Origins of Covid

[Skeptic Ginger]

Originally Posted by lionking

Arguments from incredulity are the weakest arguments.

[Steve]

Originally Posted by Skeptic Ginger

There is no credible evidence that market or any other market in Wuhan was the initial 'crossover' site. By continuing to repeat this you reinforce the falsehood.

And as for Worobey's genetic walk-back, he had missing information on the first patients and while people like Bloom politely said the walk-back had no obvious flaws, he also said it wasn't conclusive evidence.


It could have come from the lab. "Likely came from" is bull ****. No trail was found be it from frozen food to the wildlife farms to the mine in Yunnan to the caves in Laos.

As for find the furin cleavage site in the wild, sure, it was in a different bat species but recombinant coronaviruses are found in bats. That fact doesn't provide a smoking gun.

Indeed, for any source so far proposed. Each proposed source has exactly the same evidence, ie; speculation.

[Skeptic Ginger]

Originally Posted by angrysoba

You see, this is why a lot of people think that the lab leak is a conspiracy theory.

So what?

Originally Posted by angrysoba

It relies on the idea of a massive cover-up by, let's see, the Wuhan Institute of Virology, the NIH, most of the world's virologists, and Google.

Massive cover-up? What nonsense. It only requires the Chinese government and a natural self-preservation of Shi and Daszak to not want to face the music.

Originally Posted by angrysoba

It is apparently being exposed by some right-wing Senators, ivermectin proponents, anti-vaxxers and ...erm... Gab dwellers?

Again, this is not the least bit relative.

If you want to use a CT as your evidence against a lab origin hypothesis it does not belong in this thread.

[Skeptic Ginger]

Originally Posted by angrysoba

I am not remotely convinced either that you have demonstrated that the WIV made SARS-CoV2, that you know what you are talking about, or that you aren't putting forward a vast conspiracy theory. You even said that you use Duck Duck Go because Google is somehow suppressing searches for the documents you are talking about.

"Because Google is somehow suppressing searches" belongs in the other forum.

Google uses an algorithm that favors frequent hits. I often switch between DuckDuckGo and Startpage because they can turn up different results.

[Skeptic Ginger]

Originally Posted by Steve

Indeed, for any source so far proposed. Each proposed source has exactly the same evidence, ie; speculation.

I don't agree about the same amount of supporting evidence, obviously. But you are correct in that in neither origin hypotheses is there conclusive evidence.

[Skeptic Ginger]

I haven't gotten back to the specifics in the emails yet though I did link to a source summarizing what was in those early emails.

First, in this post I'm repeating the proposal's incriminating paragraph because it is relevant:

DARPA proposal

Quote:

LEAKED GRANT PROPOSAL DETAILS HIGH-RISK CORONAVIRUS RESEARCH
The proposal, rejected by U.S. military research agency DARPA, describes the insertion of human-specific cleavage sites into SARS-related bat coronaviruses....

“We will introduce appropriate human-specific cleavage sites and evaluate growth potential in [a type of mammalian cell commonly used in microbiology] and HAE cultures,” referring to cells found in the lining of the human airway, the proposal states.

You can't get a more incriminating pre-pandemic proposal.

Expert opinions in the article:

Quote:

“We will introduce appropriate human-specific cleavage sites and evaluate growth potential in [a type of mammalian cell commonly used in microbiology] and HAE cultures,” referring to cells found in the lining of the human airway, the proposal states.

Martin Wikelski, a director at the Max Planck Institute of Animal Behavior in Germany, whose work tracking bats and other animals was referenced in the grant application without his knowledge, also said it made him more open to the idea that the pandemic may have its roots in a lab. “The information in the proposal certainly changes my thoughts about a possible origin of SARS-CoV-2,” Wikelski told The Intercept. “In fact, a possible transmission chain is now logically consistent — which it was not before I read the proposal.”

And experts who disagreed:

Quote:

But others insisted that the research posed little or no threat and pointed out that the proposal called for most of the genetic engineering work to be done in North Carolina rather than China. “Given that the work wasn’t funded and wasn’t proposed to take place in Wuhan anyway it’s hard to assess any bearing on the origin of SARS-CoV-2,” Stephen Goldstein, a scientist who studies the evolution of viral genes at the University of Utah, and an author of the recent Cell article, wrote in an email to The Intercept.

Baric (N Carolina) and Shi parted ways shortly thereafter. Baric set Shi the genetically engineered mice to continue the work at the WIV. And obviously there were alternative sources of funding.


June 2021 Technology Review article discussing the not denied funding. There was plenty.

Quote:

They did share resources—for example, Baric sent the transgenic mice with human lung receptors to Wuhan. But after their initial collaboration, the two centers were more like competitors. They were in a race to identify dangerous coronaviruses, assess the potential threat, and develop countermeasures like vaccines.

Quote:

In Baric’s lab, the chimeras were studied at BSL-3, enhanced with additional steps like Tyvek suits, double gloves, and powered-air respirators for all workers. Local first-responder teams participated in regular drills to increase their familiarity with the lab. All workers were monitored for infections, and local hospitals had procedures in place to handle incoming scientists. It was probably one of the safest BSL-3 facilities in the world. That still wasn’t enough to prevent a handful of errors over the years: some scientists were even bitten by virus-carrying mice. But no infections resulted.

The WIV was reportedly doing its work in a level 2 biosafety lab.

Quote:

Two years later, Daszak and Shi published a paper reporting how the Chinese lab had engineered different versions of WIV1 and tested their infectiousness in human cells. The paper announced that the WIV had developed its own reverse-genetics system, following the Americans’ lead. It also included a troubling detail: the work, which was funded in part by the NIH grant, had been done in a BSL-2 lab. That meant the same viruses that Daszak was holding up as a clear and present danger to the world were being studied under conditions that, according to Richard Ebright, matched “the biosafety level of a US dentist’s office.”

Baric quietly weighed in:

Quote:

Since the pandemic began, Baric has not said much about the possible origins of the virus or about his Chinese counterparts. On several occasions, however, he has quietly pointed to safety concerns at the WIV. In May 2020, when few scientists were willing to consider a lab leak in public, he published a paper acknowledging that “speculation about accidental laboratory escape will likely persist, given the large collections of bat virome samples stored in labs in the Wuhan Institute of Virology, the facility’s proximity to the early outbreak, and the operating procedures at the facility.” He flagged Daszak and Shi’s BSL-2 paper, in case anyone didn’t understand what he was saying.

I say quietly because he officially he stayed on the natural spillover side of the origin argument.

Quote:

Baric says he still believes a natural spillover is the most likely cause. But he also knows the intricate risks of the work well enough to see a possible path to trouble. That is why, in May of this year, he joined 17 other scientists in a letter in the journal Science calling for a thorough investigation of his onetime collaborator’s lab and its practices. He wants to know what barriers were in place to keep a pathogen from slipping out into Wuhan’s population of 13 million, and possibly to the world.

“Let’s face it: there are going to be unknown viruses in guano, or oral swabs, which are oftentimes pooled. And if you’re attempting to culture a virus, you’re going to have novel strains being dropped onto culture cells,” Baric says. “Some will grow. You could get recombinants that are unique. And if that was being done at BSL-2, then there are questions you want to ask.”

NOTE: There is no CT here either discussed or implied.

[michaelsuede]

Yeah, you read the DARPA proposal and you realize just how insane they are, then you read the NIAID grant report and realize they simply did the DARPA proposal under the NIAID grant.

[lomiller]

]

Originally Posted by michaelsuede

The Huanan Market is literally 400 meters from the WIV.

The lab is 20Km from where the first cases were found, and the early cases are all much closer to the Wuhan Fish Market than any building occupied by WIV.

Originally Posted by michaelsuede

We have to be talking about trillion to one odds, hell maybe even gazillion to one odds, that a completely novel human infectious,

every virus that is capable of infecting humans was once a novel virus.

Originally Posted by michaelsuede

ACE2 targeting,

Viruses that target ACE2 are a thing, and SARS-COV-2 binds to the ACE2 of other animals (eg mink) more efficiently than human ACE2.

Originally Posted by michaelsuede

gene edited

Gene editing has been ruled out. The RBD is out of frame meaning it can't be read and copied reliably making it difficult for the virus to replicate. This occurs from time to time in nature, but no researcher would ever do such a thing if they wanted a viable virus.

Originally Posted by michaelsuede

furin cleavage site having

There are other corona viruses with a furin cleavage site, in fact some even have a full furin cleavage site rather than the inefficient partial furin cleavage site in SARS-CoV-2

Originally Posted by michaelsuede

400 meters away from a lab

Again 20Km from the lab. Most of the early cases were that close to the Wuhan fish market though.

Originally Posted by michaelsuede

that was working on creating that exact same virus.

There is no evidence to support such a claim. None at all.

[lomiller]

Originally Posted by michaelsuede

They moved that market and the imagery doesn't line up any more.

The lab isn't located at the WIV headquarters, and while the headquarters is a little closer it's still several Km away and on the opposite side of the river from most of the early cases. The Qyimen market is a little closer, but not as strongly implicated in early cases as the Wuhan Fish Market.

[lomiller]

Originally Posted by michaelsuede

Yeah, you read the DARPA proposal and you realize just how insane they are, then you read the NIAID grant report and realize they simply did the DARPA proposal under the NIAID grant.

They were studying the process under which these viruses can cross over into humans. Any similarity tells us they were on the right track and had correctly identified something with a real danger potential.

In fact from your own link, the sentence IMMEDIATELY after the part you quoted says:

Quote:

We found that the RBDs of these viruses differ from that of SARS-CoV-2 by only one or two residues, bind as efficiently to the hACE2 protein as the SARS-CoV-2 Wuhan strain isolated in early human cases, and mediate hACE2-dependent entry into human cells, which is inhibited by antibodies neutralizing SARS-CoV-2.

So viruses found in the wild that are have even more potential to cross over into humans and are even inhibited by SARS-CoV-2 antibodies.

Later on they say:

Quote:

Our findings therefore indicate that bat-borne SARS-CoV-2-like viruses potentially infectious for humans circulate in Rhinolophus spp. in the Indochinese peninsula.

[michaelsuede]

lomiller, I'd argue with you, but it seems like you can't comprehend what the EHA grant report says, so it would be a waste of my time.

[carlitos]

Originally Posted by michaelsuede

lomiller, I'd argue with you, but it seems like you can't comprehend what the EHA grant report says, so it would be a waste of my time.

You can't tell the difference between 400 meters and 20 Km in this thread, and you can't tell the difference between 50 years and 60 years in the moon landing thread. Maybe you shouldn't be casting aspersions on folks' comprehension skills.

[michaelsuede]

Originally Posted by carlitos

You can't tell the difference between 400 meters and 20 Km in this thread, and you can't tell the difference between 50 years and 60 years in the moon landing thread. Maybe you shouldn't be casting aspersions on folks' comprehension skills.

Great arguments bro. You really took me down.

[lomiller]

Originally Posted by michaelsuede

lomiller, I'd argue with you, but it seems like you can't comprehend what the EHA grant report says, so it would be a waste of my time.

You are clearly the one who doesn't get it. Virologists all over the world do research similar to this, and they do it so they can identify what viruses are a threat to jump species. It's important work if you want to prevent pandemics like the current one.

[dudalb]

Originally Posted by Skeptic Ginger

So what?

Massive cover-up? What nonsense. It only requires the Chinese government and a natural self-preservation of Shi and Daszak to not want to face the music.

Again, this is not the least bit relative.

If you want to use a CT as your evidence against a lab origin hypothesis it does not belong in this thread.

I think there was a cover up in CHina, but it was CHinese officials trying to cover their ass to his all the mistakes they made handling the intial outbreak.
I have noted most real life coverups are not to hide some huge evil plot, but people trying to cover up their screwups.

[dudalb]

Originally Posted by carlitos

A Humanized mouse?

You mean Pinky and the Brain are for real?

[angrysoba]

Originally Posted by dudalb

I think there was a cover up in CHina, but it was CHinese officials trying to cover their ass to his all the mistakes they made handling the intial outbreak.
I have noted most real life coverups are not to hide some huge evil plot, but people trying to cover up their screwups.

Indeed. The closing and scrubbing of the market is no doubt a good example of a cover-up that we know about.

[lomiller]

Originally Posted by dudalb

I think there was a cover up in CHina, but it was CHinese officials trying to cover their ass to his all the mistakes they made handling the intial outbreak.
I have noted most real life coverups are not to hide some huge evil plot, but people trying to cover up their screwups.

It's also entirely possible that identification of Covid as a unique disease is simply non-trivial. Even 6 weeks after the disease first enters the human population you would only expect ~200 infections and perhaps 5-10 hospitalizations. Now split that up between several hospitals and several doctors within each. Is any single doctor really going to see enough cases to distinguish Covid pneumonia from pneumonia cases by other diseases?

Maybe by week 7 (3rd week in Dec) there would be enough cases for people to begin hypothesizing there is a new virus at play, but it is still going to take time to confirm this and begin looking for the virus.

IMO while China's performance in identifying SARS-CoV-2 isn't perfect neither does it suggest any gross incompetence. If a similar new virus were to arise in Florida right now I'm not convinced it would be isolated as quickly as China isolated SARS-CoV-2

[lomiller]

Originally Posted by angrysoba

Indeed. The closing and scrubbing of the market is no doubt a good example of a cover-up that we know about.

That was part of the play book that came from SARS lessons learned. With SARS the market stayed open and continued to create new animal to human crossover events and ultimately contributed to the death toll. The lesson this time is that while the market should still be closed, cleaned and the animals disposed of, everything needs to be sampled first.

[Skeptic Ginger]

Originally Posted by dudalb

I think there was a cover up in CHina, but it was CHinese officials trying to cover their ass to his all the mistakes they made handling the intial outbreak.
I have noted most real life coverups are not to hide some huge evil plot, but people trying to cover up their screwups.

China is refusing to put the genome data back online showing all the coronaviruses the WIV had in their system.
They have refused to share the demographics and exposure history of the initial Wuhan patients.
They called for all the specimens (there were a number of them all over the country) to be destroyed.
Daszak purposefully misled the WHO investigative team to call the lab accident hypothesis a CT before it was ever investigated (according to Tedros at the WHO).
Shi at the WIV denied they had any live coronavirus cultures or live bats but evidence surfaced both existed at the WIV.
Shi claimed the 3 miners in Yunnan died of a fungal infection and subsequently both a master's thesis and a doctoral thesis surfaced contradicting that.
A grant proposal surfaced that Daszak had not properly reported on requesting funds to add the furin cleavage site to an existing strain of coronavirus that already had the ability to infect human respiratory cells.

Those are off the top of my head, there are more. Only the information on the initially infected patients fits your scenario.

[Skeptic Ginger]

More of these reports are coming out:

Jan 31st, Scientists speak out on being silenced when raising concerns about COVID lab leak theory

Quote:

Some scientists have begun speaking out about efforts to silence researchers who raised concerns about the possibility that COVID-19 could have originated in a Chinese lab.

"It shot from every direction from people who we now know were actually thinking exactly the same thing but have chosen to say the opposite, which is extraordinary," Australian Dr. Nikolai Petrovsky, a Flinders University Medicine professor, told Fox News of the backlash he received for voicing concerns that the pandemic may have originated in a lab. ...

The scientists say that there was a top-down effort aimed at protecting the scientific community from negative public attention, with fears spreading among scientists that a public realization that the pandemic may have spread due to gain-of-function research in a lab could hamper future experiments.

Quote:

Many in the scientific community who attempted to speak out about COVID-19's origins were labeled conspiracy theorists in the media and by fellow scientists early on in the pandemic, even though the possibility of human error has now gained renewed attention from experts. ...

But the scientists expressed outrage that there was more of an effort by China, some scientists and media to cover up how the pandemic may have started, leaving little hope for a push for stricter regulation.

IOW, how it started, not how it was mishandled initially.


Regardless Fox News is one of the few news sources paying attention, these researchers are from other countries in addition to being from the US:
Scientists speak out about how they were ignored, even silenced, when they suggested a lab leak in 2020

Quote:

Speaking to Fox News, scientists from the U.S., Britain, Germany, Israel and Australia have recounted that it was difficult to publish research about the possibility that the COVID-19 pandemic began due to a lab leak, and that they found themselves shunned by other scientists, even when those scientists themselves found the lab-leak theory plausible.

"We got our heads shot from every direction, from people who we now know were actually thinking exactly the same thing, but have chosen to say the opposite," Nikolai Petrovsky, a professor of medicine at Flinders University in Australia, told Fox News Digital. ...

The lab leak theory has now become mainstream, but for a long time most outspoken scientists rejected it, including those at the very top. German physicist Roland Wiesendanger called this move a betrayal of science.

"If famous and top virologists are not sticking to the truth anymore, then we have no basis in science anymore to make progress," Wiesendanger told Fox News Digital.

Quote:

Despite plenty of evidence that a lab leak was highly likely, even established medical journals refused to publish the scientists' work.

Petrovsky – who with the help of Oracle-- used their super computers to map the virus, thereby showing that it likely came from a lab – said he received blanket rejections from editors at medical journals who called his work "too hot to handle."

He was also told it would harm relations with China – a country that has such a huge influence over the medical community and research papers.

[Planigale]

Originally Posted by lomiller

It's also entirely possible that identification of Covid as a unique disease is simply non-trivial. Even 6 weeks after the disease first enters the human population you would only expect ~200 infections and perhaps 5-10 hospitalizations. Now split that up between several hospitals and several doctors within each. Is any single doctor really going to see enough cases to distinguish Covid pneumonia from pneumonia cases by other diseases?

Maybe by week 7 (3rd week in Dec) there would be enough cases for people to begin hypothesizing there is a new virus at play, but it is still going to take time to confirm this and begin looking for the virus.

IMO while China's performance in identifying SARS-CoV-2 isn't perfect neither does it suggest any gross incompetence. If a similar new virus were to arise in Florida right now I'm not convinced it would be isolated as quickly as China isolated SARS-CoV-2

I agree. We only identify a causative organism for a minority of people with pneumonia admitted to hospital maybe 10%. I was impressed that China picked up a novel virus as quickly as they did. I don't think the UK would be as good as China. China did a really good job. They picked up that there was a new syndrome, they investigated it, identified a novel corona virus on an EM of a lung biopsy, sequenced it and released the sequencing data all within a few weeks. All done very quickly with no evidence of any delay or hold up.

[Skeptic Ginger]

What nonsense! It was a pandemic that started abruptly in Wuhan and spread rapidly to hundreds of people. Hospitals were quickly filling up. The fatality rate was high where it showed up. There were milder cases but it didn't take long for the fatalities to begin.

How on Earth would any modern country miss that? China did not miss it.

I've posted before about the beginning of the SARS epidemic. We were hearing about it for a couple months as it began because healthcare workers in Guangdong were not just getting infected from patients in the hospital, they were also dying from it. No modern country would have missed that one either.

PNEUMONIA - CHINA (GUANGDONG): RFI RFI means request for information.

Quote:

Date: 10 Feb 2003
From: Stephen O. Cunnion, MD, PhD, MPH <cunnion@erols.com>

This morning I received this e-mail and then searched your archives
and found nothing that pertained to it. Does anyone know anything
about this problem?
"Have you heard of an epidemic in Guangzhou? An acquaintance of mine
from a teacher's chat room lives there and reports that the
hospitals there have been closed and people are dying."
--

Sometimes these reports don't amount to anything. That one however, did not go unnoticed.

Further down in the post:

Quote:

Commenting on the problem of pneumonia on the Mainland, Dr Yeoh said
the Department of Health has already touched base with the Guangdong
authorities to learn more about the type of infection prevalent
there. The department will also determine whether there is any
particular risk of that infection coming to Hong Kong.
He assured the public that the Government is always on the alert, as
the Department of Health has a very good communicable disease
surveillance system.

One day later multiple reports came in:

Quote:

An unidentified pneumonia virus has killed 5 people and left hundreds
hospitalized in southern China, while rumors of a surging death toll
prompted frightened residents to stock up on antibiotics, officials
said Tuesday.
Health officials said the outbreak in a region of Guangdong province
near Hong Kong had been brought under control. They said Health
Ministry investigators sent from Beijing were trying to find the
source of the disease.
Some 300 people have been hospitalized, one third of them doctors,
nurses, and other health workers, said an official of the provincial
Disease Prevention and Control Center. He said 59 of those people had
been treated and released. Officials wouldn't give any details about
who was killed by the disease or when.
Rumors that hundreds of people had died prompted residents to clear
store shelves of antibiotics and pay inflated prices for white
vinegar for use as disinfectant, officials said. Photos in Hong Kong
newspapers showed people in Guangdong wearing surgical masks in hopes
of avoiding infection. Hospitals have been given extra antibiotics,
officials said.

It was downplayed by the Chinese authorities in public messaging, that is par for the course. But you can't hide this kind of thing, you just can't. And China did not miss the first SARS outbreak.

It's not single cases of pneumonia that are treated empirically without culturing an organism. It's large or particularly deadly outbreaks. And more than a few people/agencies are monitoring for such outbreaks.

We keep a close eye on new influenza strains typically because large numbers of wild birds and poultry die. When cases show up in people, it is noticed.

One place a pandemic can start and not be noticed immediately is if said jump to humans occurs in a third world country that lacks a public health infrastructure. But once it reaches a modern country, it's not a stealthy affair. The 2009 new variant flu was picked up early on because the US has a flu detection system set up.

Name one other potentially pandemic pneumonia outbreak that went unnoticed.


ETA: None of which I might add, has any bearing on the actions the Chinese government continues to take take to obscure the origin of the COVID pandemic, and, which has nothing to do with the second issue of covering up any kind of botched initial response.

[angrysoba]

Originally Posted by lomiller

That was part of the play book that came from SARS lessons learned. With SARS the market stayed open and continued to create new animal to human crossover events and ultimately contributed to the death toll. The lesson this time is that while the market should still be closed, cleaned and the animals disposed of, everything needs to be sampled first.

Sorry, you're right. It was indeed scrubbed because it was clearly believed (probably correctly, but we cannot say for certain) that it was the epicentre of the pandemic.

The initial response to the outbreak of some unknown pathogen is to stop the spread as much as possible, rather than to try to collect specimens.

[Planigale]

Originally Posted by Skeptic Ginger

What nonsense! It was a pandemic that started abruptly in Wuhan and spread rapidly to hundreds of people. Hospitals were quickly filling up. The fatality rate was high where it showed up. There were milder cases but it didn't take long for the fatalities to begin.

How on Earth would any modern country miss that? China did not miss it.

.....

It's not single cases of pneumonia that are treated empirically without culturing an organism. It's large or particularly deadly outbreaks. And more than a few people/agencies are monitoring for such outbreaks.

We keep a close eye on new influenza strains typically because large numbers of wild birds and poultry die. When cases show up in people, it is noticed.

One place a pandemic can start and not be noticed immediately is if said jump to humans occurs in a third world country that lacks a public health infrastructure. But once it reaches a modern country, it's not a stealthy affair. The 2009 new variant flu was picked up early on because the US has a flu detection system set up.

Name one other potentially pandemic pneumonia outbreak that went unnoticed.


ETA: None of which I might add, has any bearing on the actions the Chinese government continues to take take to obscure the origin of the COVID pandemic, and, which has nothing to do with the second issue of covering up any kind of botched initial response.

At the time that China notified WHO 31/12/2019, there were 27 cases of pneumonia later attributed to a novel coronavirus with 7 of those critical across Wuhan a city of 11 million. Syndromic surveillance tends to focus on those with a severe acute respiratory syndrome, usually defined by needing ICU. With a population of 11 million one might expect 35,000 cases of pneumonia a year, weighted towards winter that is one hundred new cases per day, most of which will have no causative organism identified. At that time person to person transmission had not been confirmed. The organism was subsequently identified as a novel coronavirus 07/01/2020, SARS and MERS were excluded on 05/01/2020. By 07/01/2020 there were 44 known cases, the first death was 11/01/2020. I am afraid your statement;

Quote:

It was a pandemic that started abruptly in Wuhan and spread rapidly to hundreds of people. Hospitals were quickly filling up. The fatality rate was high where it showed up.

Is simply exaggeration, this was not the case when China announced the outbreak of a pneumonia due to an unknown pathogen.

All cases of pneumonia are treated empirically, there is a target treatment time of less than four hours from admission, so treatment is always started before the cause is known.

[angrysoba]

No time to read it now, but Michael Worobey et. al have a paper entitled "The Huanan market was the epicenter of SARS-CoV2 emergence"

https://zenodo.org/record/6299116#.YhpUK-jP1PZ

and...

"SARS-CoV2 emergence very likely resulted from at least two zoonotic events"

https://zenodo.org/record/6291628#.YhpUnOjP1PY

Should be interesting reading, and no doubt some people will dispute the findings.

I will reserve judgment until I have read them and applied my expertise in Ukrainian-Russian relations virology.

[Skeptic Ginger]

When you do read it tell us how he hypothesizes without the information China is refusing to disclose on those first cases.

[lomiller]

Originally Posted by Skeptic Ginger

When you do read it tell us how he hypothesizes without the information China is refusing to disclose on those first cases.

Would you hand over the private medical information on one of your patients to a foreign country or to internet "sleuths" trying to dig up evidence of a conspiracy?

As for the conclusions reached in these papers, there is already more then enough information already available. The suggestion that "maybe we could find something different if China would just release the complete medical history of these people" is just grasping at straws.

[angrysoba]

Originally Posted by Skeptic Ginger

When you do read it tell us how he hypothesizes without the information China is refusing to disclose on those first cases.

Well you seem to manage it okay.

Do I assume this means you are not going to read it yourself?

[Skeptic Ginger]

Originally Posted by angrysoba

Well you seem to manage it okay.

Yes, because I'm going by the mountain of evidence the origin was a lab leak. And China's refusal to share information/evidence that should exonerate them is one bit of that evidence.

Originally Posted by angrysoba

Do I assume this means you are not going to read it yourself?

If you find Worobey found the missing information about those early patients let me know and I'll read it. Otherwise, it doesn't sound like there is anything new there. All he's done is add details, not evidence, to his initial hypothesis.

His initial hypothesis BTW, was not accepted by other scientists as a smoking gun. Rather the comments were, that's interesting but not conclusive.

And while you're looking for a red herring to dismiss my POV, did you ever read Quay's analysis that showed the initial infected patients that ended up in hospitals followed in geographic proximity to the number 2 metro line that also went from the WIV into other parts of Wuhan?

Seems to me you dismissed everything Quay had to say because his specialty was breast cancer and he had a for-profit business.

BTW, I got the book, Spillover, from the library. So far I see nothing that adds to the debate in this thread.

[angrysoba]

Originally Posted by Skeptic Ginger

Yes, because I'm going by the mountain of evidence the origin was a lab leak. And China's refusal to share information/evidence that should exonerate them is one bit of that evidence.

"mountain of evidence". Sure.

Originally Posted by Skeptic Ginger

If you find Worobey found the missing information about those early patients let me know and I'll read it. Otherwise, it doesn't sound like there is anything new there. All he's done is add details, not evidence, to his initial hypothesis.

His initial hypothesis BTW, was not accepted by other scientists as a smoking gun. Rather the comments were, that's interesting but not conclusive.

They are not looking for smoking guns. They are looking for evidence and drawing conclusions based on the propensity of scientific evidence.

The lab leakers tend to make claims based on assumptions about motives ad see smoking guns all over the place.

According to Worobey, the scientists in this case find evidence that the samples from the Huanan Market point to two individual lineages presumably from two spillovers, and likely from racoon dogs.

Here is a Twitter thread from Worobey about it. Not read the paper yet. It is a pre-print, so it will be interesting to see what happens when/if it passes peer review and what other scientists make of it.

Link

Originally Posted by Skeptic Ginger

And while you're looking for a red herring to dismiss my POV, did you ever read Quay's analysis that showed the initial infected patients that ended up in hospitals followed in geographic proximity to the number 2 metro line that also went from the WIV into other parts of Wuhan?

Seems to me you dismissed everything Quay had to say because his specialty was breast cancer and he had a for-profit business.

Are you talking about Quay's Bayseian analysis?

I have skimmed through the paper and I cannot make head or tail of his argument. It just looks like he arbitrarily attaches probabilities to cherry-picked datapoints.

Originally Posted by Skeptic Ginger

BTW, I got the book, Spillover, from the library. So far I see nothing that adds to the debate in this thread.

Good. You won't find anything directly related to Covid-19 of course, because it was written a few years before it.

What I found interesting about the book was the process by which zoonotic origins are tracked down and how long it can take and how long it takes even for the virologists to make definitive statements about the route a virus takes to get from its initial host, sometimes through an amplifying animal and then to humans and how environmental pressures have made humans and wild animals more in contact and increased the chances of spillover.

However, I expect you will also be horrified and interested by the chapter on SARS and the bat hunt that the author goes on which he himself thinks is a possible route of infection.

[angrysoba]

There is some good criticism of the study from the same guys who helped expose the ivermectin fraud. The main point that one of them brings up is that while the study does make a plausible case for a market spillover there is a problem that the market was more extensively searched for clues than other areas simply because it was the presumed spillover area from the beginning. Similar amounts of exhaustive testing were not done elsewhere for this reason (not to say other places were not tested, but just not to the same extent).

[Skeptic Ginger]

Originally Posted by angrysoba

"mountain of evidence". Sure.

Yes, there is.

Originally Posted by angrysoba

They are not looking for smoking guns. They are looking for evidence and drawing conclusions based on the propensity of scientific evidence.

And that did not happen with Worobey's hypothesis. Bloomberg said, for example because it is one opinion linked to upstream, that he couldn't fault the science but it didn't prove anything.

Originally Posted by angrysoba

The lab leakers tend to make claims based on assumptions about motives ad see smoking guns all over the place.

You always want to trash me based on other people's claims. "Lab leakers" is a very broad category.

Originally Posted by angrysoba

According to Worobey, the scientists in this case find evidence that the samples from the Huanan Market point to two individual lineages presumably from two spillovers, and likely from racoon dogs.

Pure speculation, nothing more.

Originally Posted by angrysoba

Here is a Twitter thread from Worobey about it. Not read the paper yet. It is a pre-print, so it will be interesting to see what happens when/if it passes peer review and what other scientists make of it.

Link

Ah yes, and in the meantime like a lot of propaganda the headlines make it sound like this work supports more than it actually does. People soak up the headlines the same way you and others soaked up Daskin's slight-of-hand and a year when he promoted the false claim the lab leak hypothesis was a CT.

There was never any evidence the lab leak hypothesis was a CT, nor was there any evidence it was off the table.

Does it bother you at all that Daskin's cover up might be because he and Shi were both implicated in this horrible tragedy?

Daszak promoted the lab leak CT from the very beginning.
Tedros from the WHO said after the first investigation that Daskin dismissed the lab leak hypothesis before it was ever investigated.
Many scientists complained that Daszak should not be on the WHO investigative team because of his bias, perceived or real.
Many of the scientists objected to any findings with Daszak on the investigative team. And now they would like an actual investigation.
But with China holding evidence back no such unbiased investigation can take place.

Originally Posted by angrysoba

Are you talking about Quay's Bayseian analysis?

I have skimmed through the paper and I cannot make head or tail of his argument. It just looks like he arbitrarily attaches probabilities to cherry-picked datapoints.

No, not that paper. Give me a few minutes and I'll edit the link in here.

Originally Posted by angrysoba

Good. You won't find anything directly related to Covid-19 of course, because it was written a few years before it.

What I found interesting about the book was the process by which zoonotic origins are tracked down and how long it can take and how long it takes even for the virologists to make definitive statements about the route a virus takes to get from its initial host, sometimes through an amplifying animal and then to humans and how environmental pressures have made humans and wild animals more in contact and increased the chances of spillover.

However, I expect you will also be horrified and interested by the chapter on SARS and the bat hunt that the author goes on which he himself thinks is a possible route of infection.

I'm not horrified by anything in the book I've read so far because all of it is stuff I'm quite familiar with. I've been working in this field for 30+ years.

And as for tracking down the SARS origin, talk about cherry picking, look in the mirror. They discovered the proximate source of SARS within a couple months. What you are talking about and trying to make it sound like the bat source discovered in Yunnan was the proximate source, was the source that infected the proximate source.

[angrysoba]

Originally Posted by Skeptic Ginger

Yes, there is.

If you say so.

Evidence 1: It started in Wuhan.
Evidence 2: See evidence 1.

Originally Posted by Skeptic Ginger

And that did not happen with Worobey's hypothesis. Bloomberg said, for example because it is one opinion linked to upstream, that he couldn't fault the science but it didn't prove anything.

Who is Bloomberg?

Originally Posted by Skeptic Ginger

You always want to trash me based on other people's claims. "Lab leakers" is a very broad category.

Not everything is about you.

Originally Posted by Skeptic Ginger

Pure speculation, nothing more.

Have you read it?

Originally Posted by Skeptic Ginger

Ah yes, and in the meantime like a lot of propaganda the headlines make it sound like this work supports more than it actually does. People soak up the headlines the same way you and others soaked up Daskin's slight-of-hand and a year when he promoted the false claim the lab leak hypothesis was a CT.

There was never any evidence the lab leak hypothesis was a CT, nor was there any evidence it was off the table.

Does it bother you at all that Daskin's cover up might be because he and Shi were both implicated in this horrible tragedy?

Daszak promoted the lab leak CT from the very beginning.
Tedros from the WHO said after the first investigation that Daskin dismissed the lab leak hypothesis before it was ever investigated.
Many scientists complained that Daszak should not be on the WHO investigative team because of his bias, perceived or real.
Many of the scientists objected to any findings with Daszak on the investigative team. And now they would like an actual investigation.
But with China holding evidence back no such unbiased investigation can take place.

Who is Daskin?

Originally Posted by Skeptic Ginger

No, not that paper. Give me a few minutes and I'll edit the link in here.

Is this paper a recent paper? Was it published in the peer-reviewed literature? Is it taken seriously by anyone in the field of virology?

Originally Posted by Skeptic Ginger

I'm not horrified by anything in the book I've read so far because all of it is stuff I'm quite familiar with. I've been working in this field for 30+ years.

And as for tracking down the SARS origin, talk about cherry picking, look in the mirror. They discovered the proximate source of SARS within a couple months. What you are talking about and trying to make it sound like the bat source discovered in Yunnan was the proximate source, was the source that infected the proximate source.

Hmmm...? Who is cherry-picking? SARS was the exception rather than the rule for tracking down a new virus source relatively quickly from what I can gather. Most viruses take a long time to track down especially when the putative source (the market) had been scrubbed down as part of the countermeasures to the spread of the virus.

[Skeptic Ginger]

I missed the 2 hour editing window.

No, not that paper. Give me a few minutes hours (I got busy with other things) and I'll edit the link in here.

This is the paper you say you didn't understand:
A Bayesian analysis concludes beyond a reasonable doubt that SARS-CoV-2 is not a natural zoonosis but instead is laboratory derived
If you recall, you dismissed Quay not based on the paper but on the fact you weren't impressed by his background.

You yourself linked to this information on Quay while you called him unqualified:

Quote:

Dr. Steven Quay has 360+ published contributions to medicine and has been cited over 10,000 times, placing him in the top 1% of scientists worldwide. He holds 87 US patents and has invented seven FDA-approved pharmaceuticals which have helped over 80 million people....

He received his M.D. and Ph.D. from The University of Michigan, was a postdoctoral fellow in the Chemistry Department at MIT with Nobel Laureate H. Gobind Khorana, a resident at the Harvard-MGH Hospital, and spent almost a decade on the faculty of Stanford University School of Medicine.

Here's a later version of the Bayesian analysis paper:

Quote:

A small but growing number of scientists have considered another hypothesis: that an ancestral bat coronavirus was collected in the wild, genetically manipulated in a laboratory to make it more infectious, training it to infect human cells, and ultimately released, probably by accident, in Wuhan, China. For most of 2020 this hypothesis was considered a crackpot idea, but in the last few weeks, more media attention has been given to the possibility that the Wuhan Institute of Virology, located near the Wuhan city center and with a population of over 11 million inhabitants, may have been the source of the field specimen collection effort, laboratory genetic manipulation, and subsequent leak. On January 15, 2021, the U.S. Department of State issued a statement requesting the WHO investigation of the origin of COVID-19 include specific assertions related to a laboratory origin of the pandemic.2Given the strong sentiment in the scientific community in favor of a zoonosis and the massive effort undertaken by China to find the natural animal source, one can assume that any evidence in favor of a natural origin, no matter how trivial, would become widely disseminated and known. This provides a potential evidence bias within the scientific community in favor of a natural origin which isn’t quantifiable but should be kept in mind.

Here's the paper on the metro line:

Where Did the 2019 Coronavirus Pandemic Begin and How Did it Spread? The People's Liberation Army Hospital in Wuhan China and Line 2 of the Wuhan Metro System Are Compelling Answers

Quote:

The origin of the SARS-CoV-2 coronavirus that has caused the COVID-19 worldwide pandemic remains unknown. Here I report that the earliest genomic cluster is a group of four patients associated with the General Hospital of Central Theater Command of People's Liberation
Army (PLA) of China in Wuhan. This cluster contains the “Founder Patients” of both Clade A and Clade B, from which every SARS-CoV-2 coronavirus that has infected every patient with COVID-19 anywhere in the world has arisen, including the infection of the President of the United States.The observation that the genomic files for these patients were created on December 10, 2019 but the PLA Hospital did not record the collection of the specimens until weeks later is unusual andunexplained. However, it would be consistent with a vaccine challenge clinical trial (in which case files are set up in anticipation of getting samples later) or it suggests that the collection dates were actually before December 10, 2019 (in which case the reported dates for specimen collection are not accurate but may have been recorded incorrectly to suggest the infection was spreading laterthan it really was). The PLA Hospital is about one mile from the Wuhan Institute of Virology (WIV) and the closest hospital to WIV. Both the PLA Hospital and WIV are serviced by Line 2 of the Wuhan Metro System. The Hunan Seafood Market is also located adjacent to Line 2. All patients between December 1st, 2019 and early January 2020 were first seen at hospitals that are also serviced by Line 2 of the Metro system. With hospitals located near seven of the nine Metro Lines, the likelihood that all early patients were seen at hospitals only near Line 2 by chance is about 1 in 68,500 (p-value = 0.0000146). The inference then would be that the early spread of SARS-CoV-2 was through human-to human infection on Line 2. Line 2 connects to all eight other lines of the Wuhan Metro System (1, 3, 4, 6, 7, 8, 11, and Yanglu) facilitating rapid spread in Wuhan and Hubei Province, and also services both the high speed rail station (Hankou Railway Station), facilitating rapid spread throughout China, and the Wuhan International Airport (Tianhe International Airport), facilitating rapid spread throughout Asia, Europe, and to the United States. In fact, direct human-to-human spread from the Reference Sequence patient to patients around the world is suggested by an unexpectedly reduced genome base substitution rate seen in patient specimens in cities with direct flights from Wuhan.

In conclusion, Line 2 of the Wuhan Metro System services the PLA Hospital with the first genomic cluster of patients with COVID-19, the hospitals where patients first went in December 2019 and early January 2020, and is the likely conduit for human-to-human spread throughout Wuhan, China, and the world. The Hunan Seafood Market, Wuhan Institute of Virology, and the Wuhan CDC, all locations suggested to be the possible source of SARS-CoV-2 in Wuhan, are also all serviced by Line 2 of the Metro system, suggesting this public transit line should become the focus for further investigations into the origin of this pandemic.

The seafood market was ruled out early on. That it is being revisited is fine, but unfortunate it is being revisited without any new evidence like information on the earliest patients. That information is still being kept secret by the Chinese government for inexplicable reasons.


This was noted early on in the discussion and it remains relevant today:

Originally Posted by Sherkeu

Why do some here seem so against skeptics exploring and looking at various information (reliable, total propaganda, or perhaps half-truths included). Some are dead ends, some are discounted after further reading, and some lead to more pieces to be explored. Minds are changed and things evolve in time as more research is done. That is how it goes for me and I enjoy learning. YMMV.

I'll look at your last post tomorrow.

[angrysoba]

Originally Posted by Skeptic Ginger

I missed the 2 hour editing window.

No, not that paper. Give me a few minutes hours (I got busy with other things) and I'll edit the link in here.

This is the paper you say you didn't understand:
A Bayesian analysis concludes beyond a reasonable doubt that SARS-CoV-2 is not a natural zoonosis but instead is laboratory derived
If you recall, you dismissed Quay not based on the paper but on the fact you weren't impressed by his background.

You yourself linked to this information on Quay while you called him unqualified:


Here's a later version of the Bayesian analysis paper:



Here's the paper on the metro line:

Where Did the 2019 Coronavirus Pandemic Begin and How Did it Spread? The People's Liberation Army Hospital in Wuhan China and Line 2 of the Wuhan Metro System Are Compelling Answers

The seafood market was ruled out early on. That it is being revisited is fine, but unfortunate it is being revisited without any new evidence like information on the earliest patients. That information is still being kept secret by the Chinese government for inexplicable reasons.


This was noted early on in the discussion and it remains relevant today:



I'll look at your last post tomorrow.

Nice use of the passive voice there:

"The seafood market was ruled out early on" by whom?

It's funny how you complain about lab leaks being ruled out and saying that this is a nefarious plot to conceal the truth, but you state that "The seafood market was ruled out early on" as if this is an established objective fact of the universe.

[carlitos]

Paywall link to New York Times article on a study finding that covid originated in the Wuhan Wet Market (2 cases) and the Wuhan area via animal-to-human transmission. I'm working mobile and can't do a lot of excerpting now.

"New Research Points to Wuhan Market as Pandemic Origin"

This is apparently a different study from the one last november "First Known Covid Case Was Vendor at Wuhan Market ..."

[Skeptic Ginger]

I still haven't looked at your posts yet angrysoba, I will eventually. What I did do because the supposed argument that a second wet market was involved has been all over the news without any decent rebuttal is look into that.

I have a few issues and questions.

1) I have not yet seen any evidence of this second wet market. I brought this up pages back and no one has clarified where this evidence came from. The WHO report had a somewhat unclear reference to the second wet market that one of the earliest patients who had not been to the seafood market had gone to. The market was not named or even identified. A much earlier reference was made that a relative of one of the cases had been to a different market. Nothing more was said about that. And IIRC someone in this thread said they'd found another market that had evidence of COVID in a drain. No more has been said about that, in particular the source of this information and if the genome was looked at.

Nothing connects the other earlier patients to this second wet market. In fact, the note from early on which said a relative had been to another market noted none of the other earliest patients (the ones China is now refusing to share more information about) had any connection to another wet market.

2) The A & B lineages have had more than one hypothesis as to how they came to be including this one which both Andersen and Worobey were co-authors of:

Evidence Against the Veracity of SARS-CoV-2 Genomes Intermediate between Lineages A and B

Quote:

Here, we investigate the veracity of these sequences and conclude it is probable that neither C/C nor T/T genomes circulated at the start of the COVID-19 pandemic; they are likely the result of sequencing or bioinformatics issues. ...
Conclusion
As discussed in Worobey et al. (2020) (4), the repeated occurrence of numerous derived mutations on either side of a given mutation is difficult to reconcile through homoplasy events. Of the 77 mutations seen in C/C intermediate genomes, 32 (41.6%) would need to be homoplasies if these C/C intermediates actually existed. Similarly, 7 (58.3%) of the 12 mutations seen in T/T genomes would need to be homoplasies if the T/T intermediates truly existed. These apparent homoplasies can arise from issues regarding sample preparation, contamination, sequencing technology, and/or consensus calling approaches (3). In particular, it seems likely that the nucleotide of the Hu-1 lineage B reference is frequently being called at these two sites.

These findings cast substantial doubt on the veracity of C/C or T/T intermediate genomes in early 2020. We suggest that these early C/C and T/T genomes are erroneous and should be excluded from phylogenetic analyses.

Maybe I'm misunderstanding that and by intermediate genomes they mean a genome indicating A preceded B. But I am not misunderstanding the conclusion the A & B lineages may just be errors. This sentence is clear: "it is probable that neither C/C nor T/T genomes circulated at the start of the COVID-19 pandemic; they are likely the result of sequencing or bioinformatics issues."

Given how much has now been discussed in the thread about the way the sequencing can involve contamination, it makes sense. But apparently Worobey has had a change of heart, or he's had to make this fit in his new hypothesis.

3) If as Worobey claims lineage A & B came from two different markets and perhaps two different source animals, where were those source animals infected and why is there no evidence or any kind of trail? Why didn't these two (or more) infected source animals end up in other wet markets besides two in Wuhan? It's not like Wuhan is some kind of hub for wet markets. And Wuhan is a very large city, how did all the patients end up in one location?

Worobey's hypothesis ignores the problem that in looking at thousands and thousands of wild animals farmed and/or captured from the wild then sold in wet markets, no evidence of a trail has been found.

4) With SARS 1 no reservoir was found in civet cats which is what led the researchers to find the horseshoe bats. What was found was the civet cats' exposure to the bats within the market or in transit to the market. There's no evidence live bats were sold in the seafood market. Even after the market was cleaned up and shut down there was still a record of what had been sold there including which wild animals were there and bats were not on the list.

In addition, was this other wet market also closed down and cleaned up? Seems like that would be an important bit of information here. If the WHO team had found evidence of this other wet market, was it closed down? And if it was, why is there only a vague note about it in the WHO team's report?

5) With SARS 1 the virus circulated in humans for a month or so becoming more and more adapted to human to human transmission. The first patients infected directly from the two wet markets in Guangdong had milder disease. There's no evidence SARS 2 circulated among humans before abruptly turning up in Wuhan. Worobey is sure lineages A & B did not come about during human to human transmission. How does he explain the sudden introduction of severe disease readily transmitted from human to human from two separate wet markets and maybe even two separate source animals? Where did the adaptation to humans take place?

The patients infected at the seafood market did not have mild disease. Nor did they have infections with strains that were initially mild but later adapted to human to human transmission.

6) Finally and most revealing, it's a huge coincidence SARS 2 turned up in Wuhan close to the WIV and the Chinese CDC where they were also studying coronaviruses. Now the claim is it turned up twice! And in two separate lineages that were only a few mutations different! And the virus was ready to go in humans from the get-go. When you multiply rare odds by rare odds you get incredibly unlikely odds.

Where is the connection to bats the source animals in two different wet markets were exposed to? Wuhan is not exactly a source of frequent bat consumption.

Nature: Animal sales from Wuhan wet markets immediately prior to the COVID-19 pandemic

Quote:

Here we document 47,381 individuals from 38 species, including 31 protected species sold between May 2017 and November 2019 in Wuhan’s markets. We note that no pangolins (or bats) were traded, supporting reformed opinion that pangolins were not likely the spillover host at the source of the current coronavirus (COVID-19) pandemic.

Oxford News Blog: The wet market sources of Covid-19: bats and pangolins have an alibi

Quote:

This research, begun before Covid-19 focused a spotlight on these markets, was actually motivated by a study of tick-borne (no human-to-human transmission) Severe Fever with Thrombocytopenia Syndrome, which put our team in the right place at the right time to document the wild animals sold in these markets in the lead up to the pandemic. Our investigation, published today in Nature-Scientific Reports, found that both bats and pangolins had an alibi – neither was there!

Worobey is so sure these two lineages did not diverge within humans after they became infected. That could be explained if there was some other place the source animals had contact with infected bats. But where was that? And how did animals in two different Wuhan wet markets coincidentally get infected with lineages A & B, both lineages that were readily transmitted from person to person, and both lineages that were so similar genetically?

[angrysoba]

Originally Posted by Skeptic Ginger

3) If as Worobey claims lineage A & B came from two different markets ....

That is not what is being claimed, as far as I can see.

They claim it came from the same market as both lineages were present at the market.

[angrysoba]

Originally Posted by Skeptic Ginger

4) With SARS 1 no reservoir was found in civet cats which is what led the researchers to find the horseshoe bats. What was found was the civet cats' exposure to the bats within the market or in transit to the market. There's no evidence live bats were sold in the seafood market. Even after the market was cleaned up and shut down there was still a record of what had been sold there including which wild animals were there and bats were not on the list.

I don't think this is correct. There is no claim that the civets were infected in the markets.

Civets had presumably been infected with SARS somewhere close to where the bats lived, in Yunnan. (infected civets also showed up in other areas such as Shenzhen - which is where, I believe, infected civets were originally discovered, and also in Hubei, the province in which Wuhan is. This is circumstantial evidence that there is a plausible route from the countryside to Wuhan).

So nobody is looking for bats in the Huanan Market. It is irrelevant whether there were bats, live or otherwise there.

However, from what I gather Worobey et al do think that raccoon dogs were sold in the Huanan Market and they may have been infected somewhere on the wildlife trade route.

I think you should either read the Twitter thread that I linked to above in which Worobey summarizes the findings of the writers of the article (there are 18 authors altogether with impressive credentials), or maybe go straight to the paper itself.

In fact, it is one of two papers out right now which make the case for spillover.

I admit that I have not yet read them myself, and they have not been peer-reviewed yet, but I lack the competence in this field to make any critical appraisal of them. I can only go on the word of others in the field.