Origins of Covid

[angrysoba]

Originally Posted by lomiller

I don't remember the episode but I remember a discussion TWIV that said the importance of the furin cleavage site wasn't know until after scientists had seen Covid.

You could be right. I may have been thinking of the receptor-binding domain, which I suppose is Virology 101.

[angrysoba]

So the next step in the saga, is that some of the lab leakers such as Deigin and Quay and a few others, are arguing that Pekar et. al got it wrong when they claimed that lineage A and B are separate spillover events.

One of the authors of the paper has written a tweet thread explaining the process.

I honestly have no idea about this.

My thinking here, however, is that while the lab leakers seem to believe that spillover proponents (or what they call zoonati) are funded by this kind of research and are therefore desperate to protect it at all costs, it seems to me that these virologists presumably believe in what they are doing otherwise why would they be digging themselves in so deep.

Anyway, here is the thread:

Link

The lab leakers? Well, maybe they will destroy their own reputations in virology but they never had any so it is no loss for them. It is the BS asymmetry problem.

[steenkh]

Originally Posted by lomiller

Blaming the wildlife trade calls Chinese cultural practices into question, China really does not want Covid to be a result of this. They did the same thing with SARS, effectually trying to blame it on anything else until Dr Shi positively identified the exact cave SARS originated it.

Keep in mind that most of the lab leak CT's try to insinuate Dr Shi is one of the principles involved in the supposed cover-up when in fact history shows she is more than willing to engage in research the Chinese government would prefer not to come to light.

I know you have said this before, but I don’t think you can be sure that you know what the Chinese government would accept or not. There is a difference in claiming wild animals in China have produced a dangerous virus that has spread to humans, and claiming that sloppy practice in a Chinese lab caused a dangerous virus to spread to humans - quite aside from the fact that if this had happened in Dr Shi’s lab, publishing it would have severe repercussions on her own research.

On the other hand, I know nothing about Dr Shi, and I can’t possibly know for sure if she would risk her career in this way, or if her status in China is essentially untouchable, so she can publish whatever she likes.

I am content with the fact that we’ll never get to the bottom of this. I think that lab leak or not, all labs working with such viruses will tighten up their practices after Covid, and wet markets will probably be monitored in some fashion in the future, or at least the reaction will be faster next time a novel virus appear in a city with a wet market.

[GraculusTheGreenBird]

Originally Posted by lomiller

Why are you so interested in blaming China for the pandemic?

Because China is to blame for the pandemic, obviously.

It is to blame because it had full information about the Wuhan spread and that it could be transmitted between humans, yet they sat on that information for weeks until it was too late, precisely because it knew that admission would make China look bad.

The Chinese authorities knowingly and deliberately tried to cover it up for around 6 weeks, knowing full well it was transmissible between humans by mid December. Xi himself by his own admission knew all about it by 5th Jan. The government only admitted human to human transmission in their announcement in late January. They lied about it to the world for over a month.

Just before that late Jan announcement Wuhan went ahead with a 40,000 strong communal dinner, trying to set a world record, and a day or so after held a Chinese New Year festival. God knows how many people were infected just from those events.

Only when it was obviously spiralling out of control and they couldn't keep a lid on it any longer did they act meaningfully, going for the lockdown, but even then it was badly handled, allowing 5 million to leave the area before the lockdown occurred, and spreading throughout China and onwards.

In summary, both local and national governments knowingly and deliberately covered it up once recognised, lied that it was not human transmissible, and denied the scale until the news reports that were getting out were too prevalent to ignore. And even then they applied the shutdown badly, allowing it to spread globally.

China is not to blame for other countries responses, of course, but that they are to blame for its global spread is not remotely in doubt.

This is entirely separate from the lab leak theory, which may or may not be true. If it has a zoonotic origin, China is still to blame for the pandemic.

I was merely pointing out that if it were a leak from a government lab, there would be nothing that they would not do to stop that getting out. That is not a conspiracy, that is fact. That the whistleblower was eventually able to get out information about the early cases once they were in the community has no bearing on the likelihood of a lab leak being suppressed, as he was not talking about the origin.

Xi's China is not the China from 3, 5 or 10 years ago. Its a completely different beast. China spends many time more on its internal security and censorship than it does on its military, and we know how big China's military is.

Does that mean a lab leak is more likely? Not in the slightest. But if China doesn't want something to get out, it wont get out.

[angrysoba]

Originally Posted by GraculusTheGreenBird

Because China is to blame for the pandemic, obviously.

It is to blame because it had full information about the Wuhan spread and that it could be transmitted between humans, yet they sat on that information for weeks until it was too late, precisely because it knew that admission would make China look bad.

The Chinese authorities knowingly and deliberately tried to cover it up for around 6 weeks, knowing full well it was transmissible between humans by mid December. Xi himself by his own admission knew all about it by 5th Jan. The government only admitted human to human transmission in their announcement in late January. They lied about it to the world for over a month.

Just before that late Jan announcement Wuhan went ahead with a 40,000 strong communal dinner, trying to set a world record, and a day or so after held a Chinese New Year festival. God knows how many people were infected just from those events.

Only when it was obviously spiralling out of control and they couldn't keep a lid on it any longer did they act meaningfully, going for the lockdown, but even then it was badly handled, allowing 5 million to leave the area before the lockdown occurred, and spreading throughout China and onwards.

In summary, both local and national governments knowingly and deliberately covered it up once recognised, lied that it was not human transmissible, and denied the scale until the news reports that were getting out were too prevalent to ignore. And even then they applied the shutdown badly, allowing it to spread globally.

China is not to blame for other countries responses, of course, but that they are to blame for its global spread is not remotely in doubt.

This is entirely separate from the lab leak theory, which may or may not be true. If it has a zoonotic origin, China is still to blame for the pandemic.

I was merely pointing out that if it were a leak from a government lab, there would be nothing that they would not do to stop that getting out. That is not a conspiracy, that is fact. That the whistleblower was eventually able to get out information about the early cases once they were in the community has no bearing on the likelihood of a lab leak being suppressed, as he was not talking about the origin.

Xi's China is not the China from 3, 5 or 10 years ago. Its a completely different beast. China spends many time more on its internal security and censorship than it does on its military, and we know how big China's military is.

Does that mean a lab leak is more likely? Not in the slightest. But if China doesn't want something to get out, it wont get out.

I agree with all your points about China's ultimate responsibility one way or another.

I think, however, that the actions taken by both the national and local governments seem more in line with a zoonotic disease than a lab leak - particularly if we are talking about a virus that has been engineered for greater spread.

One of the problems seems to be their duplicitousness regarding the wild-life trade. It is clear that they were speaking out of both sides of their mouth by claiming they had clamped down on wild-life sales, while also turning a blind eye to it except to occasionally hand out slaps on the wrist fines.

The theory, not original to me, that sounds most plausible is that after botching the swine flu response, which resulted in such a massive culling of pigs, wild-life farms ended up making up the short-fall increasing the likelihood of spillover.

[lomiller]

Originally Posted by GraculusTheGreenBird

Because China is to blame for the pandemic, obviously.

The evidence doesn't support that.

I will say that the people responsible for the next Corona virus pandemic are the ones attacking science and scientists researching these viruses. Most of this necessarily involves Chinese scientists, so stop blaming China and maybe take a look at your own actions.

Originally Posted by GraculusTheGreenBird

It is to blame because it had full information about the Wuhan spread and that it could be transmitted between humans, yet they sat on that information for weeks until it was too late, precisely because it knew that admission would make China look bad.

This isn't true. You can't just say "there are multiple cases so it must be spreading person to person" not only is this bad science it's completely irresponsible and 9 times out of 10 will create unnecessary panic.

Originally Posted by GraculusTheGreenBird

The Chinese authorities knowingly and deliberately tried to cover it up for around 6 weeks, knowing full well it was transmissible between humans by mid December.

Again completely false. Chinese hospitals stared identifying clusters of an unknown respiratory disease around Dec 20. Nothing was known and nothing could be known about it at that time, not the cause not how it spread.


Chinese scientists tracked down the virus causing the illness and published it's genome 10 days later on Dec 30. This is an acceptable, perhaps even speedy response to tracking down and sequencing a completely new virus. From this point on research was global, so trying to blame China is nonsensical.

Obviously it would be impossible to know if it was human to human transmissible before this, but in practice you also need to be able to test for the presence of the virus before you make conclusions on how it spreads, and tests were not available until Jan 14.


Once you know who's infected you can start looking at how they got infected, and the WHO started looking at the data immediately, and a weak later concluded it was spreading person to person.

Originally Posted by GraculusTheGreenBird

Just before that late Jan announcement Wuhan went ahead with a 40,000 strong communal dinner, trying to set a world record, and a day or so after held a Chinese New Year festival. God knows how many people were infected just from those events.

So? The rest of the world continued to hold sporting events even though they had full access to all the research on the virus. The fact that it was a true respiratory virus and initial estimates on fatality rates wouldn't be available until February so it's only natural scheduled events would continue.

Originally Posted by GraculusTheGreenBird

Only when it was obviously spiralling out of control and they couldn't keep a lid on it any longer did they act meaningfully, going for the lockdown, but even then it was badly handled, allowing 5 million to leave the area before the lockdown occurred, and spreading throughout China and onwards.

Covid had spread beyond Wuhan before it was even possible to test for it's presence and long before any of it's key properties were know. China acted far more aggressively to contain Covid than any western nation would have but containing to to Wuhan was impossible from the outset.

Originally Posted by GraculusTheGreenBird

In summary, both local and national governments knowingly and deliberately covered it up once recognised, lied that it was not human transmissible, and denied the scale until the news reports that were getting out were too prevalent to ignore. And even then they applied the shutdown badly, allowing it to spread globally.

The facts and timelines produced by the WHO not only do not support this, they definitively refute it.




There are more than enough real things to criticize China for, I suggested you stick to those instead of listening to "news" outlets with an axe to grind.

[GraculusTheGreenBird]

Originally Posted by lomiller

The evidence doesn't support that.

I will say that the people responsible for the next Corona virus pandemic are the ones attacking science and scientists researching these viruses. Most of this necessarily involves Chinese scientists, so stop blaming China and maybe take a look at your own actions.

This isn't true. You can't just say "there are multiple cases so it must be spreading person to person" not only is this bad science it's completely irresponsible and 9 times out of 10 will create unnecessary panic.

Again completely false. Chinese hospitals stared identifying clusters of an unknown respiratory disease around Dec 20. Nothing was known and nothing could be known about it at that time, not the cause not how it spread.

Chinese scientists tracked down the virus causing the illness and published it's genome 10 days later on Dec 30. This is an acceptable, perhaps even speedy response to tracking down and sequencing a completely new virus. From this point on research was global, so trying to blame China is nonsensical.

Obviously it would be impossible to know if it was human to human transmissible before this, but in practice you also need to be able to test for the presence of the virus before you make conclusions on how it spreads, and tests were not available until Jan 14.


Once you know who's infected you can start looking at how they got infected, and the WHO started looking at the data immediately, and a weak later concluded it was spreading person to person.

So? The rest of the world continued to hold sporting events even though they had full access to all the research on the virus. The fact that it was a true respiratory virus and initial estimates on fatality rates wouldn't be available until February so it's only natural scheduled events would continue.

Covid had spread beyond Wuhan before it was even possible to test for it's presence and long before any of it's key properties were know. China acted far more aggressively to contain Covid than any western nation would have but containing to to Wuhan was impossible from the outset.

The facts and timelines produced by the WHO not only do not support this, they definitively refute it.


There are more than enough real things to criticize China for, I suggested you stick to those instead of listening to "news" outlets with an axe to grind.

You are wrong.

Everything I have said is a fact, is not disputed by China, and was reported in the South China Morning Post, a Chinese owned newspaper, based on Chinese state press releases.

Nothing I have said is incorrect. I knew about what would become Covid by late December, because it was reported in said newspapers.

The fact that things like the existence of the 40,000 person dinner in January, and that they knew about human transmission by mid-December are not widely known outside China doesn't make it incorrect, it just means you didn't know about it because it wasn't reported in the western press. It was reported in China and in Hong Kong.

They didn't just make up the idea of human transmission based on the fact that there were many cases, their scientists had studied the patients in hospital and in the lab and had detected human to human transmission, published scientific papers to that end (which is how we know they knew), then the government sat on that knowledge, and lied and said there was no human to human transmission. This is a fact, again reported in South China Morning Post, amongst others.

That they were able to lockdown China and Wuhan so effectively once the horse had bolted shows they had the capability at the time to do so, but simply didn't want to and preferred to cover it up.

There are indeed plenty of things to criticise China for, some that are not justified, and many that are entirely justified. This is one of those in the latter category.

China is to blame for the pandemic.

[GraculusTheGreenBird]

Originally Posted by angrysoba

I agree with all your points about China's ultimate responsibility one way or another.

I think, however, that the actions taken by both the national and local governments seem more in line with a zoonotic disease than a lab leak - particularly if we are talking about a virus that has been engineered for greater spread.

One of the problems seems to be their duplicitousness regarding the wild-life trade. It is clear that they were speaking out of both sides of their mouth by claiming they had clamped down on wild-life sales, while also turning a blind eye to it except to occasionally hand out slaps on the wrist fines.

The theory, not original to me, that sounds most plausible is that after botching the swine flu response, which resulted in such a massive culling of pigs, wild-life farms ended up making up the short-fall increasing the likelihood of spillover.

Yep, this seems likely.

I agree, in general their actions do point more toward a zoonotic spillover.

My point has always been that the lack of evidence of a lab leak in pretty much any other country in the world (ok, outside North Korea!) would indicate that a lab leak was unlikely. This is just not the case in China.

Does that help us in any way? Unfortunately not. We are still left guessing, and looking for evidence that is not yet forthcoming.

[lomiller]

Originally Posted by GraculusTheGreenBird

You are wrong.

Everything I have said is a fact, is not disputed by China, and was reported in the South China Morning Post, a Chinese owned newspaper, based on Chinese state press releases.

Everything I said is well documented fact generated by western scientists working either independently of for the WHO, not speculation or rumor that may or may not have been published in a Chinese newspaper of indeterminate journalistic quality.


When the first know cases were reported is not in doubt (Dec 11)
When hospitals first suspected they were seeing a cluster of related cases is not in doubt (Dec 19-21)
When the genetic sequence of the virus responsible was released to scientists worldwide isn't in doubt (Dec 31)
When German scientists developed the first PCR test for Covid is not in doubt (Jan 10)
the WHO was looking into whether it was human to human transmissible, On Jan 18 they said there was insufficient evidence and that they needed another week to study the question. On Jan 21 they announced that it was in fact human to human transmissible. Before this all you had was people speculating and guessing but little actual evidence.

[GraculusTheGreenBird]

Originally Posted by lomiller

Everything I said is well documented fact generated by western scientists working either independently of for the WHO, not speculation or rumor that may or may not have been published in a Chinese newspaper of indeterminate journalistic quality.


When the first know cases were reported is not in doubt (Dec 11)
When hospitals first suspected they were seeing a cluster of related cases is not in doubt (Dec 19-21)
When the genetic sequence of the virus responsible was released to scientists worldwide isn't in doubt (Dec 31)
When German scientists developed the first PCR test for Covid is not in doubt (Jan 10)
the WHO was looking into whether it was human to human transmissible, On Jan 18 they said there was insufficient evidence and that they needed another week to study the question. On Jan 21 they announced that it was in fact human to human transmissible. Before this all you had was people speculating and guessing but little actual evidence.

President Xi knew, as reported in Chinese state media, by January 5th, by his own admission.

Sure, it is correct the WHO did not know on January 18th whether it was human transmissible, because China, who already knew it was, refused to tell them.

That is a fact.

This is also not something I have just cooked up, it was reported in newspapers in March 2020, and I posted about it at that time in the main Covid science thread, e.g. http://www.internationalskeptics.com...&postcount=995

To show how apalling their attempts were to control it:

"Two days after they finally admitted it was human transmissible, they continued to hold a Lunar New Year dance performance attended by senior officials from all across Hubei. Amazingly, state media reported that the performers, some with runny noses and feeling unwell "overcame the fear of pneumonia, winning praise from the leaders.""

Xi knew, China knew, they failed to tell the WHO, and allowed it to spread because they were trying to cover it up first.

[GraculusTheGreenBird]

Originally Posted by lomiller

Everything I said is well documented fact generated by western scientists working either independently of for the WHO, not speculation or rumor that may or may not have been published in a Chinese newspaper of indeterminate journalistic quality.


When the first know cases were reported is not in doubt (Dec 11)
When hospitals first suspected they were seeing a cluster of related cases is not in doubt (Dec 19-21)
When the genetic sequence of the virus responsible was released to scientists worldwide isn't in doubt (Dec 31)
When German scientists developed the first PCR test for Covid is not in doubt (Jan 10)
the WHO was looking into whether it was human to human transmissible, On Jan 18 they said there was insufficient evidence and that they needed another week to study the question. On Jan 21 they announced that it was in fact human to human transmissible. Before this all you had was people speculating and guessing but little actual evidence.

The South China Morning Post is not some unknown newspaper of indeterminate quality, it is Hong Kong's newspaper of record, and still considered authoritative and independent.

And in this case, was simply reporting facts from Chinese state media, facts that reflected badly on China, so were extremely unlikely to be reported by said state media if they could get away with not reporting them, and impossible to be reported if they were false.

[angrysoba]

Originally Posted by GraculusTheGreenBird

President Xi knew, as reported in Chinese state media, by January 5th, by his own admission.

Sure, it is correct the WHO did not know on January 18th whether it was human transmissible, because China, who already knew it was, refused to tell them.

That is a fact.

This is also not something I have just cooked up, it was reported in newspapers in March 2020, and I posted about it at that time in the main Covid science thread, e.g. http://www.internationalskeptics.com...&postcount=995

To show how apalling their attempts were to control it:

"Two days after they finally admitted it was human transmissible, they continued to hold a Lunar New Year dance performance attended by senior officials from all across Hubei. Amazingly, state media reported that the performers, some with runny noses and feeling unwell "overcame the fear of pneumonia, winning praise from the leaders.""

Xi knew, China knew, they failed to tell the WHO, and allowed it to spread because they were trying to cover it up first.

Indeed, but the fact we now know about this cover-up and the initial cover-up when Li Wenliang was warning about about spread from the Huanan seafood market CANNOT be seen as evidence that covering up a lab leak would be easy. If anything, both points again, undermine a lab leak and suggest the Chinese government instead tried (and failed) to cover up a wild-life born spillover, and have been muddying the waters ever since.

Many times in this very thread, I've been told by lab leaker(s) that the Huanan Seafood Market has been completely refuted to the point that it is no more likely than coming from space. Yet, the initial and most plausible hypothesis, that it DID come from the wildlife trade and emerged from the Huanan Seafood Market is becoming more plausible, rather than less, and the lab leak theory is looking less plausible without some very far-fetched and far-reaching theorizing necessary to paper over the cracks.

[angrysoba]

Originally Posted by angrysoba

I think the chapter on HIV in Spillover is quite good. It goes pretty deeply into the OPV theory of AIDS (which was that oral polio vaccine used a form of the simian version of AIDS which then led to the HIV and then AIDS) and also Worobey's involvement in initially accompanying W. D. Hamilton (a prominent proponent of the theory) to Congo to find blood samples in order to see if it contained SIV. Apparently Hamilton contracted malaria on the trip and later died, and the blood samples showed no SIV.

Regarding Worobey's theory here, the TWIV team don't really ask many questions because, as they say at the end, Worobey basically answers all the ones that they planned to ask, and they apparently had a lot that they wanted to ask.

Regarding the wild animals, I don't think Worobey thinks they came from near Wuhan, as far as I remember. They could have been farmed many miles away.

I also don't think he is arguing it spilled over in multiple markets. Just one.

How did it get adapted to humans? Well, presumably there is a survivorship bias. Lineage A was not as adaptive as B, and maybe there were others that fizzled out. We know it was adapting all the time as he even mentions another variant that completely took over.

And we can hardly say he is "ignoring" the proximity of the labs. It was the very proximity of the labs that got him and Jesse Bloom to write a letter to Science saying that the lab leak theory needs to be taken seriously.

Anyway, it will be interesting to see what the peer reviewers make of it.

I think I may have forgotten to point out that Matt Ridley was one of the proponents of the theory that AIDS had come from the oral polio vaccine and not a spillover.

Well, here he is going back to that theory now. I think when we see these kinds of thought processes then it becomes pretty clear why lab leak is thought of a conspiracy theory....

[angrysoba]

I'm going to necro this thread, a little, as one of the contentious suggestions about the origins of Covid has been that all the top scientist guys - Fauci, Andersen, Farrar, Vallance, Holmes, etc... knew that the virus had come from a lab and then tried to hush it up.

Then some redacted emails came out in which it was thought that they had admitted the origins, or of making the virus, and had decided to redact those bits.

I think I may have had a bit of fun with those claiming that this is what lay under the redactions.

Anyway, now the unredacted emails have been released.

I have not read them all, but here is a thread by Angie Rasumussen in which she argues that what is going on here is a group of scientists initially wondering in horror if the virus had indeed been engineered, and then changing their mind the more they looked into it.

Link

[The Atheist]

Headline: Lab Leak Most Likely Origin of Covid-19 Pandemic, Energy Department Now Says

U.S. agency’s revised assessment is based on new intelligence

Reality:

Quote:

The conclusion from the energy department – which oversees a network of 17 US laboratories, including areas of advanced biology – is considered significant despite the fact that, as the report said, the agency made its updated judgment with “low confidence”.

In meteorological terms, that is <20%.

Still leaves US agencies that report on the pandemic 4-2 in favour of natural origins.

Murdoch priming the pump?

[Roger Ramjets]

Originally Posted by The Atheist

Headline: Lab Leak Most Likely Origin of Covid-19 Pandemic, Energy Department Now Says

U.S. agency’s revised assessment is based on new intelligence

Paywalled, and I can find no reference to it on the DOE's website. Seems like they are trying to keep it quiet...

Meanwhile

Quote:

White House national security adviser Jake Sullivan on Sunday responded to a new Wall Street Journal report that found the Department of Energy has concluded the COVID-19 pandemic most likely developed from a lab leak, saying there’s “no definitive answer” on the question.

“Here’s what I can tell you. President Biden has directed, repeatedly, every element of our intelligence community to put effort and resources behind getting to the bottom of this question,” Sullivan said on CNN’s “State of the Union.”

“If we gain any further insight or information, we will share it with Congress, and we will share it with the American people. But right now, there is not a definitive answer that has emerged from the intelligence community on this question,” the national security adviser said.

[Skeptic Ginger]

You can't say "low confidence" of a lab origin means 2-4 likelihood without saying what the confidence is for a natural spillover event. Both could be equally low confidence. I happen to think, as I have posted and supported my POV before that there is a bias begun when Peter Daszak manipulated the early conclusions. A lot of scientists don't want to believe it was a lableak.


Moving on:
Did you miss the whistleblower who reported it was the lab. He worked with EcoHealth Alliance.

Our past discussion was pretty much at a stalemate. Then I ended up in the hospital for 2 weeks with respiratory failure (autoimmune diagnosed though it was quite disturbing to read my lung CT had a "ground glass" appearance ). That was ~5 months ago. I'm not totally better but hopefully I'm getting there.

Anywho... The whistleblower articles showed up but I wasn't ready to start this debate again. I haven't read his book yet.

Here are a couple of the links I've bookmarked:

WA Times: Virus hunter for EcoHealth Alliance says COVID-19 leaked from Chinese lab

Quote:

Andrew Huff, an infectious disease epidemiologist and former vice president at the New York-based EcoHealth Alliance, said in an interview that the group was engaged in “gain-of-function” research at the Wuhan Institute of Virology in the years before the COVID-19 virus first emerged from the Chinese city in late 2019. He said he is convinced that the virus that caused the COVID-19 pandemic was manufactured at the institute’s laboratory and leaked out.

“I suspected that this was a lab leak from Day One, and as time went on, the information gaps that I had were filled,” Mr. Huff said.

Scientist who worked at Wuhan lab says Covid was man-made virus

Quote:

In his new book — The Truth About Wuhan — whistleblower Dr Huff claims the pandemic was the result of the US government’s funding of dangerous genetic engineering of coronaviruses in China.

The epidemiologist said China’s gain-of-function experiments, carried out with shoddy biosecurity, led to a lab leak at the US-funded Wuhan Institute of Virology.

“EcoHealth Alliance and foreign laboratories did not have the adequate control measures in place for ensuring proper biosafety, biosecurity, and risk management, ultimately resulting in the lab leak at the Wuhan Institute of Virology,” he said in his book, ...

That last paragraph has been thoroughly documented in this thread.


The NIH did not monitor how its money was spent regardless of Fauci's denials.
'Extremely disconcerting': NIH didn't track U.S. funds going to Chinese virus research, watchdog finds

Quote:

The National Institutes of Health failed to provide adequate oversight of an American organization that funded controversial research at the Wuhan Institute of Virology in China, according to a new government report that is sure to raise new questions about the origins of the COVID-19 pandemic.

The report is evidence of “major failures in past NIH oversight of high-risk research on enhanced potential pandemic pathogens,” Rutgers molecular biologist Richard Ebright told Yahoo News in an email.

Issued by the inspector general of the federal Department of Health and Human Services, the new report says nothing about the origins of the coronavirus. ...

But it does note that the American organization in question, the EcoHealth Alliance, should have been more rigorously scrutinized by federal officials regarding assurances that its partner lab in Wuhan was not using U.S. funds to conduct gain-of-function research, which boosts viruses to study how they might evolve in nature.

For more genetic evidence:
Thus spoke peptides: SARS-CoV-2 spike gene evolved in humans and then shortly in rats while the rest of its genome in horseshoe bats and then in treeshrews

Quote:

Abstract
SARS-CoV-2 is suspected to be the product of a natural or artificial recombination of two viruses – one adapted to the horseshoe bat and the other, donor of the spike protein gene, adapted to an unknown species. Here we used a new method to search for the original host of the ancestor of the SARS-CoV-2 virus and for the donor of its gene for the spike protein, the molecule responsible for binding to and entering human cells. We computed immunological T-distances (the number of different peptides that are present in the viral proteins but absent in proteins of the host) between 11 species of coronaviruses and 38 representatives of the main mammal clades. Analyses of pentapeptides, the presumed principal targets of T-cell non-self recognition, showed the smallest T-distance of the spike protein of SARS-CoV-2 to humans, while the rest of SARS-CoV-2 proteome to the horseshoe bat. This suggests that the ancestor of SARS-CoV-2 was adapted to bats, but the spike gene donor was adapted to humans. Further analyses suggest that the ancestral coronavirus adapted to bats was shortly passaged in treeshrews, while the donor of the spike gene was shortly passaged in rats before the recombination event.

Sure sounds like gain of function research, manipulating the genome. That is unless someone thinks the virus acquired human gene segment(s) that had been passed through treeshrews and rats, all in the wild.

[novaphile]

Originally Posted by Skeptic Ginger

You can't say "low confidence" of a lab origin means 2-4 likelihood without saying what the confidence is for a natural spillover event. Both could be equally low confidence. I happen to think, as I have posted and supported my POV before that there is a bias begun when Peter Daszak manipulated the early conclusions. A lot of scientists don't want to believe it was a lableak.


Moving on:
Did you miss the whistleblower who reported it was the lab. He worked with EcoHealth Alliance.

Our past discussion was pretty much at a stalemate. Then I ended up in the hospital for 2 weeks with respiratory failure (autoimmune diagnosed though it was quite disturbing to read my lung CT had a "ground glass" appearance ). That was ~5 months ago. I'm not totally better but hopefully I'm getting there.

Anywho... The whistleblower articles showed up but I wasn't ready to start this debate again. I haven't read his book yet.

Here are a couple of the links I've bookmarked:

WA Times: Virus hunter for EcoHealth Alliance says COVID-19 leaked from Chinese lab


Scientist who worked at Wuhan lab says Covid was man-made virusThat last paragraph has been thoroughly documented in this thread.


The NIH did not monitor how its money was spent regardless of Fauci's denials.
'Extremely disconcerting': NIH didn't track U.S. funds going to Chinese virus research, watchdog finds



For more genetic evidence:
Thus spoke peptides: SARS-CoV-2 spike gene evolved in humans and then shortly in rats while the rest of its genome in horseshoe bats and then in treeshrewsSure sounds like gain of function research, manipulating the genome. That is unless someone thinks the virus acquired human gene segment(s) that had been passed through treeshrews and rats, all in the wild.

No, no one thinks that happened in the wild.

Everyone thinks that happened in the wet markets, where all kinds of animals are packed next to each other in cages, and are handled by humans everyday.

[Skeptic Ginger]

Murdoch priming the pump? Maybe trying to distract from the Dominion lawsuit and exposed stolen election lies but it's not like Fox is the only news agency report.

Not paywalled news on the DoE report:

MSN/CNN: US Energy Department assesses Covid-19 likely resulted from lab leak, furthering US intel divide over virus origin

Quote:

Two sources said that the Department of Energy assessed in the intelligence report that it had “low confidence” the Covid-19 virus accidentally escaped from a lab in Wuhan.

Intelligence agencies can make assessments with either low, medium or high confidence. A low confidence assessment generally means that the information obtained is not reliable enough or is too fragmented to make a more definitive analytic judgment or that there is not enough information available to draw a more robust conclusion.

Like I said above:

Quote:

In 2021, the intelligence community declassified a report that showed four agencies in the intelligence community had assessed with low confidence that the virus likely jumped from animals to humans naturally in the wild, while one assessed with moderate confidence that the pandemic was the result of a laboratory accident.

I believe this represents the stalemate that this thread became:

Quote:

In May 2020, researchers at the government-backed Lawrence Livermore National Laboratory issued a classified report that found it was possible that the coronavirus escaped from a lab in Wuhan, which came at a time when that line of inquiry was considered taboo.

The US began exploring the possibility that Covid-19 spread in a laboratory as early as April 2020, though the intelligence community has noted repeatedly that a lack of cooperation from Beijing has made it difficult to get to the bottom of the question.

A total muck up because who could trust anything Trump's minions said and then you had Daszak and Fauci denying the uS funded any gain-of-function research.


As expected the GOP is having a field day with the DoE report.

[Skeptic Ginger]

Originally Posted by novaphile

No, no one thinks that happened in the wild.

Everyone thinks that happened in the wet markets, where all kinds of animals are packed next to each other in cages, and are handled by humans everyday.

Come on, move the discussion forward. If you think a spillover occurred in the wet market in Wuhan then post some new evidence of the intermediate species involved, cases circulating in an intermediate species before the spillover, data on the initial cases in WuHan that China is withholding etc. Those are some of the holes in the spillover hypothesis.

Otherwise you are just recycling stuff we debated ad nauseum. It's fine if you want to say what POV you have concluded, but don't go dismissing the whistleblower with unsupported generalities that "no one thinks". Because obviously many people have settled on the lab leak side.

[Dr.Sid]

Originally Posted by novaphile

Everyone thinks that happened in the wet markets, where all kinds of animals are packed next to each other in cages, and are handled by humans everyday.

I don't.

[The Atheist]

Originally Posted by Skeptic Ginger

You can't say "low confidence" of a lab origin means 2-4 likelihood without saying what the confidence is for a natural spillover event.

You're conflating two different things.

The DOE itself states it has low confidence.

Apparently, there are 5 other agencies (one of which is FBI) with opinions on where it started. Right now, DOE and FBI say the lab, the other 4 days natural origin.

[Aridas]

Originally Posted by The Atheist

Headline: Lab Leak Most Likely Origin of Covid-19 Pandemic, Energy Department Now Says

U.S. agency’s revised assessment is based on new intelligence

To poke a little at that -

Quote:

4/ DOE doesn’t say how they arrived at their opinion or whether they included virologists and epidemiologists in the process.

So, in short, not much way to verify much of anything. In a way, that's rather convenient for anyone more interested in backing their bias, whatever it is. Given the timing, I also sorta have to wonder if politics is in play at all, too.

Either way, CT's are likely to jump on it.

[Skeptic Ginger]

Originally Posted by The Atheist

You're conflating two different things.

The DOE itself states it has low confidence.

Apparently, there are 5 other agencies (one of which is FBI) with opinions on where it started. Right now, DOE and FBI say the lab, the other 4 days natural origin.

Citation please. I posted this, maybe you haven't read that post yet:

Quote:

In 2021, the intelligence community declassified a report that showed four agencies in the intelligence community had assessed with low confidence that the virus likely jumped from animals to humans naturally in the wild,

Anyway, it's not much of a debate at this point who holds which opinions. I put Huff's book on hold, my library has it on order.

[Sherkeu]

Originally Posted by The Atheist

You're conflating two different things.

The DOE itself states it has low confidence.

Apparently, there are 5 other agencies (one of which is FBI) with opinions on where it started. Right now, DOE and FBI say the lab, the other 4 days natural origin.

Natural origin means what? What animal? None have been found. No evidence for it.

There is, however, evidence that a Sars corona virus adapted to humans was being sequenced as part of research at the lab in Wuhan (and funded in part by the US). Wuhan WIV is THE top bats sars corona virus lab in the world. Wuhan is where the outbreak happened. The closest viruses are a thousand miles away, but are documented to have been collected and transported to the lab in Wuhan - for many years. The research was being done, not in the level 4 facilities with the most safety controls, but level 2 and 3.

So, while not definitive, what more do you need to say "likely"?
It's been the likely source this whole time.

[jt512]

Originally Posted by The Atheist

Headline: Lab Leak Most Likely Origin of Covid-19 Pandemic, Energy Department Now Says

U.S. agency’s revised assessment is based on new intelligence

In meteorological terms, that is <20%.

"Most likely" means >50%. "Low confidence" puts some upper limit on that probability.

[Planigale]

Originally Posted by Sherkeu

Natural origin means what? What animal? None have been found. No evidence for it.

There is, however, evidence that a Sars corona virus adapted to humans was being sequenced as part of research at the lab in Wuhan (and funded in part by the US). Wuhan WIV is THE top bats sars corona virus lab in the world. Wuhan is where the outbreak happened. The closest viruses are a thousand miles away, but are documented to have been collected and transported to the lab in Wuhan - for many years. The research was being done, not in the level 4 facilities with the most safety controls, but level 2 and 3.

So, while not definitive, what more do you need to say "likely"?
It's been the likely source this whole time.

BATS!

Since there is no identified precursor bat virus mentioning bats is scary but irrelevant. The failure to identify the immediate precursor virus in animals is used as an argument against a natural origin, but equally must be an argument against a laboratory escape origin.

MICE!

This paper suggests that Omicron may have evolved in mice. So perhaps we need to look for a virology laboratory that does work with mice.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718870/

Think how long it took to identify the animal origins of HIV, so it is not surprising we don't know the animal origin of SARS-CoV-2.

[The Atheist]

Originally Posted by Aridas

To poke a little at that -

So, in short, not much way to verify much of anything. In a way, that's rather convenient for anyone more interested in backing their bias, whatever it is. Given the timing, I also sorta have to wonder if politics is in play at all, too.

Either way, CT's are likely to jump on it.

That's pretty much where I am - nothing new, a purely political statement.

Originally Posted by Skeptic Ginger

Citation please.

What are you talking about? The article I linked says exactly what I typed.

Originally Posted by Skeptic Ginger

I posted this, maybe you haven't read that post yet:

I don't intend to - I'm just stating what was said.

Originally Posted by jt512

"Most likely" means >50%. "Low confidence" puts some upper limit on that probability.

Utter nonsense. Low confidence means exactly that.

Low - 20%
Moderate - 40-60%
High - 80%

They have low confidence of a likelihood.

It's a big fat nothingburger.

[jt512]

Originally Posted by The Atheist

Utter nonsense. Low confidence means exactly that.

Low - 20%
Moderate - 40-60%
High - 80%

They have low confidence of a likelihood.

It's a big fat nothingburger.

Sorry, but what you are saying is logically, mathematically, and semantically wrong. The DOE said that a lab leak most likely was the cause. "Most likely" means "more likely than not," which in turn means >50% probability. When they say they have low confidence in their conclusion, they don't mean that they have "low confidence in the likelihood" (which would be incoherent). They mean that they have low confidence in their conclusion that the cause was a lab leak. Taken together, that means that they think it "most likely"; ie, more likely than not,; ie, >50% chance, that a lab leak was the cause; but they still think that there is a substantial probability (but, necessarily, less than 50%) that the cause was other than a lab leak.

[Aridas]

Originally Posted by jt512

Sorry, but what you are saying is logically, mathematically, and semantically wrong. The DOE said that a lab leak most likely was the cause. "Most likely" means more likely than not, which in turn means >50% probability.

Normally, "most likely" used as it was in the headline could also refer to a particular option being assessed as more likely than the alternatives, which is not necessarily the same thing as greater than 50% probability - there can be more than 2 options, after all. There is something to be questioned about whether "meteorological terms" are at all applicable here, of course, and more broadly what the actual assessed probabilities are.

[jt512]

Originally Posted by Aridas

Normally, "most likely" used as it was refers to a particular option being assessed as more likely than the alternatives, which is not necessarily the same thing as greater than 50% probability - there can be more than 2 options, after all.

There is a difference between "most likely (did something)" and "the most likely (something)." When we say "X is the most likely (something)," we mean that there are more than 2 somethings and that X is the most likely of them, which could mean that P(X) < 50%. (Here, "likely" is an adjective.)

But the DOE didn't say the lab leak hypothesis was the most likely something (ie, hypothesis). It said (at least according to the Times) that "a lab leak most likely caused the pandemic." In that sentence, "most likely" means "more likely than not." (Here, "likely" is an adverb.)

To put it another way, according to the Times, the DOE did not say, "The most likely cause of the pandemic was a lab leak." They said, "The pandemic was most likely caused by a lab leak." In the former, the probability that a lab leak caused the pandemic could, in principle, be <50%; whereas, in the latter, a lab leak is asserted to be, more likely than not, the cause of the pandemic.

[Lothian]

Originally Posted by jt512

Sorry, but what you are saying is logically, mathematically, and semantically wrong. The DOE said that a lab leak most likely was the cause. "Most likely" means "more likely than not," which in turn means >50% probability. When they say they have low confidence in their conclusion, they don't mean that they have "low confidence in the likelihood" (which would be incoherent). They mean that they have low confidence in their conclusion that the cause was a lab leak. Taken together, that means that they think it "most likely"; ie, more likely than not,; ie, >50% chance, that a lab leak was the cause; but they still think that there is a substantial probability (but, necessarily, less than 50%) that the cause was other than a lab leak.

There are 8 options.
Options A to G each have a probability of 12% option H has a probability of 16%.

Which of the options is the most likely?

[Tero]

The virus we have is very close to the bat virus. Not any particular virus, but all the parts look like known virus parts.

Tracking down various variants, the bat virus remains were collected and sequenced in China. No live virus from the bat feces could be grown in lab. It's all in the Quammen book. He called and zoomed a number of scientists around the world during the pandemic year.

https://www.amazon.com/Breathless-Sc...s%2C159&sr=8-2

[Tero]

Originally Posted by Planigale

BATS!

Since there is no identified precursor bat virus mentioning bats is scary but irrelevant. The failure to identify the immediate precursor virus in animals is used as an argument against a natural origin, but equally must be an argument against a laboratory escape origin.

MICE!

This paper suggests that Omicron may have evolved in mice. So perhaps we need to look for a virology laboratory that does work with mice.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8718870/

Think how long it took to identify the animal origins of HIV, so it is not surprising we don't know the animal origin of SARS-CoV-2.

Those are the Omicron variants. The only virus we should be tracking is the original virus sequenced in the first wave of the disease in China. That is the one you would relate to any animal viruses prior to that.

[Lplus]

Originally Posted by Lothian

There are 8 options.
Options A to G each have a probability of 12% option H has a probability of 16%.

Which of the options is the most likely?

It depends if there is any political fallout for choosing H...

[Tero]

Quote:

Another source of speculation is the mere presence of the furin cleavage site.[18][118] It is absent in the closest known relatives of SARS-CoV-2 (but present in other betacoronaviruses e.g. BtHpCoV-ZJ13).[122] Scientists consider that this diversity of cleavage sites is likely the result of recombination,[118][123] and is further unsurprising since the genetic lineage of these viruses has not been adequately explored, sampled, or sequenced.[124][125] A common occurrence amongst other coronaviruses, including MERS-CoV, HCoV-OC43, HCoV-HKU1, and appearing in near-identical fashion in HKU9-1, the site is preceded by short palindromic sequences suggestive of natural recombination caused by simple evolutionary mechanisms. Additionally, the suboptimal configuration and poor targeting of the cleavage site when compared with known examples (such as HCoV-OC43 or HCoV-HKU1), along with the complex and onerous molecular biology work this would have required, is inconsistent with what would be expected from an engineered virus.

https://en.wikipedia.org/wiki/COVID-19_lab_leak_theory

[Planigale]

Originally Posted by Tero

The virus we have is very close to the bat virus. Not any particular virus, but all the parts look like known virus parts.

Tracking down various variants, the bat virus remains were collected and sequenced in China. No live virus from the bat feces could be grown in lab. It's all in the Quammen book. He called and zoomed a number of scientists around the world during the pandemic year.

https://www.amazon.com/Breathless-Sc...s%2C159&sr=8-2

There is no 'bat virus' there are many bat viruses, only a few of which have been sequenced. SARS-CoV-2 is not 'very close' to any known bat virus the closest known virus is a bat virus with about 95% sequence homology. On a similar basis humans and chimps have about 98% homology, but humans did not arise from a laboratory experiment with chimps there was a common ancestor.

With SARS it was about 5 years for the origin to be traced from a horseshoe bat virus that infected pangolins that then infected humans. The natural zoonotic spread is actually more embarassing for the Chines than a laboratory incident as it proposes virtually the same pattern of events as caused the SARS near pandemic. If the Chinese do not mend their ways, a third coronavirus outbreak seems likely.

[Skeptic Ginger]

Originally Posted by The Atheist

That's pretty much where I am - nothing new, a purely political statement.

What are you talking about? The article I linked says exactly what I typed.

I don't intend to - I'm just stating what was said.

Utter nonsense. Low confidence means exactly that.

Low - 20%
Moderate - 40-60%
High - 80%

They have low confidence of a likelihood.

It's a big fat nothingburger.

It wasn't the low confidence I was referring to, it was this unsupported conclusion you drew:

Quote:

Still leaves US agencies that report on the pandemic 4-2 in favour of natural origins.

No it did not and neither did anything else you posted.

I supported what I said, both hypotheses have a low favor.

Support your claim that "US agencies report on the pandemic" in favor of a natural origin. They don't. They favor both with equally low confidence.

As for not intending to read what I posted supporting my position, I quoted myself to make it easy for you. Did you not even read the post you replied to?

[The Atheist]

Originally Posted by jt512

When they say they have low confidence in their conclusion, they don't mean that they have "low confidence in the likelihood" (which would be incoherent).

This thread gets funnier by the post. You don't even realise how idiotic your post is, because that's exactly what they're saying.

Please do continue.

Originally Posted by Skeptic Ginger

Support your claim that "US agencies report on the pandemic" in favor of a natural origin.

Read. The. Link.

4 agencies say natural, 2 say lab.

It really is that simple.

You're right that none of them have better than low confidence, so we're exactly where we were 12 and 24 months ago.

[Ron Obvious]

Originally Posted by The Atheist

You're right that none of them have better than low confidence, so we're exactly where we were 12 and 24 months ago.

Except for the fact that a lab origin is now allowed to be discussed, apparently, rather than instantly dismissed as racist.

Small steps.