Origins of Covid

[angrysoba]

Okay, this is interesting.

This is from an older TWiV, back in the fairly early days of the pandemic. Ian Lipkin is the guest and he is calling in from China and suffering from Covid-19.

Ian Lipkin is talking with the host about how he heard about the virus in December 15th, so he has been pretty consistent in saying this.

This comes up at about the 17-minute mark. He says it was from a Chinese professor who is part of an underfunded international program called GIDEON (Global Infectious Disease Epidemiology Network).

Lipkin was one of the signatories of the Proximal Origins paper, but I think he may be somewhat on the fence about the possibility of a leak.

Interestingly, this is, I think, the first TWiV I ever listened to.

[Skeptic Ginger]

Originally Posted by angrysoba

I'm addressing a specific argument that you have made. I think it is worth examining each one if you think it is worth making the argument.

You argue that the virus could not have been so adapted to humans in a short space of time because:

a) SARS-1 took longer
b) H5N1 has taken even longer

But by that argument, SARS-1 could not have adapted so quickly because it did so quicker than H5N1.

This is a straw man. You have and continue to distort my argument. But no worries, carry on. I'll move on.

Quote:

There is an easy answer to this point: some viruses achieve pandemic potential quicker than others by mutational chance.

Obviously.

Where did the furin cleavage site come from?

Quote:

Sure. And one day, maybe we or someone will. But the "needs to explain why..." also applies to every other theory.

The evidence leans toward the lab-leak hypothesis. IIRC your main argument is that natural spillovers are more common therefore the odds are higher this was a natural spillover. Is that your main argument?

Do you agree or disagree that Worobey's hypothesis has serious problems? In particular he has used a faulty underlying premise that he's working with the earliest genomes.

Quote:

I read a whole book about it and have been following a lot of scientists talking about this. Frankly, it requires far more knowledge, and ultimately it requires the type of knowledge that I will never attain. In fact, even for the top experts, there are a LOT of areas of incomplete knowledge.

I've been working with infectious diseases including species jumps for 30 years. The knowledge is not that incomplete. Care to cite an example so I have a better idea what you are talking about?

Quote:

Then there is no point in you comparing SARS-1 and H5N1 and drawing conclusions about how possible it was to adapt to humans so quickly.

They are relevant examples in this case. You don't have to agree.

Quote:

Okay, I will have to look at that.

You still haven't??????

Quote:

So there is a bit of a contradiction here, I think.

You are expecting a viral outbreak elsewhere in the country to be easily picked up by the surveillance system.

Yet, if that is true, why did it not pick up the early (Sept-Oct) outbreak.

How do you know it didn't? What we can say is there was no evidence of an outbreak outside of Wuhan, and no evidence of initial spread from any location outside of Wuhan.

Quote:

Worobey has an answer to that, which is that the system as set up is not sensitive enough to small numbers of cases. He also, in fact, points out that even SARS-CoV2 was not identified through this system.

If the actual pandemic itself was not detected by it, we cannot assume that the virus's precursor must be.

Unless you look at the MOA/TopHap there is no point in discussing Worobey's work.

[Skeptic Ginger]

It's a pain going back to the beginning of the thread because it's saturated with the false belief the lab-leak hypothesis is a CT and with all the Trumpian and alt-right contamination of the data. So I'll just be pulling from some of the themes.

Like this one about the military games in Oct 2019 in China spreading COVID cases. We are still stuck with the paucity of data on whether ill participants were ever diagnosed with COVID. But there was this study:

The impact of the World Military Games on the COVID-19 pandemic

Quote:

There is a correlation between the number of individuals who travelled to the event and the number of COVID-19 cases in the country to which they returned. Whether this explains the rapid spread of the pandemic or not is not known definitively. However, this study shows a mathematical model to predict the number of COVID-19 cases in a country as a result of each infected individual travelling to that country.

It's also worth noting China claims the athletes brought COVID to Wuhan. That's a bit of a contradiction if they also say the first cases were in early Dec.


BBC June 2020: Coronavirus: Satellite traffic images may suggest virus hit Wuhan earlier

Quote:

Harvard researchers say satellite images show an increase in traffic outside five hospitals in the Chinese city from late August to December.

The traffic spike coincided with a rise in online searches for information on symptoms like "cough" and "diarrhoea". ...

In one case, researchers counted 171 cars parked at one of Wuhan's largest hospitals, Tianyou Hospital in October 2018.

Satellite data from the same time in 2019 showed 285 vehicles in the same place, an increase of 67%.

BBC: The author Catherine Mayer believes it's possible her late husband Andy Gill - guitarist and co-founder of Gang of Four - may have been one of the earliest to be struck down by Covid-19. He was 64.

Quote:

Andy returned from a tour in China on 23 November 2019 and fell ill in December with many symptoms of Covid-19. He died in St Thomas's hospital on 1 February. Doctors did consider whether it might be this new virus they were hearing about, but the timelines didn't seem plausible. ...

... She began doing her own detective work and discovered that his tour manager had fallen seriously ill with a respiratory infection too. And, sadly, Catherine's stepfather also died, on 22 December. "It raises all sorts of questions for me on a personal level," she says.

And further down the page:

Quote:

Debra Scott from Blackpool thinks she caught the virus in late November at her husband's school reunion, where there was "lots of hugging and handshaking".

Her symptoms included a "cough that could kill a horse" and lasted for weeks. "I kept thinking I was getting better then - boom - it floored me again and again," she says.

She was so convinced it was Covid that she sent a blood sample off to a lab for an antibody test, which came back positive.

Some of these are anecdotes, there are caveats and alternative explanations. But the evidence does corroborate the TopHap study.

[angrysoba]

Question from SG:

“Do you agree or disagree that Worobey's hypothesis has serious problems? In particular he has used a faulty underlying premise that he's working with the earliest genomes.”

Huh? The “earliest genomes”? No, the earliest available ones, maybe, but he does not claim that these were the first cases. He explicitly says the virus had infected others before it was detected.

As for that “study” in the Irish Journal of Medicine, I have already shown why that “study” is a pile of crap. It is a letter, not a study, by someone who put numbers of athletes in European countries into an Excel spreadsheet with numbers of people who had been infected about a YEAR later worldwide. I showed that if you input all the other countries’ numbers into the Excel spreadsheet then the correlation goes away. I even manually put the numbers in and posted it here, from what I remember. So for you to bring up that crap again is pretty insulting.

[angrysoba]

Here is a link to my debunking of that Irish Medical Journal letter that SG claimed was a study by the NIH….

http://www.internationalskeptics.com...postcount=2263

[angrysoba]

Originally Posted by Skeptic Ginger

IIt's also worth noting China claims the athletes brought COVID to Wuhan. That's a bit of a contradiction if they also say the first cases were in early Dec.

I don't think the claims of the Chinese government need to be taken very seriously, partly because some of these claims probably come as retaliation for the claims that the virus leaked from their labs.

In addition, it is not a contradiction if you simply acknowledge that different people in China have asserted different things, just like different people in the US and other countries have asserted different things.

As far as I can see, George Gao (et al) of the CCDC makes no mention of the Wuhan Military Games in their paper.

From what I can see, all it does is affirm that there was a high amount of virus in the Huanan Market in December 2019. suggesting it was an amplifying event. It does not claim it originated then and there. It also does not refute the idea that it originated in the market.

Latham and Wilson in the article you linked to makes some suggestion that the papers by Worobey et al and Pekar et al somehow contradict Gao et. al. I don't see the contradiction there either. By the way, do they still stand by their Mojiang Mine serial passage theory? It seems to me that this theory is now obsolete.

[Skeptic Ginger]

Originally Posted by angrysoba

Here is a link to my debunking of that Irish Medical Journal letter that SG claimed was a study by the NIH….

http://www.internationalskeptics.com...postcount=2263

Of course which is why I noted there were caveats, some of the info came from anecdotes (of which there are many more) and there were contradictions and other explanations. And for similar reasons I didn't post about the COVID antibodies in stored blood taken for other reasons.

Before you waste your time, there were criticisms of the traffic and searches for certain COVID symptoms on Weibo as well.

Coronavirus: Fact-checking claims it might have started in August 2019

All of the things posted early (and later for that matter) in the thread were criticized. Some were dismissed simply because the researchers were dismissed like Quay. Some was dismissed on the basis it appeared on a right wing site like the National Review.

The point of taking a second look is to do so with the new study information.

Again you are not moving forward. I'm looking for stuff that corroborates an earlier outbreak in Wuhan in Oct or even Sept.

It's fairly well documented there were cases in Nov. It's not just the embassy cable, and the 3 WIV workers who were never confirmed to have been hospitalized. Shi denied there were any WIV workers with pneumonia but refused to let the WHO team see any of the raw data where these workers were tested.

You might also recall that some evidence was ignored (outside of the thread) until people stopped referring to it. The fact the seafood market cases were a super-spreader event later became the claim they were the first cases. That got repeated over and over in the media until the first cases China acknowledged but later wouldn't release data on became forgotten in some circles.

I'll have to get back to this an address Worobey's claims in a bit.

[angrysoba]

Originally Posted by Skeptic Ginger

Of course which is why I noted there were caveats, some of the info came from anecdotes (of which there are many more) and there were contradictions and other explanations. And for similar reasons I didn't post about the COVID antibodies in stored blood taken for other reasons.

Not "caveats"! The "study" is meaningless. MEANINGLESS.

Originally Posted by Skeptic Ginger

Again you are not moving forward. I'm looking for stuff that corroborates an earlier outbreak in Wuhan in Oct or even Sept.

We move on when you throw that letter in the bin!

Never bring that letter up again.

Also, "I'm looking for stuff that corroborates" sounds like confirmation bias. It is a bad idea to latch onto any old crap that supports your pre-existing belief. And that letter is really really crap!

[Crazy Chainsaw]

Originally Posted by angrysoba

Not "caveats"! The "study" is meaningless. MEANINGLESS.



We move on when you throw that letter in the bin!

Never bring that letter up again.

Also, "I'm looking for stuff that corroborates" sounds like confirmation bias. It is a bad idea to latch onto any old crap that supports your pre-existing belief. And that letter is really really crap!

The Parent virus of Covid 19 came from Laos, one Laotian worker in China's great build Urinating on the ground could have gotten the Virus into the Karst and Caves under Wuhan.
Once into the Karst Geology it could have spread rapidly among wildlife in the caves.

[Skeptic Ginger]

Originally Posted by angrysoba

Not "caveats"! The "study" is meaningless. MEANINGLESS.



We move on when you throw that letter in the bin!

Never bring that letter up again.

Also, "I'm looking for stuff that corroborates" sounds like confirmation bias. It is a bad idea to latch onto any old crap that supports your pre-existing belief. And that letter is really really crap!

So you haven't looked at the MOA/TopHap material or my post looking at it in detail yet then?

[angrysoba]

Originally Posted by Skeptic Ginger

So you haven't looked at the MOA/TopHap material or my post looking at it in detail yet then?

It's almost as if people around the world have jobs and families and cannot spend their whole time reading endless studies and answering a blizzard of questions that even when answered come back again as zombie theories.

When I have time I will do it. I have no obligation to do so until then.

[Planigale]

Originally Posted by Skeptic Ginger

Of course which is why I noted there were caveats, some of the info came from anecdotes (of which there are many more) and there were contradictions and other explanations. And for similar reasons I didn't post about the COVID antibodies in stored blood taken for other reasons.

Before you waste your time, there were criticisms of the traffic and searches for certain COVID symptoms on Weibo as well.

Coronavirus: Fact-checking claims it might have started in August 2019

All of the things posted early (and later for that matter) in the thread were criticized. Some were dismissed simply because the researchers were dismissed like Quay. Some was dismissed on the basis it appeared on a right wing site like the National Review.

The point of taking a second look is to do so with the new study information.

Again you are not moving forward. I'm looking for stuff that corroborates an earlier outbreak in Wuhan in Oct or even Sept.

It's fairly well documented there were cases in Nov. It's not just the embassy cable, and the 3 WIV workers who were never confirmed to have been hospitalized. Shi denied there were any WIV workers with pneumonia but refused to let the WHO team see any of the raw data where these workers were tested.

You might also recall that some evidence was ignored (outside of the thread) until people stopped referring to it. The fact the seafood market cases were a super-spreader event later became the claim they were the first cases. That got repeated over and over in the media until the first cases China acknowledged but later wouldn't release data on became forgotten in some circles.

I'll have to get back to this an address Worobey's claims in a bit.

Presumably a stuttering outbreak with poor person to person transmission from e.g. September would fit with how you imagine an outbreak would occur if a virus had spread from an animal into humans? The isolates from December would by then have passed through many persons and have adapted to humans.

[Skeptic Ginger]

Originally Posted by angrysoba

It's almost as if people around the world have jobs and families and cannot spend their whole time reading endless studies and answering a blizzard of questions that even when answered come back again as zombie theories.

When I have time I will do it. I have no obligation to do so until then.

And yet here you are repeating old arguments.

Of course you are not obligated. The evidence is what it is whether you read it or not. It disproves Worobey's position there was a spillover beginning in the seafood market. I'm waiting for him and/or Bloom to comment on the new phylogenetics work.

I'll post about it here if I find anything.

[Skeptic Ginger]

Very interesting reading Worobey's Twitter. He's quite annoyed his* findings are being questioned, complaining the people critiquing him are not experienced virologists with research under their belts.

*I should be including K Anderson is a co-author.

Worobey repeats "earliest known" cases when that is demonstrably false because there are earlier cases China continues to withhold data on. And he continues to insist A & B lineages represent 2 separate spillover events even though at least two researchers cited in this thread now said A was the initial strain and B evolved from A.

I repeat, he ignores contradictory evidence.

Worobey mentioned Ian Lipkin claiming he heard about cases in Wuhan on Dec 15. Worobey does cite some convincing evidence Lipkin had not heard about said cases on Dec 15 because he said nothing about it on Dec 16 in a relevant meeting. It's not a piece of evidence that matters much if we toss it out.

But it seems to be odd Worobey cares to rebut Lipkin when there is other evidence the Worobey/Anderson paper does not use the earliest cases. Since I'm supposedly wrong about the paper's claims, I'll take another look at it.


The Seeker's Twitter on Mar 10th makes a detailed case for the lab-leak origin and against the natural spillover origin without mentioning the MOA/TopHap analysis.

Quote:

@TheSeeker268
·
Mar 10
There is no evidence of a single spillover, let alone two spillovers.

Besides, as one virologist tells me:
Way too much is being made of the two lineages thing. They only differ by two mutations. The virus gets that many mutations in ~10% of human transmission events. ...

The Seeker
@TheSeeker268
·
Mar 10
If it’s true that first IH-to-human cases occurred in the market, it means that the IH already had the key mutations to cross species, and perhaps the FCS region incorporated. So, the virus was already a generalist on the IH. Then, why it did not transmit widely to other animals?
The Seeker
@TheSeeker268
·
Mar 10
Why didn’t in end up in other markets besides Wuhan? Where is the trail leading to such an abrupt explosion of cases in Wuhan? Where are the intermediate strains? If it were only circulating in a few animals then how did two lineages with ultra rare mutations evolve? ...

The Seeker
@TheSeeker268
·
Mar 10
All of this makes the coincidence a lot more than just “proximity”.

In short: I think it would have to be a very unusual set of circumstances where the virus failed to emerge in other places, but Wuhan...

There's a video of Ralph Baric saying a virus could be engineered that was not detectable.

The Seeker also noted:

Quote:

One more thing to keep in mind: WIV was awarded a state-funded megaproject – with funding from the CAS and NSFC – just after the DARPA proposal was rejected.

Important if one thinks Shi and Daszak only had access to US funds.

[angrysoba]

Worobey is not “rebutting” Lipkin, he is merely questioning whether the date is accurate.

I already posted the podcast episode in which Lipkin explains how he came to know of the outbreak and also how he came to leave for China.

I think it would be very useful for Lipkin to be involved in the search for the origins of the virus by the sounds of things as he clearly has a good rapport with the Chinese scientists. Of course, if he doesn’t find a lab leak everyone who suspects it will accuse him of a conflict of interest.

[angrysoba]

Originally Posted by Skeptic Ginger

Very interesting reading Worobey's Twitter. He's quite annoyed his* findings are being questioned, complaining the people critiquing him are not experienced virologists with research under their belts.

*I should be including K Anderson is a co-author.

There are 18 authors on the paper that you definitely read.

Originally Posted by Skeptic Ginger

Worobey repeats "earliest known" cases when that is demonstrably false because there are earlier cases China continues to withhold data on. And he continues to insist A & B lineages represent 2 separate spillover events even though at least two researchers cited in this thread now said A was the initial strain and B evolved from A.

I repeat, he ignores contradictory evidence.

Worobey mentioned Ian Lipkin claiming he heard about cases in Wuhan on Dec 15. Worobey does cite some convincing evidence Lipkin had not heard about said cases on Dec 15 because he said nothing about it on Dec 16 in a relevant meeting.

It was Angela Rassmussen who was surprised that Lipkin didn't mention it. She is one of the co-authors of the paper that you definitely read.

Originally Posted by Skeptic Ginger

It's not a piece of evidence that matters much if we toss it out.

You can hardly use it as evidence of a lab leak then.

Originally Posted by Skeptic Ginger

But it seems to be odd Worobey cares to rebut Lipkin when there is other evidence the Worobey/Anderson paper does not use the earliest cases. Since I'm supposedly wrong about the paper's claims, I'll take another look at it.

Have you read it once, yet?


Expecting: Oh so here is new evidence that I missed on my first reading.

[Skeptic Ginger]

Originally Posted by angrysoba

Worobey is not “rebutting” Lipkin, he is merely questioning whether the date is accurate.

I already posted the podcast episode in which Lipkin explains how he came to know of the outbreak and also how he came to leave for China.

I think it would be very useful for Lipkin to be involved in the search for the origins of the virus by the sounds of things as he clearly has a good rapport with the Chinese scientists. Of course, if he doesn’t find a lab leak everyone who suspects it will accuse him of a conflict of interest.

He rebutted Lipkin's claim of being told on Dec 15th 2019 there was an outbreak of pneumonia (or a corona virus—whatever) in Wuhan. So we have Lipkin saying he was told and Worobey saying it doesn't add up and you questioning the claim and me saying, meh, file it away until further information comes of it.

I did not see your link to said podcast. It's not worth more time than that at the moment.

[Skeptic Ginger]

Originally Posted by angrysoba

There are 18 authors on the paper that you definitely read.

It was Angela Rassmussen who was surprised that Lipkin didn't mention it. She is one of the co-authors of the paper that you definitely read.

You can hardly use it as evidence of a lab leak then.

Have you read it once, yet?

Expecting: Oh so here is new evidence that I missed on my first reading.

Your tu quoque is a fail. Yes I did read Worobey's still-not-peer-reviewed preprint. Has it been published now? Reading something and not recalling every detail is not the same as arguing old points in the thread when a new pretty significant study is posted that you have yet to even look at. It's the whole point of opening the thread again.

Though I do need to go back to see what I thought about the 2021 paper.


So I should be saying Worobey, et al. The reason I said I should add in Anderson is because Anderson and Garry are prominent natural spillover proponents. It's not a big deal any more than it is a big deal how many authors signed on to Worobey's study.


As for using XYZ as evidence of a lab leak, this is exactly what I said about your repeated posts throughout the thread that single out something while ignoring the bigger picture.

It's not critical what Lipkin said or didn't say. Just like it was never critical what Quay published or didn't, or what was printed in the National Review.

The biggest pieces of evidence are the papers Shi published before Dec 2019, the thesis and doctorate dissertation on the miners in Yunnan, the emails and contracts involving Daszak revealed under the FOIA, the fact live bats were kept at the WIV which was denied, the removal of a database of SARS CoV genomes from net access in Sept 2019, the fact the Chinese government refuses to release data on the first infections, the attempt by Daszak to steer the WHO team away from the lab-leak hypothesis before it was investigated and his attempt to label the lab-leak investigations as CTs, the lack of any source animals found that one would expect to see by now, the fact there have been no other outbreaks across China that didn't originate in Wuhan, the fact the WIV was studying the PPVs with only level 2 biosafety precautions ... and so on.

Those are big pieces of evidence but even those need to be considered as a lot of pieces adding up, not as this piece or that piece being the key to the whole tower of evidence.

Look at the sum of the whole, which origin hypothesis has stronger evidence?

[angrysoba]

Originally Posted by Skeptic Ginger

Your tu quoque is a fail.

It is not a tu quoque.

[angrysoba]

I think this should be of interest...

Quote:

Since the identification of theSARS-CoV-2 in Wuhan, China, in January 2020 (1), the origin of the virus has been a topic of intense scientific debate and public speculation. The two main hypotheses are that the virus emerged from human exposure to an infected animal [“zoonosis” (2)] or that it emerged in a research-related incident (3). The investigation into the origin of the virus has been made difficult by the lack of key evidence from the earliest days of the outbreak—there’s no doubt that greater transparency on the part of Chinese authorities would be enormously helpful. Nevertheless, we argue here that there is much important information that can be gleaned from US-based research institutions, information not yet made available for independent, transparent, and scientific scrutiny.

The data available within the United States would explicitly include, but are not limited to, viral sequences gathered and held as part of the PREDICT project and other funded programs, as well as sequencing data and laboratory notebooks from US laboratories. We call on US government scientific agencies, most notably the NIH, to support a full, independent, and transparent investigation of the origins of SARS-CoV-2. This should take place, for example, within a tightly focused science-based bipartisan Congressional inquiry with full investigative powers, which would be able to ask important questions—but avoid misguided witch-hunts governed more by politics than by science.

In particular, the call for an independent investigation is into US researchers, particularly those in the University of North Carolnia (Baric's lab) and UCD. They also want to investigate EHA, particularly those who worked in Wuhan.

They also have an interest in the FCS:

Quote:

In fact, the assertion that the FCS in SARS-CoV-2 has an unusual, nonstandard amino acid sequence is false. The amino acid sequence of the FCS in SARS-CoV-2 also exists in the human ENaC α subunit (16), where it is known to be functional and has been extensively studied (17, 18).

Link

[The Great Zaganza]

What I'm hearing is that the NWO put the AA sequence into humans in preparation for the plandemic.

[Skeptic Ginger]

Originally Posted by The Great Zaganza

What I'm hearing is that the NWO put the AA sequence into humans in preparation for the plandemic.

This is the science thread. There is another thread in the CT forum your post probably belongs in.

[Skeptic Ginger]

Re Worobey, the issue I've haven't gotten back to the thread on is his use of a faulty underlying premise that he was operating with very early virus cases.

In this Science article, Worobey makes the case that the earliest cases were in Dec 2019 and they clustered around the seafood market.

Viewpoint: Dissecting the early COVID-19 cases in Wuhan

No one is disputing the market cluster. But it's pretty telling that the head of the Chinese CDC believes the market was where a super-spreader event took place, not where the first cases occurred.

From the article Worobey is convinced A&B lineages are evidence of 2 separate spillover events.


Preprint; Worobey et al: The Huanan market was the epicenter of SARS-CoV-2 emergence

Quote:

Abstract

Despite strong epidemiological links and the documented presence of SARS-CoV2 susceptible animals, the role of the Huanan Seafood Wholesale Market in the COVID 19 pandemic remains controversial. Using spatial analyses we show that the earliest known COVID-19 cases diagnosed in December 2019 were geographically distributed near to, and centered on, this market. This distribution cannot be explained by high densities of elderly people at greater risk of symptomatic COVID-19. This pattern was stronger in cases without, rather than with, identified epidemiological links to the Huanan market, consistent with SARS-CoV-2 community transmission starting in the surrounding area. By combining spatial and genomic data, we show that both the two early lineages of SARS-CoV-2 have a clear association with the Huanan market. We also report that live mammals, including raccoon dogs, were sold at the market in late 2019 and geospatial analyses within the market show that SARS-CoV-2-positive environmental samples were strongly associated with vendors selling live animals. Together, these analyses provide dispositive evidence for the emergence of SARS-CoV-2 via the live wildlife trade and identify the Huanan market as the unambiguous epicenter of the COVID-19 pandemic.

One sentence summary:

Geographical clustering of the earliest known COVID-19 cases and the proximity of positive environmental samples to live-animal vendors suggest that the Huanan Seafood Wholesale Market in Wuhan was the site of origin of the COVID-19 pandemic

Nowhere in the paper does Worobey, et al recognize any cases earlier than Dec 2019.

Science: Do three new studies add up to proof of COVID-19’s origin in a Wuhan animal market?

Answer, no.

Quote:

Preprints unlikely to end debate over how SARS-CoV-2 began the pandemic, but some scientists say lab-leak hypothesis has taken a “blow”

"Some scientists" have always favored the natural event. All those working to keep the lab-leak hypothesis in play and not have it snuffed out before the evidence really rules it out are not likely to have changed their minds based on these reports.


As for the raccoon dogs being sold at the seafood market, I have no issue with that fact. But let's see the follow up then hunting down where were these raccoon dogs from that were supplied to the market? Is there any evidence there could have been infected raccoon dogs anywhere?

And given how easily COVID seems to have been spread to other animal species, where are all the infected animals in China? Given the lack of cases found in any animal species in China it supports the conclusion humans were the first species infected.

[angrysoba]

Originally Posted by Skeptic Ginger

Re Worobey, the issue I've haven't gotten back to the thread on is his use of a faulty underlying premise that he was operating with very early virus cases.

The Worobey et. al paper explicitly points out in a number of places that they cannot be sure exactly when the earliest cases were and that they explicitly deny the first known case was the first actual case. In fact, they suggest that for every known case there were probably at least 10 and maybe up to 70 cases of unknown infections.

They say that the Pekar et. al paper is the one that deals with the estimates of when the virus appeared in humans.

What I did not get from looking at the paper by Kumar, et, al was exactly what was being claimed, whether it was a "proto-SARS-CoV-2" or one that was already in humans.

I have no way of knowing whether Pekar et al or Kumar et al are more likely to be correct.

[lomiller]

Originally Posted by Skeptic Ginger

No one is disputing the market cluster. But it's pretty telling that the head of the Chinese CDC believes the market was where a super-spreader event took place, not where the first cases occurred.

Nothing in your post provides evidence for this assertion.

Originally Posted by Skeptic Ginger

Nowhere in the paper does Worobey, et al recognize any cases earlier than Dec 2019.

There are no known identifiable cases earlier than Dec 11 so he's using the available data, as he should. There were almost certainly un-diagnosed cases as far back as early Nov but unknown and un-diagnosed cases are of no value to a study like this one.

[angrysoba]

Originally Posted by lomiller

Nothing in your post provides evidence for this assertion.



There are no known identifiable cases earlier than Dec 11 so he's using the available data, as he should. There were almost certainly un-diagnosed cases as far back as early Nov but unknown and un-diagnosed cases are of no value to a study like this one.

Indeed. I read through the Gao et.al. paper (CDCC) and did not find anything in it in which they “ruled out” Huanan market as a spillover location. The only thing that the paper did was confirmed that it was the site of an amplifying event, which had already been suspected. In fact the paper seems to me to be exactly what you would want in a science paper making use of available data and drawing reasonable conclusions without attendant wild speculation.

It may be the case that the Chinese government are making wild claims about covid leaking from a US lab or arriving on frozen lobsters but that was not what was written in the Gao paper.

In fact, that is obviously one of the disadvantages of being a good scientist, when people demand certain answers, good scientists will often have to say they don’t know.

“Oh YOU done know? Well I know someone who does!”

[Skeptic Ginger]

Originally Posted by angrysoba

The Worobey et. al paper explicitly points out in a number of places that they cannot be sure exactly when the earliest cases were and that they explicitly deny the first known case was the first actual case. In fact, they suggest that for every known case there were probably at least 10 and maybe up to 70 cases of unknown infections.

They say that the Pekar et. al paper is the one that deals with the estimates of when the virus appeared in humans.

This is the conclusion in the Worobey paper I have an issue with:

Quote:

Collectively these results provide incontrovertible evidence that there was a clear conduit, via susceptible live mammals for the zoonotic emergence of SARS-CoV-2 at the Huanan market towards the end of 2019. ...

And this:

Quote:

Together these analyses provide dispositive evidence for the emergence of SARS-CoV-2 via the live wildlife trade and identify the Huanan market as the unambiguous epicenter of the COVID-19 pandemic.

Another POV:
Science: Do three new studies add up to proof of COVID-19’s origin in a Wuhan animal market?

Quote:

Skeptics of the natural origin theory maintain the market cluster could merely be a superspreader event touched off when a person infected with a lab-escaped coronavirus visited it. But Worobey thinks further data could make that contention even less tenable. A more transparent analysis of the market’s genetic sampling data, in particular, might identify exactly which species of animals sold there carried the virus.

So Worobey admits more data is needed.


Back to the commentary:

Quote:

In the new preprint, Gao and colleagues analyzed 1380 samples from 188 animals in the market and the environment, including sewer wells, the ground, feather removing machines, and “containers.” They found SARS-CoV-2 in 73 samples. But because all were from the environment, not the animals themselves, they assert that humans introduced the virus to the market. The authors call the market an “amplifier,” not the source, of SARS-CoV-2.

Gao would like to move patient zero out of China altogether. He asserts the patients in Italy predate the patients in Wuhan.

Not sure where you think Gao doesn't rule out the market being more than a super-spreader event. He has asserted this from the beginning.


This was discussed in my recent link. China wants the source to be outside China. Half of the 'Western' scientists don't want the lab to be implicated for multiple reasons, especially that it hits too close to home and might implicate their own work is potentially dangerous.


I'm not seeing overwhelming evidence that the A&B lineages represent two separate introductions of the virus into humans.

Quote:

Garry had identified two different forms of SARS-CoV-2, differing by just two mutations, which he argued surfaced at different Wuhan markets in December 2019.

So A&B lineages differ by only 2 mutations yet they dismiss the possibility B descended from A?

Originally Posted by angrysoba

What I did not get from looking at the paper by Kumar, et, al was exactly what was being claimed, whether it was a "proto-SARS-CoV-2" or one that was already in humans.

I have no way of knowing whether Pekar et al or Kumar et al are more likely to be correct.

I'll get back to this.

[Skeptic Ginger]

Originally Posted by angrysoba

Indeed. I read through the Gao et.al. paper (CDCC) and did not find anything in it in which they “ruled out” Huanan market as a spillover location. The only thing that the paper did was confirmed that it was the site of an amplifying event, which had already been suspected. In fact the paper seems to me to be exactly what you would want in a science paper making use of available data and drawing reasonable conclusions without attendant wild speculation....

From my previous citation:

Quote:

2) Environmental samples collected at the market are of human origin and did not come from animals sold there.
The aim of the Chinese CDC paper was to analyse the environmental samples (swabs from surfaces etc.) that they took in and around the Huanan market after Jan 1st, 2020 (Gao et al., 2022). They concluded that the market was only an amplifying event, in part because SARS-CoV-2-positive samples were associated with stalls belonging to multiple types of vendors, including those not selling animals (the Worobey preprint argues there is a correlation). More compelling, the CDC authors found that the samples collected from the market, which Pekar and Worobey claim are from infected animals, are admixed only with human genetic material and not with genetic material from raccoon dogs or other species potentially sold at the market. The only reasonable inference is that these positive samples did not derive from the faeces or urine or exhalations of a live non-human animal. Few results would better indicate that virus-positive market samples derive from infected humans as opposed to other species.

Different people apply different levels of relevance to the same evidence. But this suggests that Gao did indeed conclude the market was a super-spreader event and not the spillover event. Gao has been consistent in this conclusion from early on in the investigation and in citations posted earlier in the thread.

Remember, Gao is pushing the theory it started elsewhere, probably Italy.

[angrysoba]

I will repeat what I said...

Originally Posted by angrysoba

Indeed. I read through the Gao et.al. paper (CDCC) and did not find anything in it in which they “ruled out” Huanan market as a spillover location. The only thing that the paper did was confirmed that it was the site of an amplifying event, which had already been suspected. In fact the paper seems to me to be exactly what you would want in a science paper making use of available data and drawing reasonable conclusions without attendant wild speculation.

What you are relying on is second-hand sources interpreting what they said.

Quote:

2) Environmental samples collected at the market are of human origin and did not come from animals sold there.
The aim of the Chinese CDC paper was to analyse the environmental samples (swabs from surfaces etc.) that they took in and around the Huanan market after Jan 1st, 2020 (Gao et al., 2022). They concluded that the market was only an amplifying event, in part because SARS-CoV-2-positive samples were associated with stalls belonging to multiple types of vendors, including those not selling animals (the Worobey preprint argues there is a correlation). More compelling, the CDC authors found that the samples collected from the market, which Pekar and Worobey claim are from infected animals, are admixed only with human genetic material and not with genetic material from raccoon dogs or other species potentially sold at the market. The only reasonable inference is that these positive samples did not derive from the faeces or urine or exhalations of a live non-human animal. Few results would better indicate that virus-positive market samples derive from infected humans as opposed to other species.

I believe this is not what they said. They:

only confirmed it was an amplifying event,
[b]they did not confirm it was only an amplifying event.

The two claims are different.

They leave a number of scenarios open such as the possibility that it came from elsewhere or that it came to the Huanan market via an intermediary.

You should read the paper yourself and not rely on others to interpret it for you. The paper is really very short.

Link

[Skeptic Ginger]

And I said Gao has had the position the market was a super-spreader event from the beginning.

Whatever's in the paper you've linked to is not the only place Gao has voiced his opinion.

[angrysoba]

Originally Posted by Skeptic Ginger

And I said Gao has had the position the market was a super-spreader event from the beginning.

Whatever's in the paper you've linked to is not the only place Gao has voiced his opinion.

So what? Whatever opinions he has expressed elsewhere is irrelevant. Clearly the paper contains that which the authors can be confident of saying. It is inaccurate to claim, as your source does, that they conclusively rule out the market.

[Skeptic Ginger]

Originally Posted by angrysoba

So what? ....

So what indeed.

Any good scientist will not deal in absolutes. Even in this debate, there is no proof one way or the other which origin hypothesis is correct.

Gao has access to the data on the early cases that China is withholding from the rest of thee world. It's in his political interest to promote the hypothesis that the origin occurred outside of China. He could provide more evidence of that fact if he truly believed the source was Italy or some other country.

In the beginning and for more than a year Daszak tried to steer the scientific community into repeating the unsupported opinion that the lab origin was a CT. More than a few scientists have described their being afraid to address the lab hypothesis because it led to being ostracized by their peers. This has all been documented in this thread.

More than a few people latched on to the Worobey study as some kind of relief they might put the lab origin hypothesis to bed. The news media reported on the study as if it were as strong of evidence as Worobey described: "incontrovertible evidence" and "unambiguous evidence." But that is an exaggeration.

When you try to make it sound like Gao only 'sort of' believes the market was a super-spreader but not a spillover event, you are biasing his position to fit your beliefs. Did he say the market might be the spillover location? No, of course not. That you are putting some kind of magical weight to the idea not denying it is the same as saying it's equivocal demonstrates that confirmation bias.

I have tried to look at the spillover evidence honestly. Had the Worobey study not claimed the A&B lineages were two separate introductions into the human population, had the researchers admitted their spatial analysis of the cases left out a lot of cases China was not releasing data on, had the report not been so overly assured of their findings, I would give that report more credence.

But they did not. The report's conclusions are overstated. And the likelihood the findings could also represent a super-spreader event is understated.


Just like the "spillover" is the default position because look how often it happens is not a convincing argument. I find the 'OMG you mean this happened only 17 miles (from the Worobey paper) from the one place in China they've been collecting these coronavirus bat specimens' to be a much stronger argument than it is some bizarre coincidence that some infected animal no one can find the source of just happened to set off a pandemic only 17 miles from the WIV.

[angrysoba]

Originally Posted by Skeptic Ginger

So what indeed.

Any good scientist will not deal in absolutes. Even in this debate, there is no proof one way or the other which origin hypothesis is correct.

Exactly. Then Latham and Wilson have no business drawing absolute conclusions that were not in the paper while claiming that those conclusions were in the paper. And you should read the paper instead of relying on them to give an accurate gloss on the paper.

[Skeptic Ginger]

From your link:

Quote:

All the four sewerage wells in the market tested positive. This suggested that either contaminated sewage may have played a role in the cluster of cases in the market or that the infected people in the market contaminated the sewage

Does that say maybe animals from the market could have been a source of the contaminated sewage?

No, it says maybe the contaminated sewage played a role in the cluster of cases.

Further down:

Quote:

These results suggested that SARS-CoV-2 might have been circulating in the market, especially the western zone, for a period of time in December 2019, leading to an extensive distribution of the virus within the market, which might have been facilitated by the crowded buyers and the contaminated environment.

Does that say a spillover event cannot be ruled out?

No.

Quote:

All the 457 animal samples tested negative for SARS-CoV-2 nucleic acid, suggesting that the animal infections with SARS-CoV-2 might be rare in the market.

That includes a lot of samples taken that include some before the market was purged of all animals.

More testing:

Quote:

Therefore, the SARS-CoV-2 sequences from environmental samples were highly similar to the clinical strains obtained during the early stage of the COVID-19 outbreak

Does that say the conclusion could be they represent a spillover event occurred at the market?

No.

Quote:

We analyzed the correlation of SARS-CoV-2 and the abundance of other species. The abundance of Homo sapiens showed the correlation to SARS-CoV-2(Figure 4), which highly suggests the SARS-CoV-2 might have derived fromHomo sapiens in the HSM. No animals were concluded, implying that no animal host of SARS-CoV-2 can be deduced.

How much more clear do you expect Gao to be?

I'm not sure why you think your interpretation of the paper is superior to the 2 PhDs' interpretation of the paper.

Quote:

Thus, the market might have acted as an amplifier due to the high number of visitors every day, causing many initially identified infection clusters in the early stage of the outbreak as indicated in the Report of WHO-convened global study of origins of SARS-CoV-2 (10). In addition, live SARS-CoV-2 viruses also existed in the environmental samples. However, no SARS-CoV-2 was detected in the animal samples from the market. Definitely, more work involving international coordination is needed to investigate the real origins of SARS-CoV-2(10), especially considering the SARS-CoV-2 positive results of samples collected in 2019 in retrospective studies of different countries (29, 30).

IOW Gao wants to see more investigating of older samples from different countries.

And you can't use your go-to excuse on these negative findings that all the testing of animals was done after all the animals were purged. Gao describes samples that reflected the actual animals in the market. And the paper documents the live virus they successfully cultured in their study all matched human virus, none matched animal viruses.

And that ties into the TopHap analysis which found the same thing: This was a human adapted virus from the very beginning of the pandemic.

[angrysoba]

Originally Posted by Skeptic Ginger

From your linkoes that say maybe animals from the market could have been a source of the contaminated sewage?

No, it says maybe the contaminated sewage played a role in the cluster of cases.

Further down:

Does that say a spillover event cannot be ruled out?

No.

That includes a lot of samples taken that include some before the market was purged of all animals.

More testingoes that say the conclusion could be they represent a spillover event occurred at the market?

No.

Absence of evidence =/= evidence of absence.

This is elementary logic and yet, your authors derived the latter from the former.

Originally Posted by Skeptic Ginger

I'm not sure why you think your interpretation of the paper is superior to the 2 PhDs' interpretation of the paper.

TWO PhDs!!!!

I guess 2 PhDs can't be wrong.

[Skeptic Ginger]

Originally Posted by angrysoba

Absence of evidence =/= evidence of absence.

This is elementary logic and yet, your authors derived the latter from the former.

What are you talking about?

Did you lose track of the discussion?

You claim Gao didn't rule out a spillover event at the market. By your measure he didn't rule out a panspermia virus either.


BTW, the Gao paper was posted before the Worobey study wasn't it? Or do I have the dates wrong? Why would you expect Gao to comment one way or the other on a spillover event at the market?

Does the Worobey study address the findings in the Gao paper? Why not? It concludes the earliest viruses don't have remnants of animal viruses.

[angrysoba]

Originally Posted by Skeptic Ginger

What are you talking about?

Did you lose track of the discussion?

You claim Gao didn't rule out a spillover event at the market. By your measure he didn't rule out a panspermia virus either.


BTW, the Gao paper was posted before the Worobey study wasn't it? Or do I have the dates wrong? Why would you expect Gao to comment one way or the other on a spillover event at the market?

Does the Worobey study address the findings in the Gao paper? Why not? It concludes the earliest viruses don't have remnants of animal viruses.

I don't contend he does.

The claim by you and Latham and Wilson is that Gao rules out a market spillover.

My claim is that Gao's paper does not do that. It merely says that their is evidence of an amplifying event there. It also says that no animal samples were found there.

I don't think anyone really disputes those points.

The dispute is on the spin you are giving it.

[angrysoba]

Originally Posted by Skeptic Ginger

Does the Worobey study address the findings in the Gao paper? Why not? It concludes the earliest viruses don't have remnants of animal viruses.

No, it does not! Why not? Because the Gao paper was posted something like one day before Worobey et al's paper came out.

How do you expect them to repond that quickly?

[Skeptic Ginger]

So Gao should have an opinion on the market being a spillover event but the Worobey group can't possibly address the Gao et al paper because they came out a day apart?

It's easy to focus on something pedantic and miss the bigger picture.

Worobey overstated the findings of their study. Nothing about being interpreted by anyone else.

More than a few Western researchers and experts have a confirmation bias toward finding a natural event, not a lab accident for the origin. I brought this up a couple posts upthread. The implications of a lab accident could have repercussions that affect the whole viral research field.

Gao has a clear motive to find an origin of the pandemic outside of Wuhan, outside of China. Why would he consider a possible spillover event at the market? That makes no sense.


None of these people except Gao are necessarily aware of their biases.


That's why the TopHap study is so important. It's also important to look at what these coronavirus researchers were doing before the pandemic. There is a lot of evidence to be found there.

[Skeptic Ginger]

From Jamie Metzl's Twitter:

Quote:

I'd love to see a respectful public dialogue between
@MichaelWorobey & Sudhir @kumar_lab re pandemic origins. If Kumar's phylogenetic analysis of #SARSCov2 evolution is correct, Worobey et al's case for "dispositive evidence" of a #COVID19 market origin cannot be defended.

He links to both papers in the next 2 Tweets.

Someone has noticed.