Origins of Covid

[lomiller]

Originally Posted by Skeptic Ginger

That's not how it works. Researchers took the data of a hundred or so genomes from patients diagnosed with COVID 19 in the months around Dec, 2019. (The details are posted in the cites upthread, the exact number of genomes investigated isn't critical to the argument.)

You claimed that the earliest know case didn't come from either of the markets in question. The technique you are describing here does not allow for such an identification. So one of your two claims MUST be wrong.

Originally Posted by Skeptic Ginger

This kind of contact tracing wasn't done.

Wasn’t done and can’t be done. The case you referred to is just one of dozens perhaps hundreds of cases in China in early Dec. It’s not reasonable to expect the virus to still be confined to it’s point of origin 4-8 weeks after it crossed over into humans, so whether an individual case was directly connected to the market is irrelevant.

What individual cases mean nothing, the greatest number of cases would still be expected to be found in the networks connected to that crossover. IOW the employees and\or suppliers to the suspect markets.

Originally Posted by Skeptic Ginger

No, the genome evidence does not support this number of cases in Sept 2019.

The case you referenced was from Dec 2019.

Originally Posted by Skeptic Ginger

The genetic trail is very clear and this did not happen.

This discussion has nothing to do with a genetic trail. You made false claims that the distribution of the virus in Dec doesn’t support the crossover point to humans not being connected to market\markets.

Originally Posted by Skeptic Ginger

What turned out to be the case and it was backed up by the WHO Report is that the initial market cluster was consistent with a super-spreader event, not the initial crossover from an animal to people. 40+% of the earliest cases (earlier than the market cluster) had no connection to any animal market.

I don't recall the WHO report calling it a super spreader event and such an event isn't required for an outbreak. Even if the crossover happened in the other market all it takes is one supplier carrying it to the fish market where it spreads from worker to worker.

[lomiller]

Originally Posted by Skeptic Ginger

How did that work out then? Did they accomplish their goal?

Watch the TWiV video up thread. They talk about this being perfectly normal reasonable research.

[lomiller]

Originally Posted by Skeptic Ginger

How many cities with wet markets do you think are in China?

A lot, since a wet market is any market that has perishable items like meat, fruit or vegetables. Don't use the term interchangeably with live animal market. There is some overlap but they are not the same thing.

[lomiller]

Originally Posted by angrysoba

Skeptic Ginger claimed that Andersen had said two lineages had been found in Wuhan in Sept 2019. When I asked for this to be supported, she assumed bad motives on my part.

wrt multiple lineages, unless we quantify how much difference there is between them we can't infer anything. The earliest samples of the virus are still 4-8 weeks removed from the jump to humans. This could be plenty of time for the "lineages" to manifest.

[Skeptic Ginger]

Originally Posted by angrysoba

This might be an interesting part:

On the question of evidence of transmission before Dec 2019:

https://youtu.be/d7kRxmEgzbQ?t=1338

They agree that there probably had been transmission prior to Dec 2019.

The interesting thing is that some lab leakers are trying to have it both ways. They argue

Premise 1: that there was probably transmission going as far back as Sept 2019 (after all, that's when the WIV took down the database, right?).

There had to be transmission somewhere in order to have 2 lineages in the first known cases.

Originally Posted by angrysoba

But then they also

Premise 2: try to rule out the market as the centre of the outbreak - "No, the first case in early Dec 2019 had no contact with the market. And 40% had no contact with the market!"

This came directly from the WHO report. It did not come from any "leakers" whoever they are.

Originally Posted by angrysoba

Therefore, it started in the WIV.

But of course, if we accept premise 1, then we negate premise 2.

No, no and no, in that order.

Originally Posted by angrysoba

The mere fact that the first known case had no contact with the market merely means that it wasn't the first case.

We know the first known case wasn't the first case.

Originally Posted by angrysoba

The non-lab leakers clearly have no problem with that part because they agree about multiple lineages predating the "first case". Therefore the markets are back in play.

Two lineages and I'm not sure who you think has a problem with this.

However, let's be clear here: The paper by Garry cited the WHO report except some of his claims were not supported by the WHO report.


In particular the claim that all the cases were tied to at least one wet market in Wuhan.

Early appearance of two distinct genomic lineages of SARS-CoV-2 in different Wuhan wildlife markets suggests SARS-CoV-2 has a natural origin; Garry

Quote:

The WHO report documented that early cases were not only linked to the Huanan market, but that other early cases were linked to different markets that sold wildlife or wildlife products. Among the first 168 diagnosed cases of COVID-19 in Wuhan with onset date prior to December 31, 2019 and a known history of exposure to wildlife markets 55.4% (93/168) reported such exposures. Of the 168 cases, 28% (47/168) had only been to the Huanan market, 22% (38/168) had exposure to another wildlife market and 4.7% (8/168) had exposure to the Huanan market and another market (Annex E2, Table 1 of WHO, 2021).

Maybe he didn't mean to imply that divvying up into various market exposures included all the known cases.

WHO Report

Quote:

For those cases where the information was available, 55.4% had a history of recent exposure to a market:28.0% to the Huanan market only, 22.6% to other markets only, and 4.8% to both. 44.6% had no history of market exposure (see Fig. 24 and Annex E4). Cases with market exposure were more evident among the early cases but exposure to other markets occurred in the earliest cases as much as exposure to the Huanan market. The case reported with the earliest onset date (8 December) had no history of exposure to the Huanan market.

Page 95 has a chart of samples from the various locations:

Quote:

Other markets in Wuhan* ... *The other markets were Dongxihu Market and Huanggang Center Market.

Only one sample collected was positive by RT-PCR so I don't see how that translates to all these other market-tied cases.

Originally Posted by angrysoba

++++++
There could have been direct spillover from a bat without an intermediary.

https://youtu.be/d7kRxmEgzbQ?t=2413

Yep.

Originally Posted by angrysoba

++++++

Cold-chain theory:

https://youtu.be/d7kRxmEgzbQ?t=2683

I get the impression that none of them think it is a good idea, and even if not true then not explanatory from where it comes from initially.

They give some explanation about why it is not crazy, but they think it is unlikely.

There was also concern of spread via frozen fish in NZ but I don't think that panned out as the most viable hypothesis.

Originally Posted by angrysoba

+++++++

The elephant in the room: Fourth scenario: lab leak

https://youtu.be/d7kRxmEgzbQ?t=3000


Marion says she asked why they took the database offline and says she was satisfied with the answer. Hmmmm...I didn't hear what the reason she said was.

Daszak also says he asks why they took down the database. Though he doesn't say what they answered.

+++++

Daszak says that if there is solid leads on people being sick then they should share it.

https://youtu.be/d7kRxmEgzbQ?t=3657

Apparently there is nothing but vague hearsay right now.

There are other discussions of these issues in this thread.

[Skeptic Ginger]

To clear up more misconceptions about what I've said:

Originally Posted by lomiller

You claimed that the earliest know case didn't come from either of the markets in question. The technique you are describing here does not allow for such an identification. So one of your two claims MUST be wrong.

[sidenote] For the record I corrected the number of genomes in the initial analysis which involved 27 full genomes and one partial genome, not 100 or so. [/sidenote]

Of the initially identified cases, many had an onset that preceded the first recognized cluster that occurred at the Wuhan Seafood Market. That is one data point.

The genome analysis which was used to walk the time clock back to the estimated true first cases is not something that identified the first known patients. The collected virus, later identified by the viral genome of the cases in the first patients was the starting place, not the endpoint. That is a second data point.

No one has of yet identified where the first crossover occurred. It could have been in a bat in Yunnan, a wild animal in some wet market somewhere in China, the WIV, or even another lab in Wuhan (I believe there are 2 other labs).

The virus had to have circulated to some extent prior to the walked back clock which found 2 lineages.

The WHO found no evidence of any outbreak prior to the one in Dec in Wuhan. I don't believe they had conclusively ruled the possibility out.

Originally Posted by lomiller

Wasn’t done and can’t be done. The case you referred to is just one of dozens perhaps hundreds of cases in China in early Dec. It’s not reasonable to expect the virus to still be confined to it’s point of origin 4-8 weeks after it crossed over into humans, so whether an individual case was directly connected to the market is irrelevant.

What individual cases mean nothing, the greatest number of cases would still be expected to be found in the networks connected to that crossover. IOW the employees and\or suppliers to the suspect markets.

These cases were identified from virus RNA collected from the nasopharynx or some other relevant site in the initial COVID 19 positive patients.

They weren't identified via contact tracing.

Originally Posted by lomiller

The case you referenced was from Dec 2019.

This discussion has nothing to do with a genetic trail. You made false claims that the distribution of the virus in Dec doesn’t support the crossover point to humans not being connected to market\markets.

What I said was that in the WHO report not all of the initially identified cases had a wet market connection. That is what the report said, it didn't originate from me. See the quote from the WHO Report in my above post.

Originally Posted by lomiller

I don't recall the WHO report calling it a super spreader event and such an event isn't required for an outbreak. Even if the crossover happened in the other market all it takes is one supplier carrying it to the fish market where it spreads from worker to worker.

The initial cluster of cases in the Wuhan Seafood Market was initially though to be the beginning of the pandemic. However when more cases came to light that occurred earlier than the market cluster, it was clear the market was not where the initial animal to human event occurred. Or at least the initial cluster was not the true initial cases.

Multiple sources have since hypothesized that rather than the initial event, a super-spreader event occurred at the Wuhan market.

[Skeptic Ginger]

Originally Posted by lomiller

Watch the TWiV video up thread. They talk about this being perfectly normal reasonable research.

Well yeah, that was the belief.

If it turns out they caused the thing they were trying to prevent, that belief needs to be seriously reevaluated.

And for the record, researchers doing this kind of work have been cautioned time and time again that they were playing with fire.

[Skeptic Ginger]

Originally Posted by lomiller

A lot, since a wet market is any market that has perishable items like meat, fruit or vegetables. Don't use the term interchangeably with live animal market. There is some overlap but they are not the same thing.

It's pretty common for live animals to be for sale at all of these markets. Often the customer buys the live animal and it is slaughtered on the spot for the customer.

We know this not just from SARS but also because the markets have been the source of more than one influenza outbreak. Also risky is anywhere people come in close contact with domestic animals. In 2009 the flu variant arose and crossed over to people from a pig farm in Mexico. Wild birds spread highly pathogenic flu strains to domestic birds (ducks and poultry) along their migration routes. That can result in the wide scale culling of those stocks.

[Skeptic Ginger]

Originally Posted by lomiller

wrt multiple lineages, unless we quantify how much difference there is between them we can't infer anything. The earliest samples of the virus are still 4-8 weeks removed from the jump to humans. This could be plenty of time for the "lineages" to manifest.

Where do you think these samples were from?

Those lineages (2) are both human coronaviruses. If we could trace the lineages back to the source, we would have the answer.

We have the virus samples and they were collected from patients in Wuhan in Dec 2019. Genetic clocks are then used to work backward to the theoretical most common ancestor in the human pandemic.

There's lots of discussion in the cited papers that there was an abrupt introduction into the human population.

[lomiller]

Originally Posted by Skeptic Ginger

Where do you think these samples were from?

Those lineages (2) are both human coronaviruses. If we could trace the lineages back to the source, we would have the answer.

Again, without quantifying how different these "lineages" are it's impossible to say if there is anything relevant or even remotely interesting in this factoid.


The distinction of human coronavirus is nonsense wrt this discussion. We don't have the immediate animal ancestor so we don't know what genetic differences characterise "human" from it's immediate animal predecessor.

[RecoveringYuppy]

Originally Posted by Skeptic Ginger

We have the virus samples and they were collected from patients in Wuhan in Dec 2019. Genetic clocks are then used to work backward to the theoretical most common ancestor in the human pandemic.

Didn't you just agree a day or two ago that this MRCA wouldn't have to be in the human pandemic??

[Skeptic Ginger]

Originally Posted by lomiller

Again, without quantifying how different these "lineages" are it's impossible to say if there is anything relevant or even remotely interesting in this factoid.

The distinction of human coronavirus is nonsense wrt this discussion. We don't have the immediate animal ancestor so we don't know what genetic differences characterise "human" from it's immediate animal predecessor.

When you read what the researchers say about the research they conducted, get back to me.

You seem to think I'm making claims when I'm essentially posting what is in the citations.

[Skeptic Ginger]

Originally Posted by RecoveringYuppy

Didn't you just agree a day or two ago that this MRCA wouldn't have to be in the human pandemic??

No, not me. Or you are misinterpreting something I posted.

Researchers, plural, used the rate of mutation (nucleotide substitution) and calculated when the COVID genomes we have probably first appeared.

It was recent, 2 separate lineages diverged early in the process. Summarized in one of the papers: either the human adaptation had some early adjusting to get a good match or the adjusting took place in the source of the crossover. We have not found the source from which the virus jumped. If we did we'd know if it was ready-adapted to human cells or sputtered about for a short time in people before becoming adapted.

It does seem to be the evidence-supported case that the cross-over was abrupt, near to the time the cases appeared, and well adapted or quickly adapted to human cells.

There is as of yet no evidence of any outbreaks anywhere except in Wuhan with the exception 6 miners were infected directly from bats a few years ago in Yunnan where they worked in caves there. There is good evidence the virus might have crossed over from bats to humans directly without need of an intermediary species. That doesn't rule an intermediary species out.

None of the bat viruses collected in Yunnan are a direct match to COVID 19. No intermediary species has been found.

I won't repeat the evidence for a lab cultured virus because people misunderstand me when I do.

[RecoveringYuppy]

So you think the human adaptation happened in humans or what?

[The Atheist]

Originally Posted by Skeptic Ginger

I won't repeat the evidence for a lab cultured virus because people misunderstand me when I do.

...none exists.

There is speculation, no evidence. If there were evidence, the case would be closed already.

Have you read Capsid's responses?

[Skeptic Ginger]

Originally Posted by RecoveringYuppy

So you think the human adaptation happened in humans or what?

I was repeating what was in the citations.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095063/

Quote:

Instead, we propose two scenarios that can plausibly explain the origin of SARS-CoV-2: (i) natural selection in an animal host before zoonotic transfer; and (ii) natural selection in humans following zoonotic transfer. We also discuss whether selection during passage could have given rise to SARS-CoV-2.

https://virological.org/t/clock-and-...27-genomes/347

Quote:

We are starting to see more structure in the tree and overall the genetic data is highly suggestive of a single-point introduction into the human population followed by sustained human-to-human transmission. This introduction was likely via either a single infected animal or a small cluster of recently infected animals directly into either a single human individual or a small cluster of human individuals. All subsequent cases are the result of human-to-human transmission with no further evidence of zoonotic transmissions.

The adaptation to humans was established right out of the gate.

Contrast this with highly pathogenic avian flu H5N1 which has been sputtering along for a couple decades now without becoming an efficient human pathogen.

[RecoveringYuppy]

So you don't agree with those citations but are just repeating them?

[Skeptic Ginger]

Originally Posted by The Atheist

...none exists.

There is speculation, no evidence. If there were evidence, the case would be closed already.

Have you read Capsid's responses?

Here we go again, denying there is any evidence supporting the lab leak when the thread is full of such evidence.

As for Capsid, yes I have been reading his posts. Seems to me they are non-committal because he doesn't find the evidence sufficient to declare anything.

A lot of people who initially discounted the lab leak scenario have begun to reconsider the hypothesis after all.

I do lean toward the lab accident hypothesis;

followed by the hypothesis some students and/or staff from the WIV became infected on a field trip to the bat caves in Yunnan Province shortly before the cases appeared in Wuhan.

I find the animal spillover the hypothesis with the least amount of evidence supporting it. There should have been a suspect species identified by now. It's been a year and a half of looking and not even a tentative source has been identified. Coronaviruses circulating in the bat colonies in Yunnan caves come the closest genetically to suggest an animal source.

Notice I don't claim any of those three hypotheses are confirmed. I do find it interesting that no matter how many times I state my position as "leaning", "favoring", or "not yet confirmed", at least 3 of you in this thread post as if I declared the lab was definitively the source.

Upon review of the thread I found one post of mine talking about the incredible tragedy from a lab leak. It was immediately followed by a clarification I was only pondering and didn't mean I thought the lab was definitively the source.

[Skeptic Ginger]

Originally Posted by RecoveringYuppy

So you don't agree with those citations but are just repeating them?

What is to agree with? These are expert opinions not shared by everyone.

Do I find them credible? Yes, certainly.

[RecoveringYuppy]

Originally Posted by Skeptic Ginger

What is to agree with? These are expert opinions not shared by everyone.

Do I find them credible? Yes, certainly.

Do you find this part credible: "small cluster of recently infected animals directly into either a single human individual or a small cluster of human individuals"?

[Skeptic Ginger]

I'm sorry for repeating myself but maybe someone here with a fresh eye for denying the lab leak hypothesis can help me find the evidence supporting this claim:

Garry: Early appearance of two distinct genomic lineages of SARS-CoV-2 in different Wuhan wildlife markets suggests SARS-CoV-2 has a natural origin. I can't find that supported in the citations he refers to.

Quote:

The WHO report documented that early cases were not only linked to the Huanan market, but that other early cases were linked to different markets that sold wildlife or wildlife products....A dispassionate science-based discourse on the topic of the origin of SARS-CoV-2 must account for this new data revealed by the WHO study showing: 1. multiple markets were linked to the early cases, and 2. divergence of SARS-CoV-2into lineages A and B was an early occurrence. ...

That is not in the WHO report that I can see.

Nor can I find this in the WHO Report:

Quote:

The WHO report documented that early cases were not only linked to the Huanan market, but that other early cases were linked to different markets that sold wildlife or wildlife products...

In a general sense one could say by default this is in the WHO Report. But definitively as asserted here, it is not there.

Quote:

Previously, Rambaut et al, (2020) noted that at the root of the phylogeny of SARS-CoV-2 are two lineages designated lineage A and B. Early lineage A viruses include SARS-Cov-2 isolate EPI_ISL_529213 sampled on 30Dec19 from a person linked to a wildlife market different than the Huanan market

That may be there, after all it is very specific as to which specimen that is. But it is one specimen, not a cluster of the not-Seafood Market specimens.

Garry is using this claim as evidence the 2 COVID lineages are neatly packaged implicating two wildlife market(s) and asserting that explains the divergent lineages.

The WHO report made no mention of two clusters connected to 2 different markets. In that report 2 markets besides the Seafood Market were named but only one revealed any COVID 19 RNA. And there is nothing which supports a cluster of cases connected to a second market.


I will not be surprised if someone can find evidence for the 2 markets = 2 lineages assertion, sometimes I can't find my glasses when they are on my head. But I would sure like to see where this assertion is coming from.

[Skeptic Ginger]

Originally Posted by RecoveringYuppy

Do you find this part credible: "small cluster of recently infected animals directly into either a single human individual or a small cluster of human individuals"?

You are asking if a particular hypothesis is credible. AFAIK the only hypothesis that seems dead in the water is that the virus was some sort of bio-weapon.

Are said hypotheses credible scenarios? Apparently. Are they definitive conclusions? Of course not.

[angrysoba]

Originally Posted by Skeptic Ginger

Here we go again, denying there is any evidence supporting the lab leak when the thread is full of such evidence.

As for Capsid, yes I have been reading his posts. Seems to me they are non-committal because he doesn't find the evidence sufficient to declare anything.

A lot of people who initially discounted the lab leak scenario have begun to reconsider the hypothesis after all.

I do lean toward the lab accident hypothesis;

followed by the hypothesis some students and/or staff from the WIV became infected on a field trip to the bat caves in Yunnan Province shortly before the cases appeared in Wuhan.

I find the animal spillover the hypothesis with the least amount of evidence supporting it. There should have been a suspect species identified by now. It's been a year and a half of looking and not even a tentative source has been identified. Coronaviruses circulating in the bat colonies in Yunnan caves come the closest genetically to suggest an animal source.

Notice I don't claim any of those three hypotheses are confirmed. I do find it interesting that no matter how many times I state my position as "leaning", "favoring", or "not yet confirmed", at least 3 of you in this thread post as if I declared the lab was definitively the source.

Upon review of the thread I found one post of mine talking about the incredible tragedy from a lab leak. It was immediately followed by a clarification I was only pondering and didn't mean I thought the lab was definitively the source.

Why is this the case? I was looking through Spillover which gives an account of the way SARS was tracked down to civet cats. Apparently it was done by a researcher from Hong Kong University in a market in Shenzhen, when he swabbed a bunch of animals (it says it was unclear how he persuaded the market traders to do it, but suggests he just paid them with cash), and then it turned up in civet cats.

This is despite the fact that SARS did not begin in Shenzhen. Apparently it was in 2003 and the first concrete evidence it was zoonotic. So this was 3 years after the initial outbreak.

Tracing it from there all the way back to bats was only done even more recently and much of the work was done by Zhengli Shi's team (hence her name Batwoman) Peter Daszak, and Linfa Wang (Batman).

This paper is from 2005...

Quote:

Bats Are Natural Reservoirs of SARS-Like Coronaviruses
Wendong Li1,2, Zhengli Shi2,*, Meng Yu3, Wuze Ren2, Craig Smith4, Jonathan H. Epstein5, Hanzhong Wang2, Gary Crameri3, Zhihong Hu2, Huajun Zhang2, Jianhong Zhang2, Jennifer McEachern3, Hume Field4, Peter Daszak5, Bryan T. Eaton3, Shuyi Zhang1,6,*, Lin-Fa Wang3,*

https://science.sciencemag.org/content/310/5748/676

[angrysoba]

This is the paper about isolating SARS from civet cats...

https://www.researchgate.net/publica...Southern_China

[The Atheist]

Originally Posted by Skeptic Ginger

Here we go again, denying there is any evidence supporting the lab leak when the thread is full of such evidence.

There isn't a shred of evidence it came from the lab, and you know it. All your bluster won't change the fact that the lab leak has zero evidence to support the idea.
_________________________

I just read a very good and balanced piece from Guardian: https://www.theguardian.com/world/20...we-know-so-far

The bit I like is the analogy of Saddam's WMD, They didn't exist, in spite of intelligence agencies demanding they did.

[Skeptic Ginger]

Originally Posted by angrysoba

Why is this the case? I was looking through Spillover which gives an account of the way SARS was tracked down to civet cats. Apparently it was done by a researcher from Hong Kong University in a market in Shenzhen, when he swabbed a bunch of animals (it says it was unclear how he persuaded the market traders to do it, but suggests he just paid them with cash), and then it turned up in civet cats.

This is despite the fact that SARS did not begin in Shenzhen. Apparently it was in 2003 and the first concrete evidence it was zoonotic. So this was 3 years after the initial outbreak.

Tracing it from there all the way back to bats was only done even more recently and much of the work was done by Zhengli Shi's team (hence her name Batwoman) Peter Daszak, and Linfa Wang (Batman).

This paper is from 2005...

https://science.sciencemag.org/content/310/5748/676

Originally Posted by angrysoba

This is the paper about isolating SARS from civet cats...

https://www.researchgate.net/publica...Southern_China

SARS 1 and SARS 2 presented with completely different circumstances.

From my infectious disease news feed I first heard of SARS in Feb 2003: Published Date: 2003-02-10 23:50:00
Subject: PRO/EDR> Pneumonia - China (Guangdong): RFI

RFI means request for information from infectious disease or other healthcare workers on the ground.

Quote:

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

Published Date: 2003-02-11 23:50:00
Subject: PRO/EDR> Pneumonia - China (Guangdong) (02)

Quote:

An unidentified pneumonia virus has killed 5 people and left hundreds
hospitalized in southern China, while rumors of a surging death toll
prompted frightened residents to stock up on antibiotics, officials
said Tuesday.
Health officials said the outbreak in a region of Guangdong province
near Hong Kong had been brought under control. They said Health
Ministry investigators sent from Beijing were trying to find the
source of the disease.
Some 300 people have been hospitalized, said an official of the provincial
Disease Prevention and Control Center. He said 59 of those people had
been treated and released. Officials wouldn't give any details about
who was killed by the disease or when. ...

So it began on the mainland in Guangdong (adjacent to Hong Kong). Infectious disease people tend to get very concerned when reports are that doctors and other healthcare workers are falling ill along with their patients combined with a high fatality rate. And that was reported initially.

China is at risk for outbreaks of new zoonosis. It is a well known hazard that these pathogens jump from domestic animals to people due to the frequent intermingling in rural China. Lots of ID experts are constantly looking for the next flu pandemic to emerge out of China in particular.

The first case of SARS was tracked back to late 2002. The ISID alert was in Feb of 2003. By June the civet cat was identified as the likely source.

SARS - WORLDWIDE (129): ORIGIN, SPECULATION

Quote:

Source: OIE press release, 28 May 2003 [edited]
<http://www.oie.int/eng/press/en_last.htm>

SARS virus in civet cat
------------------------
On the basis of recent information of the World Health Organization
which traced the SARS virus to a civet cat and 2 other small mammals
in China, the World Organisation for Animal Health (OIE) states the
following:
- as mentioned in its previous information (see press release of 11
Apr 2003), the OIE still does not dispose of any scientific evidence
to suggest that SARS-related disease has occurred in animals.
- Therefore, the OIE continues the monitoring of the evolution of the
disease and undertakes a very close collaboration with the World
Health Organization as well as with the scientists of the OIE
Reference Laboratories on the subject.

Quote:

Date: 31 May 2003
From: ProMED-mail <promed@promedmail.org>
Source: Nature 31 May 2003 [edited]
<http://www.nature.com/cgi-taf/Gateway.taf?g=5&file=/drugdisc/news/articles/423467a.html&filetype=&_UserReference=>

Virus detectives seek source of SARS in China's wild animals
-----------------------------
Researchers investigating the source of severe acute respiratory
syndrome (SARS) have turned their attention to the wild-animal
markets of southern China. The move follows reports that workers and
animals at the markets show high rates of infection with
coronaviruses, the family to which the virus believed to cause SARS
belongs.
The possible link to wild animals emerged on 23 May 2003, when a team
from the University of Hong Kong revealed that a coronavirus
resembling the SARS virus had been isolated from 6 masked palm civets
(_Paguma larvata_) and a raccoon dog (_Nyctereutes procyonoides_) in
a market in Shenzhen, in the southern Chinese province of Guangdong.
Antibodies against the virus were also found in a Chinese ferret
badger (_Melogale moschata_) from the same market.
Although the virus is not the same as that believed to cause SARS --
a member of the Hong Kong team describes it as "genetically very
close, but not identical" -- 5 out of the 10 civet handlers at the
market had antibodies against the SARS virus in their blood. A
Chinese government team has since released results showing that 66
out of 508 animal handlers tested at markets in Guangdong had
antibodies against the SARS virus.

Nothing like that has been found in Wuhan and all we know about the antibodies found in the staff and students at the WIV has been provided in a report from the Chinese government. The WHO inspection team said they were denied direct access to the bloodwork or blood specimens.

Further from ProMed:

Quote:

Microbiologist Kwok-yung Yuen, who led the Hong Kong team, notes that
in the general population, the level of antibodies against the SARS
virus is much lower. "This suggests that the virus is jumping from
wild animals to humans," he says.
Because the animal virus is similar to the SARS virus, but different
from other coronaviruses, it is now a prime suspect in the hunt for
the origins of SARS. The likelihood that the virus is moving the
other way -- from humans to animals -- is diminished by ongoing work
on genetic sequences of the 2 viruses. These analyses suggest that
the animal version has an extra stretch of 29 nucleotide bases.
"Viruses tend not to gain stretches of nucleotides when they jump
across species," says Klaus Stoehr, a SARS expert at the World Health
Organization (WHO) in Geneva.
But uncertainties remain over the exact source of the virus. Only 6
civets were present in the market, and the fact that they all had the
virus suggests that they were infected recently. "They could have
gotten it from another animal during transport to the markets," says
Zhang-liang Chen, a molecular biologist and president of the China
Agricultural University in Beijing. Chen's group did not find the
SARS virus in samples from 8 civets taken from other markets and in
the wild in Guangdong.

The link to the Nature article is no longer working. At this point in the search for the source of SARS they were hot on the trail but it wasn't confirmed.

[Skeptic Ginger]

Originally Posted by The Atheist

There isn't a shred of evidence it came from the lab, and you know it. All your bluster won't change the fact that the lab leak has zero evidence to support the idea.
_________________________

I just read a very good and balanced piece from Guardian: https://www.theguardian.com/world/20...we-know-so-far

The bit I like is the analogy of Saddam's WMD, They didn't exist, in spite of intelligence agencies demanding they did.

That highlighted bit is bizarre. Seriously.

I'm not impressed by a comparison to Saddam's WMD. There isn't anything remotely close in that analogy.

From your link:

Quote:

While it is known that dromedaries were a major reservoir host for Mers, even now the role of the animals in transmitting the virus is poorly understood.

The same was true with the Sars outbreak. While civet cats were suspected as intermediate hosts, it took years to confirm. In neither case was there was a suggestion of a lab leak. Because of that, the model of transmission via an intermediate host has remained the predominant one under consideration.

Years to confirm or not, researchers were on the right track within months of identifying the agent causing SARS.

And we're pretty sure camel's milk is a source of MERS infection. I haven't kept up beyond that re MERS.

That bit I bolded is absurd. What lab would it have been in Guangdong China? Or in Saudi Arabia?

[Lplus]

Originally Posted by The Atheist

There isn't a shred of evidence it came from the lab, and you know it. All your bluster won't change the fact that the lab leak has zero evidence to support the idea.
_________________________

I just read a very good and balanced piece from Guardian: https://www.theguardian.com/world/20...we-know-so-far

The bit I like is the analogy of Saddam's WMD, They didn't exist, in spite of intelligence agencies demanding they did.

There's no proof but there is evidence, if only circumstantial - and more than there is for a natural cause.

It seems you feel that the level of proof you require for even considering a lab leak would be akin to the smoking gun (complete with fingerprints), the empty shell case, the bullet, the dead body , and a signed confession.

[The Atheist]

Originally Posted by Lplus

There's no proof but there is evidence, if only circumstantial - and more than there is for a natural cause.

Utter nonsense.

There are some coincidences, but no evidence.

Christ, I hope none of the people who have decided it came from the lab ever get on a jury.

[zooterkin]

Several posts moved to AAH for various reasons. Please keep to the topic of the thread, and stop the bickering about the precise definition of words.

Responding to this modbox in thread will be off topic Posted By:zooterkin

[lomiller]

Originally Posted by Lplus

There's no proof but there is evidence, if only circumstantial

This question was already asked a few days ago, and as yet no one supporting the lab leak hypothesis has provided an answer so I'll ask it again.

What is the single most compelling piece of positive evidence for a lab leak?

[lomiller]

Originally Posted by Skeptic Ginger

When you read what the researchers say about the research they conducted, get back to me.

You seem to think I'm making claims when I'm essentially posting what is in the citations.

The researchers in question are suggesting that there were 2 distinct crossover events, one on each market and that the "lineages" you are referring to already existed in the original animal hosts and didn't arise in humans. Writing it as "Human Corona Virus" and bolding the word human isn't an adequate rebuttal.


Here is part of the image from the paper you linked:

[RecoveringYuppy]

Originally Posted by lomiller

This question was already asked a few days ago, and as yet no one supporting the lab leak hypothesis has provided an answer so I'll ask it again.

What is the single most compelling piece of positive evidence for a lab leak?

How about we just go for asking for a simple bullet point list of what the evidence is?
Your question doesn't seem fair for multiple reasons.

1. It would be fair to say that no origin hypothesis has compelling evidence because science as a whole considers the question unanswered.

2. Asking for a "single" piece of evidence doesn't work for questions that are supported by a range of small bit of circumstantial evidence. And, in fact, you are asking exactly the question creationists use to make it appear there is no good evidence for evolution.

3. I believe SG at least agrees the evidence is circumstantial?

Also let me clarify that it appears the (non CT) proponents of this are arguing for lab leak. The lab leak hypothesis is not at all contradictory to zoonotic origin, in fact, it is a kind of zoonotic origin hypothesis. Lab leak is where the virus arose naturally in an animal but the crossover event happened in the lab. Note that this means that quite a bit of potential evidence for natural origin does not contract the lab leak hypothesis.

[Lithrael]

He’s not going for a ‘gotcha.’ If you feel like it needs a bulleted list then make a bulleted list. I wouldn’t have a hard time making a short list of compelling points in support of evolution.

[Skeptic Ginger]

Originally Posted by lomiller

The researchers in question are suggesting that there were 2 distinct crossover events, one on each market and that the "lineages" you are referring to already existed in the original animal hosts and didn't arise in humans. Writing it as "Human Corona Virus" and bolding the word human isn't an adequate rebuttal.

Here is part of the image from the paper you linked:
http://www.internationalskeptics.com...ictureid=12836

There are multiple hypotheses and some variation within those hypotheses. Two crossover events is one variation explaining the two lineages. It's not the only way to explain the two lineages that diverged early on.

There's nothing to rebut. You apparently still have a misunderstanding about the full genomes used to walk the clock back. They can't go back beyond speculating about the crossover event without a coronavirus from the species the crossover event emerged from.

The genomes used to estimate when the crossover event occurred came from people infected with COVID 19. They didn't come from coronaviruses in animals. They are human coronaviruses.

[Skeptic Ginger]

Originally Posted by RecoveringYuppy

...

3. I believe SG at least agrees the evidence is circumstantial?

Also let me clarify that it appears the (non CT) proponents of this are arguing for lab leak. The lab leak hypothesis is not at all contradictory to zoonotic origin, in fact, it is a kind of zoonotic origin hypothesis. Lab leak is where the virus arose naturally in an animal but the crossover event happened in the lab. Note that this means that quite a bit of potential evidence for natural origin does not contract the lab leak hypothesis.

Yes.

There is a lot of evidence I think is very compelling about the lab accident. Dismissing it as "circumstantial" by some in this thread is quite the distortion of what that evidence is.

There is direct evidence the WIV was in the recent past engaged in research with live coronavirus cultures. Is that circumstantial?

There is direct evidence they lied about working with live coronavirus cultures. Is that circumstantial?

[lomiller]

Originally Posted by RecoveringYuppy

Also let me clarify that it appears the (non CT) proponents of this are arguing for lab leak. The lab leak hypothesis is not at all contradictory to zoonotic origin, in fact, it is a kind of zoonotic origin hypothesis.

A Lab leak still requires the virus to have been studied in a lab and for it's animal host to have been identified and brought to a lab. If this were the case we'd expect it to be relatively easy to find the animal host and for there to be data on the virus in existing research.

The explanation we are being given for why there is no data, no samples and no host identified is that there is a conspiracy to purge any related research from the record. At this point ANY lab-leak must have a conspiracy component to explain why there is no record of this virus ever being in a lab.

[lomiller]

Originally Posted by Skeptic Ginger

There are multiple hypotheses and some variation within those hypotheses. Two crossover events is one variation explaining the two lineages. It's not the only way to explain the two lineages that diverged early on.

That depends, as I said previously, on how different the lineages are which is a question you have never answered. The author of the paper you linked seemed to think the two linages are too far enough apart that they must have arisen in the original animal host.

Even if the lineages could have arisen in humans in an 4-8 week span, so what? How would this support your argument?

[RecoveringYuppy]

I didn't assume he was going for a gotcha and I can't make the list because I'm not one of the people making the argument.

[lomiller]

Originally Posted by Skeptic Ginger

There is direct evidence the WIV was in the recent past engaged in research with live coronavirus cultures. Is that circumstantial?

Lets play spot the moving goalposts. There is NO evidence for work with Covid-19 at WIV nor anyplace else in the world.

OF COURSE the WIV has done work with coronaviruses. China has 1 BSL-4 lab dealing with human diseases and China is a hotspot for potential Corona virus jumps to humans. The possibility of a coronavirus in China jumping from animal to humans and causing a pandemic has been recognised for at least 2 decades. This work is central to the very existence of the WIV.

China was going to be researching it and that research was going to be conducted un Wuhan. The fact that China was studying a known pandemic risk tells us nothing, nor does the fact that the risk turned out to be real.