human genetic differences with speculation that recent natural selection has led to worldwide differences in I.Q. test results, political institutions and economic development. We reject Wade’s implication that our findings substantiate his guesswork. They do not.

We are in full agreement that there is no support from the field of population genetics for Wade’s conjectures.

Originally Posted by The Atheist

The lady doth protest too much, methinks. What does that have to do with my post?

You were arguing the lab leak was "still all speculation". I was merely stating my position that the evidence supported the lab leak to a much greater degree than the natural spillover, but I'm fine with the fact there is no absolute proof yet.

[angrysoba]

Vincent Racaniello says there will be three members of the WHO Origins Committee on TWiV in three weeks.

Maybe one to look out for.

[Puppycow]

Originally Posted by angrysoba

Vincent Racaniello says there will be three members of the WHO Origins Committee on TWiV in three weeks.

Maybe one to look out for.

I feel like they are under too much political pressure from the Chinese government to dare to say anything that might allow for the possibility that it escaped from the lab.

[angrysoba]

Originally Posted by Puppycow

I feel like they are under too much political pressure from the Chinese government to dare to say anything that might allow for the possibility that it escaped from the lab.

Possibly, but they don’t work for China. If they felt differently they could resign, and virologists who interview them can also make up their own minds about whether they believe what these particular scientists are saying.

[Puppycow]

Originally Posted by angrysoba

Possibly, but they don’t work for China. If they felt differently they could resign, and virologists who interview them can also make up their own minds about whether they believe what these particular scientists are saying.

It's not so simple though. Even if they don't work directly for China, they are hardly immune to political pressure from China. Plus half the members of the team are Chinese citizens and they had veto power over anything that might make it into the report.

WHO inquiry into COVID-19 origins 'compromised by politics', say scientists awaiting overdue report

Quote:

A team of experts from the World Health Organisation (WHO) on a mission to trace the origins of the COVID-19 epidemic, intend to scrap an eagerly-awaited interim report of their mission to China. This comes amid mounting tensions between Beijing and Washington over the investigation, along with an open letter from an international group of scientists who are demanding for a new probe, according to a Wall Street Journal report. The open letter, signed by 26 distinguished academics from around the world, outlines that the WHO-led investigative report was compromised by the inherent limitations of operating under the control of Chinese authorities.

The scientists elaborate on why the investigation report might be perceived as unreliable by the scientific community, saying, "the joint team did not have the mandate, the independence, or the necessary accesses" to perform a full and unrestricted investigation into the many SARS-CoV-2 origin hypotheses proposed. These theories including a natural spillover from an animal source, as well as a laboratory/research-related incident in which the pathogen escaped a controlled setting.

The letter goes on to point out nine fundamental problems that undermine the investigation. The joint investigation "falls short of the mark", the scientists said, adding that it was essential for the international community that a full and unrestricted investigation be organized. The letter describes a detailed layout of what the investigation ought to address – from the multidisciplinary nature of the investigating team to the range of reports they should have unrestricted access to. The WHO being an international agency that relies on the collaboration of its member states, the scientists said, is limited in what it can achieve in an investigation of this kind.

The open letter is in a format that cannot easily be copy-pasted, but should be read.

[Capsid]

Garry has published this

https://virological.org/t/early-appe...ral-origin/691

He was an author on the original Andersen paper. He argues that the early appearance of two distinct lineages argues against a lab or engineered origin.

[angrysoba]

Originally Posted by Puppycow

It's not so simple though. Even if they don't work directly for China, they are hardly immune to political pressure from China. Plus half the members of the team are Chinese citizens and they had veto power over anything that might make it into the report.

WHO inquiry into COVID-19 origins 'compromised by politics', say scientists awaiting overdue report



The open letter is in a format that cannot easily be copy-pasted, but should be read.

I realize it isn't easy.

That said, my other points stand.

As far as access to a Chinese BSL-4 lab is concerned, I would expect from the outset that it is difficult to get full access.

As a thought experiment, would a US BSL-4 be open to a WHO inspection where the team gets to look at anything and everything they want?

My guess is, no.

[angrysoba]

Originally Posted by Capsid

Garry has published this

https://virological.org/t/early-appe...ral-origin/691

He was an author on the original Andersen paper. He argues that the early appearance of two distinct lineages argues against a lab or engineered origin.

Can't trust Garry! He let the Ebola out! [Of course, I am joking, but this is apparently an accusation he had levelled at him when some Ebola turned up outside of the normal area it was thought to be located].

Thanks for the link!

[Skeptic Ginger]

Originally Posted by Capsid

Garry has published this

https://virological.org/t/early-appe...ral-origin/691

He was an author on the original Andersen paper. He argues that the early appearance of two distinct lineages argues against a lab or engineered origin.

From your link:

Quote:

The majority of early cases were linked to different markets that sold wildlife or wildlife products in Wuhan.

And yet they could not find any source of initial exposure at any of the markets. The virus was found in cases earlier than the market cases and while there was a potential exposure from another market, it was a relative that had been to that market but the case had not.

There is a paper upthread addressing the 2 lineages.

I'll go back and look again. That researcher believed the cases started much earlier than the Wuhan cases but he could not explain two things, why Wuhan and why were earlier cases not detected?

[Lplus]

Originally Posted by angrysoba

I realize it isn't easy.

That said, my other points stand.

As far as access to a Chinese BSL-4 lab is concerned, I would expect from the outset that it is difficult to get full access.

As a thought experiment, would a US BSL-4 be open to a WHO inspection where the team gets to look at anything and everything they want?

My guess is, no.

Which just means any investigation of a leak near a US lab would be similarly incomplete and thus suspect.

[angrysoba]

Originally Posted by Lplus

Which just means any investigation of a leak near a US lab would be similarly incomplete and thus suspect.

No, I think it would mean that people would be suspicious. But that, in and of itself would not constitute evidence.

[angrysoba]

NYTimes:

Quote:

A group of 18 scientists stated Thursday in a letter published in the journal Science that there is not enough evidence to decide whether a natural origin or an accidental laboratory leak caused the Covid-19 pandemic.

They argued, as the U.S. government and other countries have, for a new investigation to explore where the virus came from.

The organizers of the letter, Jesse Bloom, who studies the evolution of viruses at the Fred Hutchinson Cancer Research Center in Seattle, and David Relman, a microbiologist at Stanford University, said they strove to articulate a wait-and-see viewpoint that they believe is shared by many scientists. Many of the signers have not spoken out before.

“Most of the discussion you hear about SARS-CoV-2 origins at this point is coming from, I think, the relatively small number of people who feel very certain about their views,” Dr. Bloom said.

He added: “Anybody who’s making statements with a high level of certainty about this is just outstripping what’s possible to do with the available evidence.”

The new letter stated: “Theories of accidental release from a lab and zoonotic spillover both remain viable.”

The letter in Science:

Quote:

As scientists with relevant expertise, we agree with the WHO director-general (5), the United States and 13 other countries (6), and the European Union (7) that greater clarity about the origins of this pandemic is necessary and feasible to achieve. We must take hypotheses about both natural and laboratory spillovers seriously until we have sufficient data. A proper investigation should be transparent, objective, data-driven, inclusive of broad expertise, subject to independent oversight, and responsibly managed to minimize the impact of conflicts of interest. Public health agencies and research laboratories alike need to open their records to the public. Investigators should document the veracity and provenance of data from which analyses are conducted and conclusions drawn, so that analyses are reproducible by independent experts.

In the NYTimes articel, Kristian Andersen is quoted as opposing the both-sidedness of the letter:

Quote:

Kristian Andersen, a virologist at the Scripps Research Institute in La Jolla, Calif., has been a strong proponent of the overwhelming likelihood of a natural origin. He was one of the authors of an often cited paper in March 2020 that dismissed the likelihood of a laboratory origin based largely on the genome of the SARS-CoV-2 virus that causes Covid-19. “We do not believe any type of laboratory-based scenario is plausible,” that paper stated.

Speaking for himself only, Dr. Relman said in an interview that “the piece that Kristian Anderson and four others wrote last March in my view simply fails to provide evidence to support their conclusions.”

Dr. Andersen, who reviewed the letter in Science, said that both explanations were theoretically possible. But, “the letter suggests a false equivalence between the lab escape and natural origin scenarios,” he said. “To this day, no credible evidence has been presented to support the lab leak hypothesis, which remains grounded in speculation.”

He also tweeted this

[The Atheist]

Originally Posted by angrysoba

Quote:

"Most of the discussion you hear about SARS-CoV-2 origins at this point is coming from, I think, the relatively small number of people who feel very certain about their views,” Dr. Bloom said

Gosh, now that does sound familiar.

[Skeptic Ginger]

Originally Posted by angrysoba

... As a thought experiment, would a US BSL-4 be open to a WHO inspection where the team gets to look at anything and everything they want? ....

If there was a reason, then yes.

CDC level 4 biosafety labs are inspected on a regular basis as a requirement in order to have certain biohazards like smallpox virus.

I can't get the following files to open, maybe someone else can:

Startpage search:

Quote:

https://www.who.int/csr/disease/smal...ction.pdf?ua=1
Report of WHO Biosafety Inspection Team of the Variola Virus ...
conducted in the laboratories meet the highest requirements for biosafety and biosecurity. ... laboratory level, with Principal Investigators holding responsibility in ...

https://www.who.int/csr/disease/smal...-2012.pdf?ua=1
(WHO) Biosafety Inspection Team of the Variola Virus Maximum ...
May 11, 2012 ... At the time of the inspection the laboratory was decommissioned for ... be considered to have an acceptable level of biosafety and laboratory ... and procedures for disinfecting suits and boots before leaving the animal holding ...

[The Atheist]

Originally Posted by Capsid

Garry has published this

https://virological.org/t/early-appe...ral-origin/691

He was an author on the original Andersen paper. He argues that the early appearance of two distinct lineages argues against a lab or engineered origin.

That is an excellent piece, thanks!

Originally Posted by Skeptic Ginger

And yet they could not find any source of initial exposure at any of the markets.

Garry's piece covers that:

Quote:

Certain species of animals may have been removed after the appearance of the first COVID-19 cases and the linkage of COVID-19 cases to the market, but prior to the closure of the Market on January 1, 2020.

And the real meat is the next two sentences:

Quote:

It should also be noted that environmental samples that did test positive were associated with the portion of the market where wildlife or wildlife products were sold. A temporal analysis of the early human cases at the Huanan market confirms the pattern of spread from the areas of the market where wildlife products were sold to other parts of the market.

That would appear to be extremely unlikely in the case of a lab leak, but fully in keeping with natural origin.

Looks like the case for natural infection is growing stronger.

[Skeptic Ginger]

Originally Posted by The Atheist

Gosh, now that does sound familiar.

Yes doesn't it.

[Skeptic Ginger]

Originally Posted by The Atheist

Garry's piece covers that:
And the real meat is the next two sentences:

That would appear to be extremely unlikely in the case of a lab leak, but fully in keeping with natural origin.

That is hardly conclusive of anything, and none of it is new except claiming there were different strains found in different animal markets. Maybe one of those was the patient who had a relative that had gone to a different animal market but the patient had never gone there.

Remember Daszak was off on the farmed wild animals as the nebulous source that he was going to show in his final report. Only oddly, there was no identified source there either.

WHO Points To Wildlife Farms In Southern China As Likely Source Of Pandemic

I haven't had time yet to go back to the one article that mentions the two strains. When I get my taxes done I will.

Originally Posted by The Atheist

Looks like the case for natural infection is growing stronger.

No it isn't. There are multiple pieces of evidence in this thread, and look at you, latching on to one that supports your confirmation bias.

[The Atheist]

Originally Posted by Skeptic Ginger

Yes doesn't it.

The irony of you rolling eyes at me is not lost at all. Nowhere have I stated any degree of certainty as to the origin and have taken pains to say that we still do not know.

Compare that to this post:

Originally Posted by Skeptic Ginger

I was contemplating the universe for a bit today and it struck me what devastation has occurred (and is occurring) worldwide because of a careless act in a single lab.

Then you might like to roll the eyes the other way a bit.

[angrysoba]

Originally Posted by Skeptic Ginger

Remember Daszak was off on the farmed wild animals as the nebulous source that he was going to show in his final report. Only oddly, there was no identified source there either.

I am pretty sure Daszak never said the final report was going to show that.

My understanding was that given what they had found so far, this was going to be the theory they were going to pursue. Obviously the hunt for the source is continuing.

[Puppycow]

Originally Posted by angrysoba

I realize it isn't easy.

That said, my other points stand.

As far as access to a Chinese BSL-4 lab is concerned, I would expect from the outset that it is difficult to get full access.

As a thought experiment, would a US BSL-4 be open to a WHO inspection where the team gets to look at anything and everything they want?

My guess is, no.

I think the latest thinking among proponents of the lab-leak hypothesis is that it more likely escaped from a BSL-2 or BSL-3 lab.

Originally Posted by Puppycow

Origin of Covid — Following the Clues

Quote:

The real problem, however, was not the unsafe state of the Wuhan BSL4 lab but the fact that virologists worldwide don’t like working in BSL4 conditions. You have to wear a space suit, do operations in closed cabinets and accept that everything will take twice as long. So the rules assigning each kind of virus to a given safety level were laxer than some might think was prudent.

Before 2020, the rules followed by virologists in China and elsewhere required that experiments with the SARS1 and MERS viruses be conducted in BSL3 conditions. But all other bat coronaviruses could be studied in BSL2, the next level down. BSL2 requires taking fairly minimal safety precautions, such as wearing lab coats and gloves, not sucking up liquids in a pipette, and putting up biohazard warning signs. Yet a gain-of-function experiment conducted in BSL2 might produce an agent more infectious than either SARS1 or MERS. And if it did, then lab workers would stand a high chance of infection, especially if unvaccinated.

Much of Dr. Shi’s work on gain-of-function in coronaviruses was performed at the BSL2 safety level, as is stated in her publications and other documents. She has said in an interview with Science magazine that “The coronavirus research in our laboratory is conducted in BSL-2 or BSL-3 laboratories.”

The lower the BSL level, the greater the potential for escape, as the safety measures are more relaxed.

Anyway, if it escaped, it seems likely that it escaped not from the new BSL-4 facility but from the BSL-2 or BSL-3 laboratories, as that is where Dr. Shi says they did their coronavirus research.

[Chris_Halkides]

Preprint. "Here, we show that O-glycosylation near the furin cleavage site is mediated by specific members of the GALNT enzyme family and is dependent on the novel proline at position 681 (P681)."

This is from the abstract to the preprint, which has not yet been peer-reviewed. I am still attempting to understand this paper, but I thought it might be germane to the discussion of the proline in the PRRA sequence. O-glycosylation can occur at serine or threonine residues, and IIUC T678 is a possible location for this post-translational modification. Glycosylation decreases furin cleavage.

[Capsid]

Originally Posted by Chris_Halkides

Preprint. "Here, we show that O-glycosylation near the furin cleavage site is mediated by specific members of the GALNT enzyme family and is dependent on the novel proline at position 681 (P681)."

This is from the abstract to the preprint, which has not yet been peer-reviewed. I am still attempting to understand this paper, but I thought it might be germane to the discussion of the proline in the PRRA sequence. O-glycosylation can occur at serine or threonine residues, and IIUC T678 is a possible location for this post-translational modification. Glycosylation decreases furin cleavage.

Thanks! The final remark in the discussion says that loss of the proline may cause increased infectivity, therefore arguing against including it in an engineered virus.


Sent from my iPad using Tapatalk

[Skeptic Ginger]

Originally Posted by angrysoba

I am pretty sure Daszak never said the final report was going to show that.

My understanding was that given what they had found so far, this was going to be the theory they were going to pursue. Obviously the hunt for the source is continuing.

NPR: WHO Points To Wildlife Farms In Southern China As Likely Source Of Pandemic

Quote:

China shut down those wildlife farms in February 2020, says Peter Daszak, a disease ecologist with EcoHealth Alliance and a member of the WHO delegation that traveled to China this year. During that trip, Daszak says, the WHO team found new evidence that these wildlife farms were supplying vendors at the Huanan Seafood Wholesale Market in Wuhan with animals....

Those wildlife farms, including ones in the Yunnan region, are part of a unique project that the Chinese government has been promoting for 20 years now.

"They take exotic animals, like civets, porcupines, pangolins, raccoon dogs and bamboo rats, and they breed them in captivity," says Daszak.

The agency is expected to release the team's investigative findings in the next two weeks. In the meantime, Daszak gave NPR a highlight of what the team figured out.

"China promoted the farming of wildlife as a way to alleviate rural populations out of poverty," Daszak says. The farms helped the government meet ambitious goals of closing the rural-urban divide, as NPR reported last year.

"It was very successful," Daszak says. "In 2016, they had 14 million people employed in wildlife farms, and it was a $70 billion industry."

[Skeptic Ginger]

Originally Posted by Capsid

Thanks! The final remark in the discussion says that loss of the proline may cause increased infectivity, therefore arguing against including it in an engineered virus.

Here is what was posted upthread: Published in Mar, published in June 2020: On the origin and continuing evolution of SARS-CoV-2

Nature Mar 2020: The proximal origin of SARS-CoV-2

From your link above:

Quote:

Introduction
Our previous commentary on the Proximal Origins of SARS-CoV-2 (Andersen et al., 2020) concluded that, “SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus." The possibility of a laboratory release or Lab Leak was also considered, but it was determined that a natural origin of SARS-CoV-2 is much more likely.

So it acknowledges the source posted upthread.

No one here anyway is arguing for a purposefully constructed virus. That's the same thing Daszak throws out hoping to distract from the other two options.


I'm still doing taxes, this is a short break. I'll have to look at the claims in Andersen et al's paper from last year. Because there are still some holes in the hypothesis.

[angrysoba]

Originally Posted by Skeptic Ginger

NPR: WHO Points To Wildlife Farms In Southern China As Likely Source Of Pandemic

Yes, but read again...

Quote:

During that trip, Daszak says, the WHO team found new evidence that these wildlife farms were supplying vendors at the Huanan Seafood Wholesale Market in Wuhan with animals....

It only says that wildlife farms were supplying vendors.

It says literally nothing about whether they had been shown to be the trail for Covid.

I remember what was said at the time, only that they know who the vendors are and that should be the next stage of the research.

There was literally never any suggestion that they had found the Covid trail and that it would appear in the report. That was never promised.

[angrysoba]

Originally Posted by Skeptic Ginger

No one here anyway is arguing for a purposefully constructed virus. That's the same thing Daszak throws out hoping to distract from the other two options.

You are always attributing motive and machinations to Daszak.

The point is that yes indeed the claim is often made that this is the result of GoF.

I am sure you have said the same thing.

What is all the talk of the furin cleavage site about? - To some extent the claim is of a manipulated virus.

What is all the talk of the way the virus seems so suitable to human transmission? The claim is of a manipulated virus.

The point is that proponents of the lab leak are using multiple hyotheses so you cannot pretend that this is a strawman.