Origins of Covid

[The Atheist]

Originally Posted by Sherkeu

Why do some here seem so against skeptics exploring and looking at various information...

I don't see anyone arguing the evidence shouldn't be examined, no matter how unreliable it may be.

It's the jumping to conclusions on little or no evidence I object to.

Originally Posted by Samson

If the virus jumped from Wuhan bats the dna evidence would be clear.
If the virus jumped from the Wuhan lab the Chinese government would punish any country that asked them to investigate by punishing that country's wine industry.

What a load of cobblers - the trade dispute with Australia goes back long before Covid.

Have they stopped buying Australian coal?

Originally Posted by Orphia Nay

How do we know the virus wasn't perfect when it jumped if we don't know the source / what it jumped from?

The idea the virus was "perfect" is as dumb as Trump's claims about his perfect phone calls.

The evidence is enormous that the virus wasn't only not perfect, but barely able to survive in human populations, because it wouldn't have had any evolutionary pressure to evolve, and it's evolving very quickly.

[lomiller]

Originally Posted by Skeptic Ginger

If it came from a pangolin/bat recombination event, why are there no papers declaring eureka? We're done here, we know the origin

Maybe because scientific papers rarely contain the word “eureka”

Originally Posted by angrysoba

I need to point out, again, that this was already very well known about the virus. It doesn't "corroborate" what Dr Quay says. Papers had already been published. Like this one...

https://www.nature.com/articles/s41591-020-0820-9

I posted that before, and you ignored it.

And more recently, the papers I linked up-thread
https://www.nature.com/articles/s41598-020-78703-6

Quote:

Our analysis confirmed that the 228 bp long sequence within the SARS-CoV-2 S protein (Fig. 2A) is likely to be an integrated sequence resulting from recombination between some strains similar to Bat-CoV-RaTG13 (NCBI accession No. MN996532) and some strains similar to Pangolin-CoV-2019 (NCBI accession No. MT121216; Table 1, Fig. 1D, Figs. S1C, S2). This recombination was significant in 6 independent statistical tests (Table 1). Moreover, we further validated of this recombination by performing sliding window analysis on sequence differences (Fig. S3) between SARS-CoV-2 and other coronaviruses proximal to SARS-CoV-2 in the phylogenetic tree (Fig. 1A). The recombination event was also validated by genetic distance analyses (Table 2).

https://www.nature.com/articles/s41467-021-21240-1

Identifies a new Covid relative circulating in bats in Thailand. They suggest that Covid-19’s bat ancestor could come from a much wider area than is currently being looked at, and this includes places like Thailand where bats and Pangolins live in the same areas.

Furthermore, they report Covid-19 reactive antibodies not just in bats but in a Pangolin as well indicating Covid-19 or a very close relative may be circulating there.

[Skeptic Ginger]

Originally Posted by Orphia Nay

Have they looked at a primate in China being the source for a lab bite?

I haven't seen anything suggesting the lab had primates. It was primates in zoos that were infected from their zookeepers.

[Skeptic Ginger]

Originally Posted by lomiller

Maybe because scientific papers rarely contain the word “eureka”

You don't think that would have been in the news?

Originally Posted by lomiller

And more recently, the papers I linked up-thread
https://www.nature.com/articles/s41598-020-78703-6

https://www.nature.com/articles/s41467-021-21240-1

Identifies a new Covid relative circulating in bats in Thailand. They suggest that Covid-19’s bat ancestor could come from a much wider area than is currently being looked at, and this includes places like Thailand where bats and Pangolins live in the same areas.

Furthermore, they report Covid-19 reactive antibodies not just in bats but in a Pangolin as well indicating Covid-19 or a very close relative may be circulating there.

I saw all this and no one is disputing that a slew of COVID related gene segments exist in the wild. And I don't think you can find a post of mine that said it was 'my opinion' (meaning not an opinion in a paper I posted) that the lab is definitively the source. Nor has any paper so far said a natural event was definitively the cause.

"Genomic recombination events may reveal" not 'has revealed'.

"Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins."

These are important sources. That's why they belong in the discussion.


Maybe I need to remind people the title of this thread is "Origins of Covid". The title is not, 'the origin of Covid was the lab'.

Let's go back to the beginning of this discussion. You made a statement the virus had to have come from the pangolin.

Originally Posted by Skeptic Ginger

Has that been narrowed down? I thought there were one or more possible animals besides the pangolin.

Originally Posted by lomiller

...
Most of the virus is closely related to the bat virus, however the spike structure of that virus is unlikely to infect humans. The spike protein of covid-19 is very closely related genetically and structurally to one found in Pangolins but the rest of the Pangolin virus is considerably more distant from Covid-19.

Pangolins were in the market where the first major outbreak started so the simplest answer is that's where the recombination occurred, and then it jumped to humans. There may be other potential places the recombination occurred but they appear more complicated and unlikely

Originally Posted by Skeptic Ginger

But keep in mind the wet market was not the original source of the pandemic.

Newsweek 04-27-20 ...

There's a lot in this Newsweek article, more than usual for a news magazine. The whole next section is worth a read.

Evidence it could have happened in the lab, my point being the lab has not been ruled out. Also, I haven't seen a source confirming pangolins were for sale at the market. Maybe there is one?

And I added that the argument against the origin being in the lab was that lab manipulation could be spotted genetically. But passing the virus through other animal species would not be visible.

Originally Posted by lomiller

The bat virus is Covid-19's closest know relative, it's significantly more closely related to Covid-19 than the Pangolin virus. Only the spike protein came from the Pangolin virus.

It's possible the recombination event joined the two happened in yet another species, but given Pangolin's presence at the epicenter of the original outbreak the simplest solution is that it occurred in Pangolins. Either way Pangolins are involved because that is the apparent source of the spike protein. ...

Except the pangolin has not been shown to have been present at the epicenter of the original outbreak.

Originally Posted by lomiller

This has been achieved to a relatively high degree. It's possible there are still some missing steps, but what we already know is more than enough to say it's unlikely it would have been in a lab in the first place.

Covid-19 is very much a new virus. How would a lab even get hold of it before it started circulating? It's a very infectious virus that can infect many different animal species. I don't find it credible that it was just sitting around waiting for a laboratory to pick it up and study. It's infectious enough that it would have begun circulating widely among animals almost the moment it came into existence and found it's way into humans shortly after. If it were not so infectious than the "escaped from a lab" story wouldn't make sense either.

This has been addressed but to summarize, no one is suggesting it was sitting around in the lab. IF if did happen in the lab mechanisms for this happening have been described.

Originally Posted by Skeptic Ginger

@lomiller: No it is not all recombination. That is playing a role with COVID, but it is not the only thing going on.

Meaning you have recombination event or events and you also have mutations: shift and drift.

Originally Posted by Skeptic Ginger

...The Lancet 2015 editorial: China's medical research integrity questioned.

Just a reminder. I went on to show an initial coverup happened with SARS.

The point of all this is: no paper has said the origin was definitively a pangolin in Wuhan. If we had that the discussion would be over. I find Quay's paper compelling. Some people here find evidence the pangolin as a source is compelling.

No one can explain the coincidence the outbreak occurred in Wuhan of all the cities in China if it wasn't the lab.

[Skeptic Ginger]

Originally Posted by lomiller

Minds are changes by published results, not the insistence that we need to be “skeptical” of the results that have already been published.

Much harm is done by purveyors of pseudo-science claiming to simply be "skeptics exploring and looking at various information". Climate science deniers, anti-vaxers, truthers, birthers and flat earthers would all describe themselves as "skeptics" who are just looking for reliable explanations.

Accusing people in this thread of being CTers does not move the discussion further.

This strawman is why there is a barrier to discussion here.

[RecoveringYuppy]

Originally Posted by Skeptic Ginger

Accusing people in this thread of being CTers does not move the discussion further.

This strawman is why there is a barrier to discussion here.

The strawman was in Sherkeu's post:

"Why do some here seem so against skeptics exploring and looking at various information"

ETA: Is there a word for when you've been "ninja'd" before the post you were replying to was even posted?

[Cavemonster]

Originally Posted by Skeptic Ginger

No one can explain the coincidence the outbreak occurred in Wuhan of all the cities in China if it wasn't the lab.

I think it might be a coincidence, but not such a huge one.

There are 23 provinces of mainland China. About a third of them are more rural. Hubei is pretty central to the populace parts of the country.
Wuhan is the 9th largest city in the country.

Many cities and provinces had been phasing out wet markets for the last 20 years. If a wet market played a role, as many seem to suspect, it would have been less likely to happen in cities where the practice is banned or more actively discouraged.

https://en.wikipedia.org/wiki/Wet_market#Asia

Yes, as has been noted, the closest bat form of the virus seems to be tracked elsewhere, but Wuhan would be an excellent candidate for initial spread conditions.

[Skeptic Ginger]

Originally Posted by RecoveringYuppy

The strawman was in Sherkeu's post:

"Why do some here seem so against skeptics exploring and looking at various information"...

There are a couple people here, I don't believe you are one of them. It doesn't matter.


Moving on, some things need clearing up:

Originally Posted by lomiller

You were the one arguing "more evolution was needed" earlier in the thread. I told you several pages back that because we now know the spike from the Pangolin virus is ALREADY efficient at attaching to human ACE2 bindings that the resulting virus would be very infectious to humans as soon as the recombination event occurred.

The argument that this is a natural event is that this spike stricture was unknown prior to research into Covid-19 so no one knew it could infect humans until mid 2020. No researcher could have been working with it in 2019, and even if they were they would have had zero reason to expect it would help create a more infectious version of a bat virus.

I've been reading a bit about the genetics of COVID 19, I'll post the inks and specifics later. But there is a general principle here that needs addressing.

There is a bat strain that is about 97ish% a match for COVID. And either all or just the spike protein of the pangolins is about the same, 97%.

Given the genetics and assuming a recombinant event, it does not get you to COVID-19. It's not close enough. I brought this up earlier, chimpanzee DNA is ~99% match for human DNA. And look how different we are.

I had to look again to be sure and this source says 98.8%. (I might have quoted the wrong number earlier).

Quote:

Humans and chimps share a surprising 98.8 percent of their DNA.

With the bat COVID relative being ~97% different from COVID-19, you can't just take the pangolin COVID relative and end up with a virus capable of infecting human cells no matter how you recombine the viruses.

It's not that simple to say we found this specific segment in the pangolin that solves the problem. It doesn't. Unless we find a much closer match than either the bat or the pangolin coronaviruses, we don't have the animal source for the jump.

97% might sound like a very close match, but as far as genomes go, it's not close. Chimpanzees are not like Neanderthals, they are not close enough to breed with humans (think in vitro). 98.8% is not close enough.

I'll post about what I found tomorrow that will make this a bit more clear, but people need to stop thinking we have the answer just because pangolin coronavirus has a specific spike protein gene.


As for it being a natural event, the evidence is clear that it was. But such recombinant events can be coaxed in the lab and that is what there is at least some question the researchers were working with coronaviruses where such a 'natural' event could have taken place.

The point of this thread is to look at the evidence that is out there supporting the origin of COVID 19. The point is not to prove the origin was or was not the WIV. I can lean in one direction, that doesn't mean I can't lean in the other direction should that evidence surface.

You all can also lean in one direction. The point here is not to 'prove' a person right or wrong. The point is to discuss the evidence with an open mind.

[Skeptic Ginger]

Originally Posted by Cavemonster

I think it might be a coincidence, but not such a huge one.

There are 23 provinces of mainland China. About a third of them are more rural. Hubei is pretty central to the populace parts of the country.
Wuhan is the 9th largest city in the country.

Many cities and provinces had been phasing out wet markets for the last 20 years. If a wet market played a role, as many seem to suspect, it would have been less likely to happen in cities where the practice is banned or more actively discouraged.

https://en.wikipedia.org/wiki/Wet_market#Asia

Yes, as has been noted, the closest bat form of the virus seems to be tracked elsewhere, but Wuhan would be an excellent candidate for initial spread conditions.

If you could explain how an individual was infected elsewhere and just happened to come to Wuhan before infecting anyone from where they were infected... it makes no sense.

An earlier article by Dr Quay mapped out the first cases there was genetic evidence for and they clustered around one particular mass transit line. The line goes to the WIV, near the seafood market where a superspreader event took place, and a hospital where the first cluster was recognized.

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

Before anyone gets antsy to dismiss this, he shows his work like any good epidemiologist would. Go to the link to see the genomes he looked at, where he got them and how he traced the clade lineages. This one is a pre-print where the other one is labeled a working paper. I don't know if this one has been submitted to any journal publisher yet but I'll look.

Quote:

The origin of the SARS-CoV-2 coronavirus that has caused the COVID-19 worldwide pandemic remains unknown. Here I report that the earliest genomic cluster is a group of four patients associated with the General Hospital of Central Theater Command of People's Liberation Army (PLA) of China in Wuhan. This cluster contains the “Founder Patients” of both Clade A and Clade B, from which every SARS-CoV-2 coronavirus that has infected every patient with COVID-19 anywhere in the world has arisen, ...

This shows the specifics of where the first cases occurred. They cluster near the WIV. And remember the wet market was not the source of the original species jump.

[Capsid]

Originally Posted by Skeptic Ginger

I haven't seen anything suggesting the lab had primates. It was primates in zoos that were infected from their zookeepers.

Pedantic mode, but humans are primates too.

[Capsid]

I think it's a stretch to argue that the human and chimps genome similarity yet different phenotypically, can be applied to virus genome homology.

[steenkh]

Originally Posted by Skeptic Ginger

97% might sound like a very close match, but as far as genomes go, it's not close. Chimpanzees are not like Neanderthals, they are not close enough to breed with humans (think in vitro). 98.8% is not close enough.

Is that really true? I would say that in a recombination event, the only thing that is needed is that the two combining RNA strings will be able to make up 100% of the SARS-CoV-2 genome. This could be done by, say 97% of bat virus, and 3% pangolin.

[angrysoba]

Some members of the WHO investigation seem to be completely ruling out the most ridiculed hypothesis, that of the cold chain theory:

Quote:

World Health Organization investigators have downplayed a Chinese theory that coronavirus was brought to Wuhan through frozen food, underlining the charged geopolitics surrounding the roots of Covid-19.

Vladimir Dedkov from the Pasteur Institute in St Petersburg, Russia, and Fabian Leendertz, an emerging diseases specialist at Germany’s Robert Koch Institute, both told the Financial Times that it was extremely unlikely the first cases of Sars-Cov-2 identified in Wuhan in 2019 entered the city on frozen or refrigerated goods.

The two were part of the WHO team that travelled to Wuhan in January to investigate the origins of the pandemic. But in the press conference that concluded the visit last month, the WHO did not rule out the theory, which has been pushed hard by China’s government and state media.

“We know that the virus can persist and survive in conditions that are found in these cold and frozen environments, but we don’t really understand if the virus can then transmit to humans,” Peter Ben Embarek, the head of the investigation, said at the time.

Back on home ground in Russia, however, Dedkov was more definitive. He said samples of frozen food from the Huanan seafood market in Wuhan, which had tested positive for Sars-Cov-2, were probably contaminated by humans rather than the other way round.

“It’s very difficult to imagine a situation where all this [contaminated] food came to one market in China, and not the biggest one at that, from different countries and it all started from there,” Dedkov said. “We aren’t taking it out of consideration but we think it’s very unlikely given the facts we know today.”

From the Financial Times (you can probably see the full article if you answer some survey):
Link

Besides, such a theory could only explain how the virus had got to Wuhan (and presumably to other sources), but not its origins:

Quote:

Leendertz in Germany told the FT in a separate interview that although the transmission of Covid-19 via frozen foods was theoretically possible, the role of cold-chain transport was not the most important question.*

“If you transport a virus fresh or frozen, the virus is not born from a piece of plastic. It’s about where the virus is from before that. Cold chain is never the source,” he said.

Embarek also told the journal Science that frozen food “was not a possible route of introduction”.

“There were no widespread outbreaks of Covid-19 in food factories around the world,” he added.

[angrysoba]

This WSJ article is a summary of some of the recent articles that suggest a natural origin:

Quote:

As a World Health Organization team digs into the origin of the Covid-19 pandemic, other scientists are unearthing tantalizing new clues suggesting that the virus behind it evolved naturally to infect humans.

At least four recent studies have identified coronaviruses closely related to the pandemic strain in bats and pangolins in Southeast Asia and Japan, a sign that these pathogens are more widespread than previously known and that there was ample opportunity for the virus to evolve.

One of them is by Edward C. Holmes, Kristian G. Andersen, Andrew Rambaut and Robert F. Garry. (All of them were apparently sent Quay's paper, but none of them seem to be interested in it. In addition, they are all pretty annoyed with Ailin Chan and Matt Ridley, Bill Maher, Bret and Hayley Weinstein, Yuri Deigin etc... for promoting the escaped from a lab theory).

Of course, if you look at Twitter, you'll see plenty of people claiming that these guys are all in some kind of circling the wagons situation.

But...

Quote:

The amino acid change also suggests a natural viral evolution, said James Weger-Lucarelli, a Virginia Tech virologist who led the study that identified that amino acid change. It was posted on a preprint server, meaning that it hadn’t been peer reviewed, and has been submitted to a journal for publication.

And...

Quote:

Scientists now should mount an aggressive search for the origin of the pandemic virus wherever horseshoe bats roost, said Linfa Wang, professor of emerging infectious diseases at Duke-NUS Medical School in Singapore and a senior author of one of the bat studies. These bats, which carry coronaviruses, are found in tropical and temperate regions of Asia, the Middle East, Africa and Europe, he said, adding, “I am convinced that the ancestral virus came from bats.”

...

Chinese scientists reported soon after the pandemic began that the Wuhan Institute of Virology had a virus whose genome is a 96.2% match with that of the Covid-19 virus. But the difference between the two viruses would have been too great for researchers to successfully engineer the pandemic virus, said Dr. Wang, who is an expert in bat-borne viruses.

“It would explode your calculator,” he said of the difference. “If the best scientists all worked for me for the rest of my life, I would not be able to create it.”

Of course, Lin-Fa Wang is no doubt one of those who would be seen as covering for the Wuhan lab given that he is has co-written papers with Zhengli Shi and Peter Daszak, etc... and was the lead investigator on the paper that I cited in post 6 about the Covid-19 similar virus found in bats in Thailand...

The thing is, I think we are back to the idea that while it could have come from a lab, the view of these viruses that they are ready to emerge from nature at almost any moment, is one that most of the professional virologists seem to agree on. It is certainly the impression I have reading Quammen's book.

I think the alternative view is really that pretty much all the virologists in the world, particularly those who have done so much work on SARS, MERS, and Ebola, Nipah, and Hendra, are conspiring to cover-up a mistake of one of their colleagues.

[lomiller]

Originally Posted by Skeptic Ginger

And I don't think you can find a post of mine that said it was 'my opinion' (meaning not an opinion in a paper I posted) that the lab is definitively the source. Nor has any paper so far said a natural event was definitively the cause.

IOW “I’m not saying, I’m just saying”. Sorry but this isn’t the least bit convincing. ANY science can be overturned with the next new discovery. When we have an explanation that works we don’t “keep the door open” to alternative expansions with no evidence behind them just because new evidence “could come along”. We change our minds WHEN there is evidence for these alternative theories, not before.

Originally Posted by Skeptic Ginger

"Genomic recombination events may reveal" not 'has revealed'.

Many, perhaps most scientific conclusions tend to be low key until they are replicated. It’s a pretty good practice to follow.

Originally Posted by Skeptic Ginger

No one can explain the coincidence the outbreak occurred in Wuhan of all the cities in China if it wasn't the lab.

Texas sharpshooter fallacy. Take any event you want, and if you do enough digging you will find coincidences. These coincidences mean nothing unless you predicted them ahead of time and properly constrained your data so finding one was actually unlikely. If you take 10 000 events that each have a 1 in 100 chance of occurring and look at a single sample you’d expect to find 100 “coincidences”

[lomiller]

Originally Posted by Skeptic Ginger

Given the genetics and assuming a recombinant event, it does not get you to COVID-19. It's not close enough. I brought this up earlier, chimpanzee DNA is ~99% match for human DNA. And look how different we are.

You are simply re-hashing a point I made earlier in the thread. I’ve been very specific that RaTG14 is NOT a direct Covid-19 ancestor and that an actual Covid-19 ancestor has yet to be isolated. This makes it more than a little difficult for any lab to have been working with this ancestor 2 years ago.

Originally Posted by Skeptic Ginger

And either all or just the spike protein of the pangolins is about the same, 97%.

Not as relevant. The recombination event may not have involved the entire spike protein, and even if it did it may have been subject to considerable evolutionary stress before it jumped to humans. What’s more important here are specific sequences. The 2019 Pangolin virus may have directly provided the distinctive features of the spike or it may have been a close relative of the virus that did. Unlike RaTG13 both are possible.

Originally Posted by Skeptic Ginger

There is a bat strain that is about 97ish% a match for COVID.

RaTG13 is a relative of the ancestor of Covid-19 but not a direct ancestor. The paper I linked above says it’s 96% similar (but I’ve seen it rounded up to 97% as well). This 96% slightly higher than the new Covid-19 relative they found in Thailand which was 95.5% similar. They also suggest that close Covid-19 relatives could be located anywhere from Japan to Eastern Europe so RaTG13 being found in China may be a red herring. The actual ancestor may come from a much larger area, with SE Asia being a distinct possibility.

Originally Posted by Skeptic Ginger

As for it being a natural event, the evidence is clear that it was. But such recombinant events can be coaxed in the lab and that is what there is at least some question the researchers were working with coronaviruses where such a 'natural' event could have taken place.

Such “research” would have had to have been something along the lines of “lets infect a host with multiple, randomly chosen, poorly characterized viruses and see what happens!” Even someone things there could be value, a handful of such experiments in a lab doesn’t compare the nature doing millions of such experiments every day. Finally there is the issue of how they obtained a corvid ancestor that is previous unidentified , difficult to find and may not even exist in China.

In the absence of evidence to the contrary, we chose the simplest expiation. The simplest explanation, by far, is that this is a natural event that occurred out in the wild. There is no reason to suspect it’s any different from any of recombination events that have resulted in novel viruses throughout the history of the planet.

Originally Posted by Skeptic Ginger

You all can also lean in one direction. The point here is not to 'prove' a person right or wrong. The point is to discuss the evidence with an open mind.

How is this different than a Proponent of Intelligent design arguing that since it’s impossible to prove evolution we should keep an open mind. Remember while science piles up more and more evidence it’s actually impossible for it to truly prove anything, but what it can do is pile evidence in favor of one answer to the point where we can completely discount the proposed alternative until it can present positive evidence of it’s own.

There is not compelling positive evidence for the lab hypothesis. It’s also more complicated requires people to know about undiscovered viruses and be doing research that wouldn’t make sense. This means it can be and will be discounted and discredited by people doing actual science until such a time as evidence can be produces. It’s not a scientifically valid explanation at this point and doesn’t belong in this thread.

[lomiller]

Originally Posted by steenkh

Is that really true? I would say that in a recombination event, the only thing that is needed is that the two combining RNA strings will be able to make up 100% of the SARS-CoV-2 genome. This could be done by, say 97% of bat virus, and 3% pangolin.

The Pangolin virus or a close relative is thought to have contributed a few hundred of the base pairs that make the spike protein. This could be much less than 3% of the whole genome. This virus is also still a Corona virus and therefor still a Covid relative, so it would have had a lot of common RNA with both Covid's direct ancestor, just not as much as RaTG13

[lomiller]

Originally Posted by angrysoba

Some members of the WHO investigation seem to be completely ruling out the most ridiculed hypothesis, that of the cold chain theory:


From the Financial Times (you can probably see the full article if you answer some survey):
Link

Besides, such a theory could only explain how the virus had got to Wuhan (and presumably to other sources), but not its origins:

Worth noting that this theory is a more plausible example of "face saving" in that frozen food would take culpability away from the cultural practice of live animals in wet markets.

[Skeptic Ginger]

Originally Posted by Capsid

Pedantic mode, but humans are primates too.

I know but thanks. I try to say non-human primates but it gets tedious.

I was hoping you'd join this thread. I'm interested in your take.

[Skeptic Ginger]

Originally Posted by Capsid

I think it's a stretch to argue that the human and chimps genome similarity yet different phenotypically, can be applied to virus genome homology.

What other analogy can I use to point out 97% is not close enough?

[Skeptic Ginger]

Originally Posted by steenkh

Is that really true? I would say that in a recombination event, the only thing that is needed is that the two combining RNA strings will be able to make up 100% of the SARS-CoV-2 genome. This could be done by, say 97% of bat virus, and 3% pangolin.

But we have no evidence of the recombination result that suggests we have found the source.

We have a partial match in bats and a partial match in pangolins. We don't have a combined match that is close enough to jump.

[Capsid]

Originally Posted by Skeptic Ginger

I know but thanks. I try to say non-human primates but it gets tedious.

I was hoping you'd join this thread. I'm interested in your take.

I don't think we have enough information. There are so many possibilities. There are lots of bats and lots of viruses. Bat caves are cleaned out of bat guano for copper mining and those individuals got sick. Plenty of opportunities there for virus mixing and adaptation to humans.


Sent from my iPhone using Tapatalk

[Capsid]

Originally Posted by Skeptic Ginger

What other analogy can I use to point out 97% is not close enough?

I don't have one. Virologists don't tend to use analogies, they just look at sequence trees and nod their heads.


Sent from my iPhone using Tapatalk

[lomiller]

Originally Posted by Capsid

I don't think we have enough information. There are so many possibilities. There are lots of bats and lots of viruses. Bat caves are cleaned out of bat guano for copper mining and those individuals got sick. Plenty of opportunities there for virus mixing and adaptation to humans.


Sent from my iPhone using Tapatalk

This isn't really the case. The changes that allow Covid to spread in humans could not have evolved in a bat because the spike structure attaches poorly to bat ACE2 receptors.

Similarly the virus could not have spread to humans and evolved from there because the spike that can attach to bat ACE2 doesn't readily attach to human ACE2.

It also doesn't seem to be a case of it evolving into an intermediate form that can infect either, because the Covid-19 spike contains the distinct signature of recombination with a virus that infects Pangolines.

This gives us a really good idea about what happened. A host, almost certainly a Pangolin, was infected by both viruses. The two viruses attacked the same cell, which in RNA viruses commonly causes genetic material from one to get spliced into the other. (Recombination) The result was a bat virus with a spike that that strongly resembled the one in the Pangolin virus.

This had to have happened in a host where that spike structure could attack to the ACE2 binding domain, or the virus would not have been able to propagate any further. It could have been something other than a Pangolin but that would have required BOTH viruses to jump to another species before the recombination event.

The most likely case is the Pangolin itself because the spike was already evolved to attach to Pangolin ACE2 binding and one of the viruses already circulated regularly in Pangolins so all that would have been required is for a sick Pangolin to come into contact with the bat virus.

Since the new virus already had a spike suitable for infecting Pangolins it could have spread and perhaps even evolved in them until one of the infected animals ended up in the Wuhan market where the virus jumped to humans.

From there it would take ~8 weeks before it became clear there was a new virus circulating. Since it started in the market, most of the initial spread would have been between workers and visitors but there was sufficient time for cases to have spread away from the market as well.

[Sherkeu]

Originally Posted by lomiller

This isn't really the case. The changes that allow Covid to spread in humans could not have evolved in a bat because the spike structure attaches poorly to bat ACE2 receptors.

Similarly the virus could not have spread to humans and evolved from there because the spike that can attach to bat ACE2 doesn't readily attach to human ACE2.

It also doesn't seem to be a case of it evolving into an intermediate form that can infect either, because the Covid-19 spike contains the distinct signature of recombination with a virus that infects Pangolines.

So when the scientists found viruses in Yunnan that are able to infect directly (in human cell cultures) and SARS-related antibodies from local villagers, then why not?

I'm not saying it happened for SARS-CoV-2, but it does seem to happen for SARS-related viruses- at least the ones in that cave in Yunnan. (it doesnt seen to happen in other bat populations tested)

Even recently, for SARS-CoV-2, the Chinese scientists do not rule out direct infection:

From a paper this year (submitted 9/20, published 1/2021):
https://www.sciencedirect.com/scienc...475?via%3Dihub

Quote:

Bat coronavirus (CoV) RaTG13 shares the highest genome sequence identity with SARS-CoV-2 among all known coronaviruses, and also uses human angiotensin converting enzyme 2 (hACE2) for virus entry. Thus, SARS-CoV-2 is thought to have originated from bat. However, whether SARS-CoV-2 emerged from bats directly or through an intermediate host remains elusive.

[angrysoba]

Originally Posted by Skeptic Ginger

What other analogy can I use to point out 97% is not close enough?

Here’s the he thing:

The closeness is what is giving rise to the lab hypothesis in the first place. This is why they are suggesting that either it is a similar virus or the Ratg13 that has been given supercharged in the lab.

It seems most virologists are discounting it on the basis that creating SARS CoV 2 from that particular virus would involve science not yet known, and are thus dismissing the lab leak or at the very least saying it makes it highly unlikely.

If you’re saying it is not close at all then it seems you are agreeing with them that it diminishes the lab leak theory.

On the other hand it seems that the wide distribution of SARS CoV-similar viruses makes the likelihood that another family member in the wild is the culprit.

[angrysoba]

Originally Posted by Sherkeu

So when the scientists found viruses in Yunnan that are able to infect directly (in human cell cultures) and SARS-related antibodies from local villagers, then why not?

I'm not saying it happened for SARS-CoV-2, but it does seem to happen for SARS-related viruses- at least the ones in that cave in Yunnan. (it doesnt seen to happen in other bat populations tested)

Even recently, for SARS-CoV-2, the Chinese scientists do not rule out direct infection:

From a paper this year (submitted 9/20, published 1/2021):
https://www.sciencedirect.com/scienc...475?via%3Dihub

Assumption alert (IANAV): I’m assuming the Ratg13 virus required a much higher viral load than SARS CoV 2. Maybe the workers had to be in very close proximity to a lot of the stuff in a confined space breathing it in.

On the other hand, SARS CoV 2 shows signs of “better adaptation to humans” hence the “hypothesis” that it was this virus that had been subjected to gain of function experiments.

The virologists are drawing different conclusions, from what I can gather saying that this type of discovery points to the fear that there were way more similar viruses out there getting ever closer to creating a new pandemic given the opportunities of recombining within wildlife, farmed, and domestic animals.

Organizations such as EcoHealth Alliance and others have been worrying about how ecological destruction and of course wet markets, etc... are increasing the chances that one of the similar viruses spills over.

I think it comes to a different view of what the Wuhan Institute of Virology is doing.

[angrysoba]

Originally Posted by lomiller

Worth noting that this theory is a more plausible example of "face saving" in that frozen food would take culpability away from the cultural practice of live animals in wet markets.

Yes, I was thinking something along those lines.

Even if the lab is cleared, there are many aspects of this that point the finger at China in general.

Another one is that the virologists have been pointing to the sensitivity that surrounds whichever region this virus is seen to originate from.

[Skeptic Ginger]

Originally Posted by lomiller

IOW “I’m not saying, I’m just saying”. Sorry but this isn’t the least bit convincing. ANY science can be overturned with the next new discovery. When we have an explanation that works we don’t “keep the door open” to alternative expansions with no evidence behind them just because new evidence “could come along”. We change our minds WHEN there is evidence for these alternative theories, not before.

I stated that the jury is still out and you are not convinced I mean it? Stop with the accusations please.



Moving on. This was interesting. There is at least one paper in Nature (posted above) that concludes there can't be a direct jump from bats to humans. I've been looking at papers from the WIV written before Nov 2019 to see what they were researching at the lab.

PLoS 2017 WIL: Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus

Quote:

Abstract
A large number of SARS-related coronaviruses (SARSr-CoV) have been detected in horseshoe bats since 2005 in different areas of China. However, these bat SARSr-CoVs show sequence differences from SARS coronavirus (SARS-CoV) in different genes (S, ORF8, ORF3, etc) and are considered unlikely to represent the direct progenitor of SARS-CoV. Herein, we report the findings of our 5-year surveillance of SARSr-CoVs in a cave inhabited by multiple species of horseshoe bats in Yunnan Province, China. The full-length genomes of 11 newly discovered SARSr-CoV strains, together with our previous findings, reveals that the SARSr-CoVs circulating in this single location are highly diverse in the S gene, ORF3 and ORF8. Importantly, strains with high genetic similarity to SARS-CoV in the hypervariable N-terminal domain (NTD) and receptor-binding domain (RBD) of the S1 gene, the ORF3 and ORF8 region, respectively, were all discovered in this cave. In addition, we report the first discovery of bat SARSr-CoVs highly similar to human SARS-CoV in ORF3b and in the split ORF8a and 8b. Moreover, SARSr-CoV strains from this cave were more closely related to SARS-CoV in the non-structural protein genes ORF1a and 1b compared with those detected elsewhere. Recombination analysis shows evidence of frequent recombination events within the S gene and around the ORF8 between these SARSr-CoVs. We hypothesize that the direct progenitor of SARS-CoV may have originated after sequential recombination events between the precursors of these SARSr-CoVs. Cell entry studies demonstrated that three newly identified SARSr-CoVs with different S protein sequences are all able to use human ACE2 as the receptor, further exhibiting the close relationship between strains in this cave and SARS-CoV. [/b]This work provides new insights into the origin and evolution of SARS-CoV and highlights the necessity of preparedness for future emergence of SARS-like diseases.

Was this all theoretical or was this based on lab experiments only a couple years before the pandemic? Or was it based on finding and collecting the relevant strains?

From the body of the paper:

Quote:

We have carried out a five-year longitudinal surveillance (April 2011 to October 2015) on SARSr-CoVs in bats from a single habitat in proximity to Kunming city, Yunnan province, China, which was mainly inhabited by horseshoe bats....

The full-length genome sequences of all 15 SARSr-CoVs from the surveyed cave were screened for evidence of potential recombination events....

That is all collecting and analyzing wild virus.


Then we get to experiments:

Quote:

... when Vero E6 cells* were respectively infected with the two successfully rescued chimeric SARSr-CoVs, WIV1-Rs4231S and WIV1-Rs7327S, and the newly isolated Rs4874, efficient virus replication was detected in all infections (Fig 7). To assess whether the three novel SARSr-CoVs can use human ACE2 as a cellular entry receptor, we conducted virus infectivity studies using HeLa cells** with or without the expression of human ACE2. All viruses replicated efficiently in the human ACE2-expressing cells. The results were further confirmed by quantification of viral RNA using real-time RT-PCR (Fig 8).

Research was done with cultured bat virus, they did not collect live bats in this report. But they did demonstrate that bat coronavirus could replicate in human cells.

That doesn't mean they created COVID-19, only that they were working with CoV that could infect humans.

*Green Monkey cells used to culture viruses
**Henrietta Lacks cells Human cells that don't die out, used to culture and test viruses.


Nature 2013: Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor

Quote:

Abstract
...attempts to isolate the progenitor virus of SARS-CoV from bats have been unsuccessful. ...Here we report whole-genome sequences of two novel bat coronaviruses from Chinese horseshoe bats (family: Rhinolophidae) in Yunnan, China: RsSHC014 and Rs3367. These viruses are far more closely related to SARS-CoV than any previously identified bat coronaviruses, particularly in the receptor binding domain of the spike protein. Here we report whole-genome sequences of two novel bat coronaviruses from Chinese horseshoe bats (family: Rhinolophidae) in Yunnan, China: RsSHC014 and Rs3367. These viruses are far more closely related to SARS-CoV than any previously identified bat coronaviruses, particularly in the receptor binding domain of the spike protein. Most importantly, we report the first recorded isolation of a live SL-CoV (bat SL-CoV-WIV1) from bat faecal samples in Vero E6 cells, which has typical coronavirus morphology, 99.9% sequence identity to Rs3367 and uses ACE2 from humans, civets and Chinese horseshoe bats for cell entry. ...

More importantly:

Quote:

Preliminary in vitro testing indicates that WIV1 also has a broad species tropism. Our results provide the strongest evidence to date that Chinese horseshoe bats are natural reservoirs of SARS-CoV, and that intermediate hosts may not be necessary for direct human infection by some bat SL-CoVs.

Not that the virus came from a cave in Yunnan, but that there were cultures of risky viruses at the WIV. And the virus would be completely natural, not one that was even a chimera made in the lab.


Again I point out the initial outbreak was in the neighborhood of the WIV.

[angrysoba]

Did they have dangerous viruses in the lab? Sure, it's a BSL-4 lab.

Did they have SARS CoV2 in the lab? No evidence.

So what is the theory here?

[Samson]

In its simplest and ideal form, the testable proposition would be that if the WIV did not exist, this pandemic would not be happening.

[angrysoba]

I wanted to return to this...because I have been looking into it...

Originally Posted by Skeptic Ginger

I posted this upthread:

But I wanted to post this from a link in that paragraph to a blog: Matt Ridley, Rational Optimist*Does that sound like there are no virologists questioning the WHO investigation?

Quote:

However, the public scientific consensus had been slowly shifting even before the announcement. A growing number of top experts including (ordered alphabetically by last name) Drs Francois Balloux, Ralph S. Baric, Trevor Bedford, Jesse Bloom, Bruno Canard, Etienne Decroly, Richard H. Ebright, Michael B. Eisen, Gareth Jones, Filippa Lentsoz, Michael Z. Lin, Marc Lipsitch, Stuart A. Newman, Rasmus Nielsen, Megan Palmer, Nikolai Petrovsky, Angela Rasmussen, and David A. Relman have stated publicly (several in early 2020) that a lab leak remains a plausible scientific hypothesis to be investigated, regardless of how likely or unlikely. We informed and obtained consent from each expert for their inclusion in this list.

Remember that my question before was which virologists support the lab leak theory.

The above list is actually what reminds me of a Gish Gallop, because the assumption is that each of the names mentioned above, represent the following:

a) they are virologists
b) they support the theory that the virus leaked from a lab

However,
Francois Balloux is not a virologist and in the video, from 7:55 he says, “Where did it come from? There are many viruses around in China and can jump around...the most likely is a natural spillover from an animal? Did it come from a lab? It’s difficult to say, no evidence it has been manipulated...” etc... He DOES NOT support the lab leak theory.

Ralph S. Baric, I don’t know if he is a virologist as such, but in the paper cited by Ridley he says, “How, then, did the virus emerge? Anderson et al. cite multiple lines of strong evidence that argue, instead, in favor of various mechanisms of natural selection, either in an animal host before the virus was transmitted to humans or in humans after the zoonotic transmission event(s). These possibilities will be reviewed below. Nevertheless, speculation about accidental laboratory escape will likely persist, given the large collections of bat virome samples stored in labs in the Wuhan Institute of Virology, the facility’s proximity to the early outbreak, and the operating procedures at the facility”. Hardly strong support for a lab leak. In fact, looking on Twitter, it seems a lot of people think he is part of the conspiracy given his work with Zheng-li Shi.

Trevor Bedford, in the very source that Ridley uses, Bedford says: “I've written before that #COVID19 has no evidence of genetic engineering and the "bioweapon" theory has no grounds. See, for example https://twitter.com/trvrb/status/1224207086013149184. In this thread I wanted to directly address the theory of escape from lab in Wuhan. 1/21” and “We have public figures making televised statements promoting this lab escape theory and I believe it needs to be addressed directly. Not because it has evidence, but because a vacuum permits these theories room to expand. 2/21”

Okay, look, I said before that I checked a few and got some similar results. I am getting bored and annoyed by this.

Almost all of Ridley’s claims regarding “A growing number of top experts... have stated publicly (several in early 2020) that a lab leak remains a plausible scientific hypothesis to be investigated” turn out to be them saying the almost complete opposite.

This is exactly the kind of thing we see in conspiracy theorizing. Someone says something like, “Yes, I think we need to look into it” and a conspiracy theorist seizes on the comment to say that this person supports the conspiracy theory.

I predict that anyone going through the other names in the list will find very similar results. But of course it is time-consuming to look into each one. Pure, pure Gish Gallop on the part of Matt "climate change is not a problem lets keep burning fossil fuels" Ridley!

Yet the biggest proponents of this theory are way, way out of their field.

Bill "vaccines are bad" Maher
Bret "vaccines are at least dodgier than we hear; the election fraud claims need to be looked into; I became famous after being cancelled and now have made a career out of appearing on Joe Rogan, hanging out with Jordan Peterson, questioning the natural origins of Covid, coming up with crackpot theories about evolution and angering Richard Dawkins, the left is the real problem even though I totally am a liberal, honest!" Weinstein.
Steven "not even other conspiracy theorists take my paper seriously" Quay.


etc...

[angrysoba]

Originally Posted by Samson

In its simplest and ideal form, the testable proposition would be that if the WIV did not exist, this pandemic would not be happening.

Wut?

[Sherkeu]

What were the results of the serology tests on the lab workers?
Surely they were all tested as soon as possible. I can't find anything on it.

The first confirmed patient in Wuhan was December 8- Man, mid forties, office worker.. He said his parents went to a wet market (a different one). Parents tested negative. No other contact tracing information was given.

Upon hearing the man describe how his parents went to the wet market, Peter Daszak said:

Quote:

Daszak said the Chinese scientists, looking into the case as part of the government's response, assured the WHO team the patient's parents had tested negative for the disease, yet the Chinese did not appear to have traced the parents' contacts in that market.
"If you find out the patients are negative, it is not obvious to contact-trace them. But it is worth doing now because we understand something of the spread of Covid around Wuhan," Daszak said.
This patient had no known connection to the Huanan seafood market..

How about the people in his office building, his apartment building, his local takeout place, his friends, etc.. ? This 40-something man did not live in a parental bubble. Why focus on the parents who tested negative? Odd, yes?

Seems other scientists were surprised at the lack of info into this first patient:

Quote:

Other scientists expressed surprise and even disbelief that the further investigations, into both the first patient's contact history and the supply chain to the Huanan market that the WHO sought, had apparently not already been performed by China.
Professor Maureen Miller, an infectious disease epidemiologist at Columbia University, said: "It's implausible that this research has not been done. It's not realistic, given they have world-class scientists there, and the technology invested in over the last 20 years. They are sophisticated, they understand transmission pathways, and have been working on them for years."

(CNN article here)

[Skeptic Ginger]

Originally Posted by angrysoba

I wanted to return to this...because I have been looking into it...

Remember that my question before was which virologists support the lab leak theory.

So your premise is you are not hearing about any virologists that suspect the lab ergo there are none?

Do you think the virologists in the WIV are free to speak up? Think other virologists in China are free to speak up?

I don't see where this line of inquiry, 'majority vote' can go very far given the limitations.

But do carry on. However this:

Originally Posted by angrysoba

This is exactly the kind of thing we see in conspiracy theorizing. Someone says something like, “Yes, I think we need to look into it” and a conspiracy theorist seizes on the comment to say that this person supports the conspiracy theory.

Has no place in this thread. You are ridiculing people instead of addressing specific evidence.

And I can certainly cite the opposite, remember Project Steve?

Originally Posted by angrysoba

I predict that anyone going through the other names in the list will find very similar results. But of course it is time-consuming to look into each one. Pure, pure Gish Gallop on the part of Matt "climate change is not a problem lets keep burning fossil fuels" Ridley!

Yet the biggest proponents of this theory are way, way out of their field.

Bill "vaccines are bad" Maher
Bret "vaccines are at least dodgier than we hear; the election fraud claims need to be looked into; I became famous after being cancelled and now have made a career out of appearing on Joe Rogan, hanging out with Jordan Peterson, questioning the natural origins of Covid, coming up with crackpot theories about evolution and angering Richard Dawkins, the left is the real problem even though I totally am a liberal, honest!" Weinstein.
Steven "not even other conspiracy theorists take my paper seriously" Quay.


etc...

No one has brought up any of these people here. Why do you keep insisting on dragging CTs into this thread. Please stop.

If you think any discussion of the possible origin within the WIV belongs in the CT forum, post over there.

[angrysoba]

Originally Posted by Skeptic Ginger

So your premise is you are not hearing about any virologists that suspect the lab ergo there are none?

Do you think the virologists in the WIV are free to speak up? Think other virologists in China are free to speak up?

Another goalpost shift.

"Where are the virologists who support the lab leak theory?"
"There are loads: look at these."
"They're not virologists and/or they don't support it!"
"So? So? Maybe there are others who have to keep quiet! Also, the ones who don't support it are compromised by big money, China and other stuff"
"So are we talking about a conspiracy?"
"You're not allowed to say conspiracy. That's my rule! That's for another forum!"

Originally Posted by Skeptic Ginger

I don't see where this line of inquiry, 'majority vote' can go very far given the limitations.

It isn't "majority vote". Again, this is a mischaracterization. The issue is whether we are talking about relevant experts vs. non-relevant experts.

Originally Posted by Skeptic Ginger

But do carry on. However this:
Has no place in this thread.

And I can certainly cite the opposite, remember the Steve Project?

I don't know what that is.

[Skeptic Ginger]

Originally Posted by angrysoba

Did they have dangerous viruses in the lab? Sure, it's a BSL-4 lab.

Did they have SARS CoV2 in the lab? No evidence.

So what is the theory here?

I just posted evidence. Care to address the specific viruses the WIV was studying prior to 2019?

Post #229

[angrysoba]

Originally Posted by Skeptic Ginger

No one has brought up any of these people here. Why do you keep insisting on dragging CTs into this thread. Please stop.

If you think any discussion of the possible origin within the WIV belongs in the CT forum, post over there.

Really? You haven't brought up Steven Quay?

Except here...

Originally Posted by Skeptic Ginger

This is from the Aussie version of Spectator. I think the US version if they are related is a right-leaning news magazine.

Covid cuckoo clock - Australia is stuck in a viral Groundhog Day

It's mostly about treatments saying if you can't beat them treat them while lamenting shut down economies. But there is this:
There's an assertion that Western universities are involved in a coverup. That plus the Steven Quay paper really drift off into CT territory. ( Bolded just so you know I am trying to be objective here even though I know some of you don't believe that.)

Is there a link to the Quay paper here? The number 99+% certainty rings a bell.

Originally Posted by Skeptic Ginger

Here are the two Quay papers:

Zenodo. Where Did the 2019 Coronavirus Pandemic Begin and How Did it Spread? The People’s Liberation Army Hospital in Wuhan China and Line 2 of the Wuhan Metro System Are Compelling Answers. Steven Carl Quay. October 28, 2020. doi: 10.5281/zenodo.4119262

Zenodo. A Bayesian analysis concludes beyond a reasonable doubt that SARS-CoV-2 is not a natural zoonosis but instead is laboratory derived. Dr. Steven Quay. January 29, 2021.

https://zenodo.org/record/4477081#


In the acknowledgements:


From the executive summary:So Zhengli Shi's own work.


Controls:


So no gradual changes in the human infection and earlier I posted a reference to the fact that the genetic evidence is this pathogen has only been in the human population recently.

So it was a perfect match on the first jump? Quay compares this to SARS (1) which was not.

I'm going to leave it to the people in this thread who "are not impressed" to sift through this scientific paper and find the faults in it. I'm not seeing them.

Oh wait...

[angrysoba]

Originally Posted by Skeptic Ginger

I just posted evidence. Care to address the specific viruses the WIV was studying prior to 2019?

Post #229

Okay, how similar were these viruses?

Do you have a name for them?

[Skeptic Ginger]

Originally Posted by Samson

In its simplest and ideal form, the testable proposition would be that if the WIV did not exist, this pandemic would not be happening.

That's not testable is it?