Origins of Covid

[Skeptic Ginger]

Originally Posted by angrysoba

September infections of Covid?

That makes no sense.

This has clearly not reached the level of established fact otherwise it would be part of any working theory of the origins of Covid.

Besides, if the cases were in September it would torpedo your claim the Wuhan Games led to the outbreaks in Italy.

I'm not sure how other researchers were supposed to incorporate in their work research only recently published.

How would cases in Sept mean the military games in Oct couldn't have spread the virus worldwide?

[lomiller]

Originally Posted by Skeptic Ginger

The ones China at first admitted to then later refused to share any of the demographic data about. Demographic as in the things an epidemiologist would look at to track down the source of an outbreak.

That sounds a lot like 9\11 CT that argues early, erroneous, statements prove that latter more accurate information are really part of a coverup. The earliest confirmed case was recorded on Dec 11, non-confirmed or speculative cases before this date should not be used in these studies.

[angrysoba]

Originally Posted by Skeptic Ginger

The ones China at first admitted to then later refused to share any of the demographic data about. Demographic as in the things an epidemiologist would look at to track down the source of an outbreak.

Can you be more specific with dates and locations?

[angrysoba]

Originally Posted by W.D.Clinger

On my reading of the paper by Caraballo-Ortiz et al., they are not suggesting any humans had been infected with SARS-CoV-2 in September 2019, or even in October. So far as I can tell, their methods are incapable of determining when the first human infections occurred. In the following quotation, they are talking about the evolution of the Most Recent Common Ancestor (MRCA) of SARS-CoV-2. With my highlighting:

Right! This would not be inconsistent, then, with Worobey's paper, as far as I can tell.

When I looked through the paper, and I am not competent to judge the science of the paper, I could not find any reason for thinking it would favour the lab leak over spillover.

Indeed. It would even answer the questions the lab leakers often ask which is why the virus was ready for human to human transmission immediately. The answer would be, it wasn't.

[angrysoba]

Originally Posted by Skeptic Ginger

I'm not sure how other researchers were supposed to incorporate in their work research only recently published.

How would cases in Sept mean the military games in Oct couldn't have spread the virus worldwide?

I was referring to your link that said it was in Italy in September 2019.

The article was from November 2020.

Is this still considered plausible? Genuine question as I have no idea. It refers to some people who were screened for lung cancer.

Were these contaminated samples?

[angrysoba]

No evidence of Covid infections in blood donors in Wuhan from Sept-Dec 2019.

Quote:

we reviewed SARS-CoV-2 antibody results from these donors who donated several times from September 2019 to June 2020, partly tested in a previous published study, no one was found a significant increase in S/CO of antibodies against SARS-CoV-2. Our findings showed no SARS-CoV-2 specific antibodies existing among blood donors in Wuhan, China before 2020, indicating no evidence of transmission of COVID-19 before December 2019 in Wuhan, China.

Link

[carlitos]

Just out in Science, seems like Covid-19 came from the seafood market.

Quote:

Abstract

Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports but later this conclusion became controversial. We show the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2 susceptible mammals were sold at the market in late 2019 and, within the market, SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals. While there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred via the live wildlife trade in China, and show that the Huanan market was the epicenter of the COVID-19 pandemic.

[The Atheist]

Still no evidence of the Great Lab leak?

Colour me unsurprised.

[angrysoba]

Originally Posted by carlitos

Just out in Science, seems like Covid-19 came from the seafood market.

So what you are saying is... the Wuhan Institute of Virology infected some wildlife animals and sent them to the seafood market, and then it became a pandemic?

I knew this was suspicious!

[angrysoba]

By the way, the Pekar paper, also peer-reviewed and published at the same time, did look at the TopHap analysis (Caraballo-Ortiz et. al and Kumar et. al) as well as Jesse Bloom's paper (which I think I mentioned in this thread when Worobey strongly criticized it in a Twitter thread). However, I have no idea how to judge these types of analyses, so I will just quote the part that talks about it and leave it for others...

Quote:

Even though sequence similarity to closely related sarbecoviruses alone is insufficient to determine the SARS-CoV-2 ancestral haplotype, this similarity can inform phylodynamic inference. Rather than rely on outgroup rooting [fig. S18B and (18)], we developed a rooting method that assigns the recCA as the progenitor of the inferred SARS-CoV-2 MRCA (fig. S18C). As opposed to the unconstrained rooting, the recCA root favored a lineage A haplotype over lineage B, although support for C/C was unchanged (Table 1). Our results were insensitive to the method of breakpoint identification in the recCA (supplementary text).

The A.1 and A+C29095T proposed ancestral haplotypes were strongly rejected by all the phylodynamic analyses, even when rooting with recCA or bat sarbecovirus outgroups, which include both C18060T and C29095T (Table 1 and data S3). Hence, WA1-like and 20SF012-like haplotypes cannot plausibly represent the MRCA of SARS-CoV-2 as previously suggested (19–21): the similarity of these genomes to the recCA is due to C-to-T reversions. Haplotypes not reported in Table 1 were similarly rejected (data S3).

We inferred the tMRCA for SARS-CoV-2 to be 11 December 2019 (95% HPD: 25 November–12 December) using unconstrained rooting. It has been suggested that a phylogenetic root in lineage A would produce an older time of most recent common ancestor (tMRCA) than a lineage B rooting (21). Therefore, we developed an approach to assign a haplotype as the SARS-CoV-2 MRCA and inferred the tMRCA (i.e., A, B, C/C, A.1 or A+C29095T) (fig. S18D). The tMRCA was consistent with the recCA-rooted and fixed ancestral haplotype analyses (table S2 and supplementary text).

We infer only three plausible ancestral haplotypes: lineage A, lineage B, and C/C. However, the inability to reconcile the molecular clock at the outset of the COVID-19 pandemic with a lineage A ancestor without information from related sarbecoviruses (e.g., the recCA) requires us to question the assumption that both lineages A and B resulted from a single introduction.

[Skeptic Ginger]

Andersen, Garry and Worobey are all listed as authors of that paper. And interestingly Garry is a "co-founder of Zalgen Labs, a biotechnology company developing countermeasures to emerging viruses." All of these people are interconnected to the whole research community that is funded by and involved in the research that might have resulted in the lab accident.

I'm not saying that means we should dismiss any rebuttal to the TopHap research. But it is important to keep that bias in mind that there were 2 spillovers at the seafood market.

With that in mind, these discrepancies are interesting:

Quote:

The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October–8 December)

That's a large range meaning the Nov 18th date isn't as precise as it sounds.

And:

Quote:

These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans prior to November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported.

Doesn't Worobey's paper rely on the virus being widespread before the first cases were reported? That's how he accounts for the earliest cases that were not connected to the market.

It's still hard to discount lineage B evolving from lineage A given other researchers suggest that happened. The two lineages are very closely related. If they came from 2 different spillover events how is that any more likely than the lineages split after they were in the human population?

Say lineage A spilled over into humans. CoV2 then continued to evolve in the hypothesized source animal. Then lineage B spilled over into humans.

How is that more likely than B evolved as a variant of A after it was in the human population?


What is one thing this paper supports? The virus jumped into the human population already well adapted to person to person spread.

The paper may be a follow up that questions the TopHap analysis. I await the author's reply. In the meantime the BBC reminds readers: There is no definitive piece of evidence - no Covid-positive bat or a confirmed first human case - to show conclusively how it started.

Quote:

The authors of this new report point out that none of those were, or could have been, manipulated to become Sars-Cov-2. But some scientists do not entirely accept that conclusion, including Prof David Relman, of the US's Stanford University.

"I see this [new report] as a deliberate effort to marshal all the possible information in support of what is a perfectly good hypothesis - natural spillover - but [it's] not balanced and objective," he told BBC News. ...

"What we don't need right now is for scientists to insist on their favourite explanation in the absence of new, solid data," says Prof Relman.

"Sars-Cov-2 has not been found in any natural animal host. Let's just cool it and demand a proper investigation."

[The Atheist]

Originally Posted by angrysoba

So what you are saying is... the Wuhan Institute of Virology infected some wildlife animals and sent them to the seafood market, and then it became a pandemic?

I knew this was suspicious!

Those Chinese are sneaky little *******.

Next they'll be using dolphins to sniff out subs.

[angrysoba]

Originally Posted by Skeptic Ginger

Andersen, Garry and Worobey are all listed as authors of that paper. And interestingly Garry is a "co-founder of Zalgen Labs, a biotechnology company developing countermeasures to emerging viruses." All of these people are interconnected to the whole research community that is funded by and involved in the research that might have resulted in the lab accident.

]

I’ll get to the other stuff later, but for now, are you really doing this?

This is like something I would expect from anti-vaxxers. (“How much are they taking from Big Pharma, huh?”). Remember that earlier you were fairly confidently claiming that these papers would not pass peer review. But now they have, so I guess we are to assume that the peer reviewers are also being paid off too? Do you see how this the route to conspiracy theory?

[Skeptic Ginger]

Originally Posted by angrysoba

I’ll get to the other stuff later, but for now, are you really doing this?

This is like something I would expect from anti-vaxxers. (“How much are they taking from Big Pharma, huh?”). Remember that earlier you were fairly confidently claiming that these papers would not pass peer review. But now they have, so I guess we are to assume that the peer reviewers are also being paid off too? Do you see how this the route to conspiracy theory?

No it isn't like anti-vaxxer stuff. Maybe to you with a serious bias from the start it was spillover it seems that way.

I did not say they wouldn't pass peer review, I said it will be interesting to see the rebuttal analyses. There are holes in the work.

But we don't need to see that now since those rebuttals have been in the media.

You seem to be operating on some assumption being published means one's conclusions were well supported. If that were the case half the research would never be published.

As I quoted above:

Quote:

"It's not true that we don't know where it came from - we just don't know how it got into humans," says Glasgow University virologist Prof David Robertson.

It is widely accepted that an ancestor of the virus originally circulated harmlessly in wild bats. But it is vital to discover how, where and exactly when that first made its way into a person to prevent a similar future outbreak.

There is no definitive piece of evidence - no Covid-positive bat or a confirmed first human case - to show conclusively how it started. That may never be known, but the scientists who wrote this latest report want to clarify the available evidence and what it means.

Comparing me to an anti-vaxxer shows your preference to avoid the actual debate.

What about the discrepancy re circulating low levels of disease put forth as Worobey's explanation for early cases he ignored in his research?

What about the fact nothing yet has been definitive? Worobey claims the idea his work is wrong is as unlikely as being struck by lightening. Isn't that over the top demonstrating he's simply ignoring evidence that doesn't fit his conclusions?


Why don't you debate the issues instead of trying to make me look stupid? I am not stupid and you'll get nowhere with that approach except maybe some local cheerleading by other members in this thread.


BTW, hope you're staying safe. It looks like cases exploded in Japan.

[Skeptic Ginger]

MedicalExpressNews: WHO says all theories still on table after studies point to natural COVID origin

Quote:

The World Health Organization on Wednesday welcomed new studies concluding that COVID-19 first emerged at an animal market in China's Wuhan, but insisted it was too early to rule out other theories.

"All hypotheses remain on the table," WHO emergencies director Michael Ryan told reporters from the UN health agency's Geneva headquarters. ...

Two peer-reviewed studies published in Science Tuesday claimed to have tipped the balance in the debate about the virus's origins, concluding it must have been introduced naturally through the wildlife trade at the Wuhan market. ...

Maria Van Kerkhove, WHO's technical lead for COVID-19, welcomed the studies, as well as another one published this week looking at environmental samples.

WHO experts, she said, had already evaluated the studies, which were previously posted as "preprints" before being vetted by scientific peer review.

"These are good analyses," she told reporters, but stressed that more studies on the ground in China and beyond were needed before any final conclusions could be drawn.

So no, my pointing out Worobey is overstating his case is not like an anti-vaxxer. It's not a CT.

[angrysoba]

Originally Posted by Skeptic Ginger

MedicalExpressNews: WHO says all theories still on table after studies point to natural COVID origin

So no, my pointing out Worobey is overstating his case is not like an anti-vaxxer. It's not a CT.

That is not what looks like a CT. This is...

Originally Posted by Skeptic Ginger

Andersen, Garry and Worobey are all listed as authors of that paper. And interestingly Garry is a "co-founder of Zalgen Labs, a biotechnology company developing countermeasures to emerging viruses." All of these people are interconnected to the whole research community that is funded by and involved in the research that might have resulted in the lab accident.

What does the highlighted mean? Does it mean we cannot trust them? If so, then that is the purpose of peer review. An independent scrutinzing of the methods of the research. Not that peer review is perfect. Not by a long shot. A lot of crappy research sails through peer review when the data is not properly analyzed.

But you said that Worobey et al. "ignore" early cases.

As far as I can tell this is just not true at all, and throwing that around is pretty obnoxious and suggests that you think they are engaged in some kind of scientific malpractice.

Worobey et al are completely up front about the fact that they only have the first known cases to go on.

Are you asking them why they are not investigating the unknown cases? The clue should be in the question. If they don't have access to that data then they can only go on what they have. This is not unusual in science. Data is almost always going to be incomplete.

Originally Posted by Skeptic Ginger

BTW, hope you're staying safe. It looks like cases exploded in Japan.

Thanks, I appreciate it. Yes, numbers are extremely high here now. Fortunately deaths are relatively low.

Likewise, I hope you are well.

[angrysoba]

Originally Posted by Skeptic Ginger

With that in mind, these discrepancies are interesting:
That's a large range meaning the Nov 18th date isn't as precise as it sounds.

No, maybe not. But I don't think it is much of an objection. Worobey et. al say:

Quote:

In a related study, we infer separate introductions of SARS-CoV-2 lineages A and B into humans from likely infected animals at the Huanan market (38). We estimate the first COVID-19 case to have occurred in November 2019, with few human cases and hospitalizations occurring through mid-December (38).

In other words, "around 18 November 2019 (23 October–8 December)". It hardly seems to be a problem.

Originally Posted by Skeptic Ginger

And: Doesn't Worobey's paper rely on the virus being widespread before the first cases were reported? That's how he accounts for the earliest cases that were not connected to the market.

Not "widespread" but circulating. And they say that:

Quote:

One of the key findings of our study is that ‘unlinked’ early COVID-19 patients, those who neither worked at the market or knew someone who did, nor had recently visited the market, resided significantly closer to the market than patients with a direct link to the market. The observation that a substantial proportion of early cases had no known epidemiological link had previously been used as an argument against a Huanan market epicenter of the pandemic.

Originally Posted by Skeptic Ginger

It's still hard to discount lineage B evolving from lineage A given other researchers suggest that happened. The two lineages are very closely related. If they came from 2 different spillover events how is that any more likely than the lineages split after they were in the human population?

Maybe it cannot be discounted. However, the presence of both within the stalls and in proximity does increase the chances that the Huanan Market was likely a locus. My understanding, from looking at other virologists commenting on this is that this did not begin with an animal being infected by a bat in a stall, but animals already infected brought into the market having been infected in the supply chain, either at a farm or en route, suggesting also that supply chain workers could also have been infected somewhere along the line.

Quote:

A recent preprint (24) confirms the authenticity of the CCDC report (data S1) and records additional positive environmental samples in the southwestern area of the market selling live animals. This report also documents the early presence of the A lineage of SARS-CoV-2 in a Huanan market environmental sample. This, along with the lineage A cases we report in close geographical proximity to the market in December, challenges the suggestion that the market was simply a superspreading event, which would be lineage-specific. Rather, it adds to the evidence presented here that lineage A, like lineage B, may have originated at the Huanan market then spread from this epicenter into the neighborhoods surrounding the market and then beyond.

Originally Posted by Skeptic Ginger

Say lineage A spilled over into humans. CoV2 then continued to evolve in the hypothesized source animal. Then lineage B spilled over into humans.

How is that more likely than B evolved as a variant of A after it was in the human population?

I don't know. Maybe more analysis can be done here and presumably it all depends on how much it holds up.



Personally, I doubt very much that this is the final word on the origins of Covid. I think it seems too premature for that and obviously more investigation will be needed to track down the wildlife route origin, if, in fact, that is how it got to Huanan in the first place.

I think the point for now is that it makes a pretty plausible case that Huanan is a very likely candidate for the origin of the virus's emergence.

[angrysoba]

So of course, the question is going to be, well where is the animal(s) that brought the virus?

Yes, it is true that none have yet been found despite "80,000 animals being tested", but as this person on Twitter points out, the markets had clearly been selling a lot of wild life which was never tested.

In addition, very soon after the outbreak it seems there was a rush to close wildlife farms and a mass extermination of animals there. This is not unusual in pandemics in fact, and certainly does point to the Chinese government finding a wildlife route to be a plausible explanation for the pandemic.

This article came out in February of 2020:

Quote:

Nearly 20,000 wildlife farms raising species including peacocks, civet cats, porcupines, ostriches, wild geese and boar have been shut down across China in the wake of the coronavirus, in a move that has exposed the hitherto unknown size of the industry.

Until a few weeks ago wildlife farming was still being promoted by government agencies as an easy way for rural Chinese people to get rich.

But the Covid-19 outbreak, which has now led to 2,666 deaths and over 77,700 known infections, is thought to have originated in wildlife sold at a market in Wuhan in early December, prompting a massive rethink by authorities on how to manage the trade.

China issued a temporary ban on wildlife trade to curb the spread of the virus at the end of January and began a widespread crackdown on breeding facilities in early February.

Why would China have reacted like this unless they saw the likelihood of it being caused by the wildlife trade?

[Dr.Sid]

Originally Posted by angrysoba

Why would China have reacted like this unless they saw the likelihood of it being caused by the wildlife trade?

My thought on this part only. I don't think there is any relation to what really happened to how China is reacting. This is public reaction. Something China thinks we want it to do. And probably what China wanted to do anyway. Even if covid haven't started in the market, prior infections certainly did, and future ones might.

Also Chinese government is criminal conspiracy from the beginning. Somebody supporting official position should prove his independence to greater than usual extent.

[angrysoba]

Originally Posted by Dr.Sid

My thought on this part only. I don't think there is any relation to what really happened to how China is reacting.

You think that China shut down the wild life farms because "we" wanted them to do so? Wow! Good for China then, to finally start taking "us" into consideration. Usually they tell "us" to go **** ourselves and stop interfering in their domestic issues.

Do you really think that?

Originally Posted by Dr.Sid

This is public reaction. Something China thinks we want it to do.

Public relations? This is something you know, or something you suspect but have decided to categorically state as if it is common knowledge?

Again, I am quite surprised you immediately think that China is thinking of "us" when doing this. My understanding is that China does not want to implicate the wildlife trade, and have made up all kinds of their own conspiracy theories such as how the virus leaked from a US lab or that it began in Italy or came to China on frozen food or lobsters from Maine, etc...

Originally Posted by Dr.Sid

And probably what China wanted to do anyway. Even if covid haven't started in the market, prior infections certainly did, and future ones might.

Yes, they did. That in itself should influence your priors.

Originally Posted by Dr.Sid

Also Chinese government is criminal conspiracy from the beginning. Somebody supporting official position should prove his independence to greater than usual extent.

I'm not supporting the official position at all. The idea it originated in the Huanan Market is NOT the official position of the Chinese goverment.

Quote:

China’s top epidemiologist said Tuesday that testing of samples from a Wuhan food market, initially suspected as a path for the virus’s spread to humans, failed to show links between animals being sold there and the pathogen. Gao Fu, director of the Chinese Center for Disease Control and Prevention, said in comments carried in Chinese state media, “It now turns out that the market is one of the victims.”

Link

Their actions implicate the market and the wildlife trade while their statements officially deny it.

They also deny the lab leak scenario as well, of course.

But you should remember, if you are going to make claims like those you have about China doing things for public relations, that their official position is NOT that the market is the centre of the outbreak.

[Lplus]

Originally Posted by angrysoba

So of course, the question is going to be, well where is the animal(s) that brought the virus?

Yes, it is true that none have yet been found despite "80,000 animals being tested", but as this person on Twitter points out, the markets had clearly been selling a lot of wild life which was never tested.

In addition, very soon after the outbreak it seems there was a rush to close wildlife farms and a mass extermination of animals there. This is not unusual in pandemics in fact, and certainly does point to the Chinese government finding a wildlife route to be a plausible explanation for the pandemic.

This article came out in February of 2020:



Why would China have reacted like this unless they saw the likelihood of it being caused by the wildlife trade?

The obvious answer to that is because it would point the finger away from the real cause.

[angrysoba]

Originally Posted by Lplus

The obvious answer to that is because it would point the finger away from the real cause.

You laugh, but that is exactly what is being proposed, and that they probably wanted to do it anyway, because that is how pandemics start and they want to prevent future pandemics.

[Lplus]

Originally Posted by angrysoba

You laugh, but that is exactly what is being proposed, and that they probably wanted to do it anyway, because that is how pandemics start and they want to prevent future pandemics.

Pity they didn't do it after the SARS 1 outbreak then.

[angrysoba]

Originally Posted by Lplus

Pity they didn't do it after the SARS 1 outbreak then.

Indeed. My understanding is that there actually had been some moves to do this.

BUT... there was also a swine flu epidemic. This article is from Dec 17th 2019 (not long before we learned of Covid-19) and it was to do with an ongoing swine flu epidemic ranging from China that ended up going into other neighbouring countries.

Quote:

WULONGQIAO, China — A devastating disease spreading from China has wiped out roughly one-quarter of the world’s pigs, reshaping farming and hitting the diets and pocketbooks of consumers around the globe.

China’s unsuccessful efforts to stop the disease may have hastened the spread — creating problems that could bedevil Beijing and global agriculture for years to come.

To halt African swine fever, as the disease is called, the authorities must persuade farmers to kill infected pigs and dispose of them properly. But in China, officials have been frugal to the point of stingy, requiring farmers to jump through hoops to seek compensation from often cash-poor local governments.

As a result, Chinese officials are not reaching farmers like Peng Weita. When one of his pigs suddenly died three months ago from swine fever, he said, he quickly slaughtered his other four dozen before they could fall sick as well. But he buried them and took a big loss rather than reporting the deaths to the government for compensation.

“Three years of costs were all for nothing,” Mr. Peng said.

His loss was the government’s as well. Because he did not report the episode, local officials could not make sure he followed all the steps necessary to halt the spread, like burying carcasses a considerable distance from the farm. Mr. Peng said he probably buried them too close to his farm but declined to discuss details of the disposal.

The epidemic shows the limits of China’s emphasis on government-driven, top-down solutions to major problems, sometimes at the expense of the practical. It has also laid bare the struggle of a country of 1.4 billion people to feed itself.

Link

I remember on This Week in Virology (TWiV) hearing someone explain that this massive swine flu epidemic that wiped out so many pigs, led to... guess what? The ramping up of the wildlife trade to make up the shortfall in food and income for farmers.

[Dr.Sid]

Originally Posted by angrysoba

You think that China shut down the wild life farms because "we" wanted them to do so? Wow! Good for China then, to finally start taking "us" into consideration. Usually they tell "us" to go **** ourselves and stop interfering in their domestic issues.

Do you really think that?

Yes. Not that we want them to do it. But that they think we are expecting it. Like this:

Sir ! There is a new disease spreading in Wuhan apparently from a seafood market !
Ah, Wuhan ? Isn't that where our new virus lab is ? Don't tell me it's our fault !
We can't tell sir !
Yeah .. as expected .. we can't admit it is either way. But we should do something, right ? To save face.
Certainly, sir ! What about regulating those damn markets, those places are terrible !
Oh, why we didn't do it already anyway ? It's not like farmers will revolt, right ? Ha ha ha.
They know we would just shoot them, sir ! Ha ha ha.
Ah, and don't forget to purge the lab documents, just to be sure.
I've already ordered that, sir.

[angrysoba]

Originally Posted by Dr.Sid

Yes. Not that we want them to do it. But that they think we are expecting it. Like this:

Sir ! There is a new disease spreading in Wuhan apparently from a seafood market !
Ah, Wuhan ? Isn't that where our new virus lab is ? Don't tell me it's our fault !
We can't tell sir !
Yeah .. as expected .. we can't admit it is either way. But we should do something, right ? To save face.
Certainly, sir ! What about regulating those damn markets, those places are terrible !
Oh, why we didn't do it already anyway ? It's not like farmers will revolt, right ? Ha ha ha.
They know we would just shoot them, sir ! Ha ha ha.
Ah, and don't forget to purge the lab documents, just to be sure.
I've already ordered that, sir.

Okay, so are you just going to go with something you made up as the origin of Covid?

Mmmkay.

[Dr.Sid]

Originally Posted by angrysoba

Okay, so are you just going to go with something you made up as the origin of Covid?

Mmmkay.

Not at all. That's just why I think China's action against wet markets is irrelevant. IMHO they would do it even if they knew it came from lab.
Why so angry ?

[angrysoba]

Originally Posted by Dr.Sid

Not at all. That's just why I think China's action against wet markets is irrelevant. IMHO they would do it even if they knew it came from lab.
Why so angry ?

Not angry, but wondering why you are posting this speculative drivel and not acknowledging the corrections I have made to your claims or answered questions I have asked you. It makes me think you are not arguing in good faith, and maybe not very well versed in the topic so you are resorting to bluster and tone policing instead of the topic at hand.

I

[Skeptic Ginger]

Originally Posted by angrysoba

No, maybe not. But I don't think it is much of an objection. Worobey et. al say:

In other words, "around 18 November 2019 (23 October–8 December)". It hardly seems to be a problem.

Not "widespread" but circulating. And they say that:

All of this is speculation on Worobey's part. I will repeat what I said before: There are a number of holes in Worobey's study and he simply makes stuff up to fit his round data in a square hole.

One key giveaway to his significant bias is him claiming how his and the other study makes a lab-leak origin as unlikely as a lightning strike, (or however he worded it). Give me a break, that is a narcissistic overstatement. He is certain he knows.

But a lot of people involved, like Andersen and Tedros, have commented the lab-leak has not been ruled out.

It's not useful to debate where Worobey has filled in the blanks sans evidence. Best if we debate the new evidence rather than repeating what we've already discussed ad nauseum about Worobey's holes in his evidence..


Take the following for example:

Quote:

Maybe it cannot be discounted. However, the presence of both within the stalls and in proximity does increase the chances that the Huanan Market was likely a locus. My understanding, from looking at other virologists commenting on this is that this did not begin with an animal being infected by a bat in a stall, but animals already infected brought into the market having been infected in the supply chain, either at a farm or en route, suggesting also that supply chain workers could also have been infected somewhere along the line.

What is it you are talking about here? Both lineages can be traced to the market, is that right? When you say "within the stalls" was that people who worked in those stalls?

There were no bats at that market. It wasn't on the menu in many Wuhan homes. We had a long discussion early in the thread when 'bat soup' was suggested as the problem.

Yes, there had to have been a supply chain. So where is evidence of infected animals outside of the market? Outside of Wuhan? How did an infected animal handler not infect anyone except at the market?

The odds are not in favor of this hypothesis for two reasons:

There is no trail, none zilch. Even given the Chinese scrubbing and closing the market would not erase the trail of COVID to Wuhan.

And Worobey can only speculate about those earliest cases. They may have a direct link to the WIV or to the CCDC lab near the market. We don't know and neither does Worobey.

Quote:

I don't know. Maybe more analysis can be done here and presumably it all depends on how much it holds up.

Personally, I doubt very much that this is the final word on the origins of Covid. I think it seems too premature for that and obviously more investigation will be needed to track down the wildlife route origin, if, in fact, that is how it got to Huanan in the first place.

I think the point for now is that it makes a pretty plausible case that Huanan is a very likely candidate for the origin of the virus's emergence.

I agree, we don't have the final word. Plausible, maybe. But missing evidence is pretty damning, IMO. Where do you expect this missing animal trail is going to be found if it hasn't already?

China might not want that trail found but like early cases of COVID in Dec 2019 were leaked by health care providers, no cases of COVID-like pneumonia outside of Wuhan were leaked.

Now consider what evidence China might be hiding.

The raw data on the lab workers' COVID tests was not shown to the WHO inspectors.

They have yet to release all the coronavirus genome data they have quashed.

They won't release information on the earliest cases.

Those things could go a long way toward ruling out the lab ... or incriminating it.

[Roger Ramjets]

Originally Posted by angrysoba

The epidemic shows the limits of China’s emphasis on government-driven, top-down solutions to major problems,

I'm wondering what other method of dealing with 'major problems' would be more appropriate. Pretend there's no problem and hope it goes away by itself?

[angrysoba]

Originally Posted by Roger Ramjets

I'm wondering what other method of dealing with 'major problems' would be more appropriate. Pretend there's no problem and hope it goes away by itself?

Well indeed. These are not my words, of course, but of the article that I was quoting about the swine flu epidemic that prefigured Covid.

[angrysoba]

Originally Posted by Skeptic Ginger

All of this is speculation on Worobey's part. I will repeat what I said before: There are a number of holes in Worobey's study and he simply makes stuff up to fit his round data in a square hole.

One key giveaway to his significant bias is him claiming how his and the other study makes a lab-leak origin as unlikely as a lightning strike, (or however he worded it). Give me a break, that is a narcissistic overstatement. He is certain he knows.

But a lot of people involved, like Andersen and Tedros, have commented the lab-leak has not been ruled out.

I don't think the phylogenetic analysis is "speculation". I don't know much about how this kind of thing is done, but would you accept dismissing the TopHap analysis as "speculation"?

Besides, Worobey did not do the analysis. It was Pekar. Presumably you could work your way through the supplementary materials or contact them to find out how they arrived at the emergence date. It would be meaningless to me because I do not have the competence to understand these things. Hopefully it will all be open to other scientists who want to do their own calculations.

Originally Posted by Skeptic Ginger

Take the following for example:
What is it you are talking about here? Both lineages can be traced to the market, is that right? When you say "within the stalls" was that people who worked in those stalls?

I believe so, but I could be wrong.

Originally Posted by Skeptic Ginger

There were no bats at that market. It wasn't on the menu in many Wuhan homes. We had a long discussion early in the thread when 'bat soup' was suggested as the problem.

I don't think any of the scientists of the spillover scenario have ever talked about bat soup. If there was any "long discussion" about bat soup it was probably a strawman or someone talking very ignorantly about the situation.

If my memory is mistaken, I would be happy for you to find the discussion again.

Nobody is suggesting bats were in the market.

Originally Posted by Skeptic Ginger

Yes, there had to have been a supply chain. So where is evidence of infected animals outside of the market? Outside of Wuhan? How did an infected animal handler not infect anyone except at the market?

There isn't any.

Originally Posted by Skeptic Ginger

The odds are not in favor of this hypothesis for two reasons:

There is no trail, none zilch. Even given the Chinese scrubbing and closing the market would not erase the trail of COVID to Wuhan.

And Worobey can only speculate about those earliest cases. They may have a direct link to the WIV or to the CCDC lab near the market. We don't know and neither does Worobey.

Yes, maybe, but it seems odd that we are now moving the lab leak itself from the primary suspect based on X, Y and Z reasons to a completely different lab based only on proximity. Remember that the reasons for suspecting the WIV were that it was BSL-4, worked on coronaviruses and was in Wuhan. So the CCDC, well, it is in Wuhan and close to the market where all the cases were found. The rationale seems very weak in comparison.

Originally Posted by Skeptic Ginger

I agree, we don't have the final word. Plausible, maybe. But missing evidence is pretty damning, IMO. Where do you expect this missing animal trail is going to be found if it hasn't already?

China might not want that trail found but like early cases of COVID in Dec 2019 were leaked by health care providers, no cases of COVID-like pneumonia outside of Wuhan were leaked.

Now consider what evidence China might be hiding.

The raw data on the lab workers' COVID tests was not shown to the WHO inspectors.

They have yet to release all the coronavirus genome data they have quashed.

They won't release information on the earliest cases.

Those things could go a long way toward ruling out the lab ... or incriminating it.

Could you be more specific here. Which earliest cases do you know of that China has been refusing to release?

[angrysoba]

Discussion about the two papers on a podcast with Kristian Andersen and Michael Worobey:

YouTube Video This video is not hosted by the ISF. The ISF can not be held responsible for the suitability or legality of this material. By clicking the link below you agree to view content from an external website.

I AGREE

[Skeptic Ginger]

Originally Posted by angrysoba

I don't think the phylogenetic analysis is "speculation". I don't know much about how this kind of thing is done, but would you accept dismissing the TopHap analysis as "speculation"?

What was speculated about in both studies was the missing data on the earliest cases, not the analysis in either study.

TopHap didn't fill in any missing data blanks. When you analyze thousands of genomes for the genetic trail your conclusions are based on very strong data. When you base your study on the earliest cases and you are missing the key gemomes/cases your data is weak.

Quote:

Besides, Worobey did not do the analysis. It was Pekar. Presumably you could work your way through the supplementary materials or contact them to find out how they arrived at the emergence date. It would be meaningless to me because I do not have the competence to understand these things. Hopefully it will all be open to other scientists who want to do their own calculations.

Sigh ... From the Pekar/Worobey et al study:

Quote:

The earliest lineage A viruses, Wuhan/IME-WH01/2019 and Wuhan/WH04/2020, were sampled on 30 December 2019 and 5 January 2020, respectively

Those are not the earliest lineage A virus genomes, they are the earliest genomes except for the true 'earliest' genomes the Chinese refuse to disclose. Look how late the viruses were sampled.

You continue to ignore the problem of this missing key data. Over and over you repeat the same things while ignoring this problem.

If your phylogenetic analysis used a small sample size then it can be greatly affected by missing data, especially if that missing data consists of a group of genomes all from the earliest cases.

Worobey, as good of a scientist as he clearly is, is displaying an incredible amount of confirmation bias here in how he discusses the strength of his conclusions. What he should be saying is the two studies do come at the problem from different angles and corroborate each other, but our research was limited by the missing earliest cases.

That is how you report research, at the end of your conclusions you add the study's limitations. That is standard protocol in a research report. You don't run around all excited overstating the significance of your findings.

I have to run to the store. I'll try to address the rest when I get back.

[Roger Ramjets]

Originally Posted by Skeptic Ginger

From the Pekar/Worobey et al study: Those are not the earliest lineage A virus genomes, they are the earliest genomes except for the true 'earliest' genomes the Chinese refuse to disclose.

Which are of course the proof that Covid came from a lab. Why else would the Chinese refuse to disclose these true 'earliest' genomes?

[lomiller]

Originally Posted by Skeptic Ginger

What was speculated about in both studies was the missing data on the earliest cases, not the analysis in either study.

This seems like an odd choice of wording to me. Can something be missing if it never existed in the first place?

The data on the earliest cases don't exist, nor is there any valid reason to think it should exist. Describing it as "missing" sounds like you are trying to imply someone is covering up something.

[No Other]

Originally Posted by angrysoba

This is like something I would expect from anti-vaxxers. (“How much are they taking from Big Pharma, huh?”). Remember that earlier you were fairly confidently claiming that these papers would not pass peer review. But now they have, so I guess we are to assume that the peer reviewers are also being paid off too? Do you see how this the route to conspiracy theory?

Peer review is not robust. Peer Review exhibits the same weaknesses as Institutions that accept monies from various sources... money talks and money keeps various minds from exploring certain possibilities. The problem started when the lab leak hypothesis people were told to prove there was a leak without demanding the same from the zoonotic side (I say demanding because for some reason the default is that COVID-19 is zoonotic which is totally arbitrary). Given that labs have used GOF to "create" things we will never know, the default should be that new virus' be initially suspected as lab created. If nature is at work, it will be found.

[lomiller]

Originally Posted by No Other

Peer review is not robust. Peer Review exhibits the same weaknesses as Institutions that accept monies from various sources... money talks and money keeps various minds from exploring certain possibilities.

"Mainstream science is suppressing the truth!!!" is the catercorner of virtually every pseudoscience and conspiracy theory out there.

Originally Posted by No Other

The problem started when the lab leak hypothesis people were told to prove there was a leak without demanding the same from the zoonotic side (I say demanding because for some reason the default is that COVID-19 is zoonotic which is totally arbitrary).

The lab leak side was asked to provide evidence, and so far it hasn't managed to come up with any.

As for why zoonotic crossover is the default, it's something that has been happening for billions of year and there are infection outbreaks and epidemics that start this way every single year. Every virus that infects humans likely crossed over from some other species at some point. Conversely there isn't a single recorder example of a novel virus coming from a lab leak.

Originally Posted by No Other

Given that labs have used GOF to "create" things we will never know, the default should be that new virus' be initially suspected as lab created.

It's been explicitly proven that Covid wasn't created in a lab.

I don't know where you got you mistaken impressions about GoF research, but it's a critical tool in identifying what viruses are a risk to jumping to humans. Not knowing what viruses could jump from other animals and kill you isn't going to save you from it happening.

[angrysoba]

Originally Posted by No Other

Peer review is not robust. Peer Review exhibits the same weaknesses as Institutions that accept monies from various sources... money talks and money keeps various minds from exploring certain possibilities. The problem started when the lab leak hypothesis people were told to prove there was a leak without demanding the same from the zoonotic side (I say demanding because for some reason the default is that COVID-19 is zoonotic which is totally arbitrary). Given that labs have used GOF to "create" things we will never know, the default should be that new virus' be initially suspected as lab created. If nature is at work, it will be found.

This is what I am saying about it sounding like an anti-vaxx argument.

If I say, "This peer-reviewed RCT shows the effectiveness of Vaccine A", then anti-vaxxers will say, "Nah, the writers and peer reviewers and journals are paid off by Big Pharma so none of the RCTs can be trusted."

I am fine with saying that there are all kinds of flaws with the peer-review system. Indeed, there are, and we have seen examples of that with people submitting to low-quality journals with fraudulent data on things like Ivermectin. There is a good book called Science Fictions which goes into the problems of peer review (and much else besides such as bias, negligence and hype). But please note that in the case of Ivermectin, researchers actually looked into and evaluated the methods and data of the research before determining that the science was bad (if not outright fraudulent.).

If you simply dismiss a paper on a priori grounds that any paper that argues for a zoonotic spillover must be the result of a conspiracy by Big Pharma, then there is almost no point in you being in the discussion, because you have determined your conclusion first and based it upon unknowable surmising that you have no evidence for (you do NOT know whether the peer-reviewers were paid off, nor do you know that this is the case with the authors of the papers).

[The Atheist]

Looks like case closed to me:

Quote:

The virus almost-certainly jumped from wildlife into humans in the Huanan Seafood Wholesale Market in Wuhan, the papers argue. The authors have even found the most likely section of the market. They have old photos of caged raccoon dogs – known carriers of Covid-19 – being sold there.

Quote:

If the Covid-19 virus originated in a lab, as some conspiracy theories suggest, you’d expect a single introduction into humans – rather than two distinct viral lineages. And both strains were found in samples taken from Huanan market.

https://www.stuff.co.nz/national/exp...ovid19s-origin