Origins of Covid

[angrysoba]

That was typical state department wording in a public information page and like I said, one can ignore things that aren't relevant like the militarized stuff. Yes, I said this was during Trump's 4 years

Just use these sources as part of the whole. There are sources claiming it was the lab and other sources saying it wasn't. We don't have a definitive answer, IMO. Though there is some good evidence coming out in this thread that it wasn't the lab.

If you don't buy any information coming from the US defense agencies, can you believe anything coming from China? There are issues with both.

What is there to believe? I want evidence.

What I don't trust is Trump-era propaganda, and frankly that webpage looks like it. The only claim that is vaguely interesting is the one about sick staff at Wuhan, but it isn't sourced, and you still haven't given any evidence about that. There is no reason to take it at face value. Give me a credible source on that, and then we can talk.

Not yet. There is the evidence posted elsewhere that through satellite images there was activity around the Wuhan hospital and an uptick of net searches for pneumonia and other related terms in August of 2019 suggesting COVID began spreading that month. The wet market was a super-spreader event but not the source.

Ah! So, is that now something we can look into?

I guess not.

So where is the evidence?

What are we left with?

Absolutely nothing!

 

[Skeptic Ginger]

...you expected us to believe it was causing an increase in online searches.

I don't expect you or anyone else to believe anything. I'm also not opposed to posting rebuttal information myself. See post #76.

I do expect to not be dismissed with ad hominems (not you specifically) and to not have the debate hand-waved off, dismissing it as a CT before you've made much of an effort to see what the evidence is or what the ongoing discussion is.

I especially expect people to follow the discussion they inject themselves into and not comment about the flu coming before COVID when the discussion is about the cars in the hospital parking lots in August. OTOH, see post #76 since that particular piece of the debate has been resolved, at least to my satisfaction.

 

[angrysoba]

Here's an important point:

One of the supposedly compelling pieces of evidence is that the outbreak - or at least the emergence - of Covid-19 began in Wuhan when the idea is that it came from bats that dwell in caves in Yunnan Province. But that's like 100s of kilometres away! How is it possible that a coronavirus found in bats travelled 100s of kilometres!!!?!?!? How is it even possible?!?!

The theory then is that Wuhan Institute of Virology scientists to Yunnan, extracted the coronavirus from the bats, went back to Wuhan and let the virus escape because of shoddy protocols and then kept quiet about it because of "face" (*yawn*!)...

Except, why were they down in Yunnan in the first place? Well, because that is where SARS Cov1 was thought to have come from. So is that where SARS Cov1 emerged? No, it emerged in Guandong Province. But that's like 100s of kilometres away! How is it possible that a coronavirus found in bats travelled 100s of kilometres!!!?!?!? How is it even possible?!?!

Could it be that Guandong and Wuhan are both big cities and transport hubs, and that vast amounts of travellers and produce from all over China pass through there every day?

No! I want to ruminate instead on important questions of the concept of face. That's what scientists do after all...

 

[Skeptic Ginger]

To see why the Aug hospital parking lots and net searches is no longer being considered, see post #76, save yourselves some unnecessary stress.

Again trying to move the discussion forward. I cited this Nature article from 2015 a frew posts back: A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence.

I don't pretend to understand some of the specifics in this paper but I understand the gist of this description of how the researchers are manipulating the coronaviruses they are working with.

Viruses, cells, in vitro infection and plaque assays.
Wild-type SARS-CoV (Urbani), mouse-adapted SARS-CoV (MA15) and chimeric SARS-like CoVs were cultured on Vero E6 cells (obtained from United States Army Medical Research Institute of Infectious Diseases), grown in Dulbecco's modified Eagle's medium (DMEM) (Gibco, CA) and 5% fetal clone serum (FCS) [details snipped] Human lungs for HAE cultures were procured under University of North Carolina at Chapel Hill Institutional Review Board–approved protocols. HAE cultures represent highly differentiated human airway epithelium containing ciliated and non-ciliated epithelial cells as well as goblet cells. The cultures are also grown on an air-liquid interface for several weeks before use, as previously described26. Briefly, cells were washed with PBS and inoculated with virus or mock-diluted in PBS for 40 min at 37 °C. After inoculation, cells were washed three times and fresh medium was added to signify time '0'. Three or more biological replicates were harvested at each described time point. No blinding was used in any sample collections nor were samples randomized. All virus cultivation was performed in a biosafety level (BSL) 3 laboratory with redundant fans in the biosafety cabinets, as described previously by our group2. All personnel wore powered air purifying respirators (Breathe Easy, 3M) with Tyvek suits, aprons and booties and were double-gloved.

On to the figures/charts.

Figure 1: SARS-like viruses replicate in human airway cells and produce in vivo pathogenesis.

Figure 3: Full-length SHC014-CoV replicates in human airways but lacks the virulence of epidemic SARS-CoV. (Similar to H5N1 which is still a potential flu pandemic threat.)

Figure 4: Emergence paradigms for coronaviruses.

Existing data support elements of all three paradigms.

1) bat to intermediate animal to humans
2) bat directly to humans
3) :

The data from chimeric SARS-like viruses argue that the quasi-species pools maintain multiple viruses capable of infecting human cells without the need for mutations (red circles). Although adaptations in secondary or human hosts may be required for epidemic emergence, ....

And an interesting addendum:

30 March 2020 Editors’ note, March 2020: We are aware that this article is being used as the basis for unverified theories that the novel coronavirus causing COVID-19 was engineered. There is no evidence that this is true; scientists believe that an animal is the most likely source of the coronavirus.

It depends on one's definition of "engineered". What these researchers demonstrated was how a human pandemic might occur and to do that they manipulated SARS-like coronaviruses.

They also note how carefully they maintained isolation when dealing with these dangerous viruses. What we don't know from this is was the Wuhan Institute just as careful?

Did the WHO look at those employees' and students' antibodies demonstrating no COVID 19 leaked. Yes, I am dismissing the Wuhan researchers claims without evidence backing those claims up that none of the viruses in their lab resembled the pandemic virus.

And what explains the coincidence that the initial outbreak was near the Wuhan lab? You know, "Of All The Gin Joints In All The Towns In All The World, She Walks Into Mine." There are thousands of wet markets in China. There are thousands of places people interact with animals where a species jump could occur. SARS 1 species jump was nowhere near Wuhan regardless the Institute was not there in 2003. Wuhan is nowhere near the bat caves.

I think that is the biggest question that needs an answer before we can rule out a lab accident.

 

[Sherkeu]

Here's an important point:

One of the supposedly compelling pieces of evidence is that the outbreak - or at least the emergence - of Covid-19 began in Wuhan when the idea is that it came from bats that dwell in caves in Yunnan Province. But that's like 100s of kilometres away! How is it possible that a coronavirus found in bats travelled 100s of kilometres!!!?!?!? How is it even possible?!?!

The theory then is that Wuhan Institute of Virology scientists to Yunnan, extracted the coronavirus from the bats, went back to Wuhan and let the virus escape because of shoddy protocols and then kept quiet about it because of "face" (*yawn*!)...

Except, why were they down in Yunnan in the first place? Well, because that is where SARS Cov1 was thought to have come from. So is that where SARS Cov1 emerged? No, it emerged in Guandong Province. But that's like 100s of kilometres away! How is it possible that a coronavirus found in bats travelled 100s of kilometres!!!?!?!? How is it even possible?!?!

Could it be that Guandong and Wuhan are both big cities and transport hubs, and that vast amounts of travellers and produce from all over China pass through there every day?

No! I want to ruminate instead on important questions of the concept of face. That's what scientists do after all...

Of course it could be. The original SARS obviously traveled --and given the distance to the source was not a likely place for it start its' spread.

There are currently 113 cities in China with over 1 million people in the urban areas. It could have emerged anywhere, even outside of China, though it would be more likely in a closer city or one with some close 'supply' chain relation to the area. The difference with Wuhan is that we KNOW these SARS-related viruses went there, purposely, multiple times over many years, from persons having direct contact with the people, animals, and caves at the source. And so a theory that those travels contributed to the emergence there becomes more likely- however it happened. I am perplexed that it sounds so conspiratorial.

Going by just the 'main hub' train stations (of the 5500 they have), Yunnan to Guangdong is one main hub away. Wuhan looks like three hubs away.

https://flic.kr/p/2kEJpff https://www.flickr.com/photos/155114068@N02/

 

[angrysoba]

Of course it could be. The original SARS obviously traveled --and given the distance to the source was not a likely place for it start its' spread.

There are currently 113 cities in China with over 1 million people in the urban areas. It could have emerged anywhere, even outside of China, though it would be more likely in a closer city or one with some close 'supply' chain relation to the area. The difference with Wuhan is that we KNOW these SARS-related viruses went there, purposely, multiple times over many years, from persons having direct contact with the people, animals, and caves at the source. And so a theory that those travels contributed to the emergence there becomes more likely- however it happened. I am perplexed that it sounds so conspiratorial.

Going by just the 'main hub' train stations (of the 5500 they have), Yunnan to Guangdong is one main hub away. Wuhan looks like three hubs away.

[qimg]https://live.staticflickr.com/65535/50977770886_6cc1078dc4_z.jpg[/qimg]https://flic.kr/p/2kEJpff https://www.flickr.com/photos/155114068@N02/

But I think this misses another point. It seems only fairly recently have the researchers led by Shi Zhengli discovered that the original SARS came from Yunnan Province, and yet it turned up in Guanzhou City, so it clearly travelled far from its origin. This is the most important point. Where it emerges is not necessarily where it originates!

However, as I posted previously, the types of coronaviruses that share almost all of the genetic make-up of SARS Cov2 are found over wide areas of China, South-East Asia and even in Japan (probably elsewhere as well). We have no reason for thinking that the one that orginated in Yunnan is the one that has emerged as SARS Cov2. There could likely be several areas from which it broke out.

[Sorry, I meant to say that Guangzhou is the city in Guandong Province, and Wuhan is the city in Hubei Province.]

 

[RecoveringYuppy]

People are so quick to label something as a CT after new evidence surfaces if they first went with the CT

Which evidence is new? Bullet point descriptions would be fine.

 

[angrysoba]

Did the WHO look at those employees' and students' antibodies demonstrating no COVID 19 leaked. Yes, I am dismissing the Wuhan researchers claims without evidence backing those claims up that none of the viruses in their lab resembled the pandemic virus.

That's not how this works!

You have made the claim that there were sick workers. The WHO said they found no evidence of that. Then you say, "I don't believe it!"

First, why don't you show evidence that there were sick workers at the lab!

And what explains the coincidence that the initial outbreak was near the Wuhan lab? You know, "Of All The Gin Joints In All The Towns In All The World, She Walks Into Mine." There are thousands of wet markets in China. There are thousands of places people interact with animals where a species jump could occur. SARS 1 species jump was nowhere near Wuhan regardless the Institute was not there in 2003. Wuhan is nowhere near the bat caves.
I think that is the biggest question that needs an answer before we can rule out a lab accident.

Yeah, and Guanzhou is nowhere near the bat caves either. So it couldn't have emerged there, by this line of reasoning.

Also, the Wuhan Institute did exist in 2003. It didn't have the BSL-4 lab until 2018, according to Wikpedia. So the idea is that now that the Institute has finally created a far more secure facility, now it escapes?

 

[angrysoba]

Which evidence is new? Bullet point descriptions would be fine.

Apparently what's new is:

1. Look how close the Wuhan Institute of Virology is to Wuhan
2. Then a bunch of debunked ****

ETA: Oh and the Chinese... well, you just can't trust them on anything because of the "face" thing. They're all liars!

 

[RecoveringYuppy]

SARS 1 species jump was nowhere near Wuhan regardless the Institute was not there in 2003

Could you clarify: What wasn't where in 2003?

 

[Skeptic Ginger]

Here's an important point:

One of the supposedly compelling pieces of evidence is that the outbreak - or at least the emergence - of Covid-19 began in Wuhan when the idea is that it came from bats that dwell in caves in Yunnan Province. But that's like 100s of kilometres away! How is it possible that a coronavirus found in bats travelled 100s of kilometres!!!?!?!? How is it even possible?!?!

The theory then is that Wuhan Institute of Virology scientists to Yunnan, extracted the coronavirus from the bats, went back to Wuhan and let the virus escape because of shoddy protocols and then kept quiet about it because of "face" (*yawn*!)...

That's a serious misunderstanding of the origin of SARS. And just what do you think they were doing with all these coronavirus strains in the Institute?

Except, why were they down in Yunnan in the first place? Well, because that is where SARS Cov1 was thought to have come from. So is that where SARS Cov1 emerged? No, it emerged in Guandong Province. But that's like 100s of kilometres away! How is it possible that a coronavirus found in bats travelled 100s of kilometres!!!?!?!? How is it even possible?!?!

Let's look at your hypothesis sans your incredulity sarcasm. And you really shouldn't dismiss the 'face saving' in the Chinese culture when there are so many papers written on how it makes medical research from China of uncertain value. But whatever...

Moving on: SARS 1 was traced to a wet market. SARS 2 was not traceable to the Wuhan (sea food) wet market it was initially thought to have originated in.

Hint: it's not about train stations or even population hubs. Surprisingly, we actually have a pretty good idea how SARS got to the Guangdong wet markets.

And don't forget, COVID has not been traced to any wet market so far. But I'll indulge the hypothesis anyway.

Molecular epidemiology, evolution and phylogeny of SARS coronavirus

Subsequently, SARS-related CoVs (SARSr-CoVs) were found in palm civets from live animal markets in Guangdong and in various horseshoe bat species, which were believed to be the ultimate reservoir of SARSr-CoV.

No such animal source was identified in Wuhan so far.

Overall, it is observed that the SARSr-CoV genomes from bats in Yunnan province of China possess the highest nucleotide identity to those from civets. ...

Our current model on the origin of SARS is that the human SARS-CoV that caused the epidemic in 2002/2003 was probably a result of multiple recombination events from a number of SARSr-CoV ancestors in different horseshoe bat species.

So recombination events in the bats. That was paradigm #3.

Also SARS was found in palm civet cats in the markets, but not in palm civet cats in the wild. The cats were infected from bats in the market where they were both for sale.
Were there bats for sale in the Wuhan market? I haven't checked yet. I'm waiting for the surprise.


Do they sell bats in the Wuhan Seafood Market?

That search turned up this oddity: Wiki: Huanan Seafood Wholesale Market

Phylogenetic analysis indicates that pangolins are a potential reservoir host rather than the intermediate host of SARS-CoV-2. While there is scientific consensus that bats are the ultimate source of coronaviruses, SARS-CoV-2 originated from a pangolin, jumped back to bats, and then jumped to humans, according to phylogenetic analysis.

I'm going to let someone else explore that rabbit hole.

Looks like there are over 100 wild animal species sold in that market.

Bats were initially suggested to be the source of the virus, although it remains unclear if bats were sold there.[28][29][30][31] ...

[30] Camero, Katie (6 February 2020). "Scientists Link China Coronavirus to Intersection of Humans and Wildlife". Wall Street Journal. ISSN 0099-9660. Retrieved 28 March 2020. Some researchers said bats weren't being sold at the Huanan market in Wuhan...The U.S. Centers for Disease Control and Prevention and the World Health Organization said they couldn't confirm if bats were present at the market.

So patient zero didn't get infected in the Huanan market and it isn't even certain bats were sold there. [Bats and palm civet cats were sold in the markets where SARS originated and the palm civet cats are a documented source of SARS.]


We're back where we started, sort of. The market has been ruled out as the initial source. The wet markets are common all over China but the ones where bats and pangolins are most likely to be sold in the same market are in Southern China. You can probably find pangolins for sale in Wuhan but it is uncommon compared to other parts of China. And even if it were common, it's still a highly unlikely coincidence that the place this pangolin-human interface was, was in Wuhan. "Of all the gin joints" and all that.

 

[Sherkeu]

But I think this misses another point. It seems only fairly recently have the researchers led by Shi Zhengli discovered that the original SARS came from Yunnan Province, and yet it turned up in Guanzhou City, so it clearly travelled far from its origin. This is the most important point. Where it emerges is not necessarily where it originates!

However, as I posted previously, the types of coronaviruses that share almost all of the genetic make-up of SARS Cov2 are found over wide areas of China, South-East Asia and even in Japan (probably elsewhere as well). We have no reason for thinking that the one that orginated in Yunnan is the one that has emerged as SARS Cov2. There could likely be several areas from which it broke out.

From what I have read, when looking at the whole genome, the closest related virus to SARS-CoV-2 continues to be RaTG13, collected from a cave in Yunnan.
I have not seen any conflicting research that proposes a closer 'whole genome' match. There could be, or might be in the future.

If you are aware of new data, let me know.

 

[Skeptic Ginger]

But I think this misses another point. It seems only fairly recently have the researchers led by Shi Zhengli discovered that the original SARS came from Yunnan Province, and yet it turned up in Guanzhou City, so it clearly travelled far from its origin. This is the most important point. Where it emerges is not necessarily where it originates!

See my last post, I'll let you catch up. And it wasn't recent. The source of SARS was discovered more than a decade ago.

However, as I posted previously, the types of coronaviruses that share almost all of the genetic make-up of SARS Cov2 are found over wide areas of China, South-East Asia and even in Japan (probably elsewhere as well). We have no reason for thinking that the one that orginated in Yunnan is the one that has emerged as SARS Cov2. There could likely be several areas from which it broke out. ...

I'm pretty sure your source did not say "share almost all of the genetic make-up of SARS Cov2" or if it did it's not a legit source.

But yeah, why did it happen in Wuhan if it could have happened anywhere?

 

[Skeptic Ginger]

Which evidence is new? Bullet point descriptions would be fine.

1) It did not originate in the sea food wet market

2) The concern over the highly unlikely coincidence it began in Wuhan now that we know more about the genome and potential animal sources.

3) The species transfer of SARS to people occurred after the palm civet cats and bats were commonly sold in wet markets together in southern China.

If we accept pangolins as the intermediary source, (maybe they initially traded virus back and forth between bats), one still has to explain why the outbreak would occur in Wuhan where the lab is.

 

[Skeptic Ginger]

Could you clarify: What wasn't where in 2003?

The Wuhan Institute of Virology in its present form:

In 2003, the Chinese academy of Sciences approved the construction of China's first biosafety level 4 (BSL–4) laboratory at the WIV. The construction of the WIV's National Bio-safety Laboratory was completed at a cost of 300 million yuan ($44 million) in collaboration with the French government's CIRI lab at the end of 2014.[2][4] The new laboratory building has 3000 m2 of BSL-4 space, and also 20 BSL-2 and two BSL-3 laboratories.[5]

In response to SARS a large part of the research was located in Wuhan. I'm not sure what's currently going on at the Beijing facility that also studied SARS at the time.

SARS did not emerge in Wuhan. Why would SARS 2 coincidentally emerge near the lab?

 

[Bob001]

.....
SARS did not emerge in Wuhan. Why would SARS 2 coincidentally emerge near the lab?

I'm willing to say that WHO scientists know more about this than I -- or most other people -- ever could, and they have concluded that it's very unlikely that covid came from a Wuhan lab. China is a densely populated country in which people move freely from one giant city to another, usually by rail. It might not even have started in Wuhan. Why should it be a surprise that a disease could originate somewhere and travel elsewhere? Coincidences do happen.
https://www.cnn.com/2021/02/14/health/who-mission-china-intl/index.html

 

[angrysoba]

That's a serious misunderstanding of the origin of SARS. And just what do you think they were doing with all these coronavirus strains in the Institute?

Huh? What?

Let's look at your hypothesis sans your incredulity sarcasm. And you really shouldn't dismiss the 'face saving' in the Chinese culture when there are so many papers written on how it makes medical research from China of uncertain value. But whatever...

You posted a link to the Lancet that said nothing about face, and then one blog post written by some random laowai called China Mike that you said was a "paper" on the topic.

This is not evidence. It's an ac hoc narrative to support a hypothesis which I am not necessarily ruling out (although the WHO scientists who visited Wuhan are ruling it out, so I feel a little arrogant even allowing it to be an option for me), but want to see some actual support for.

Besides, what I really want you to do is post some support for your claim that scientists in Wuhan got sick.

I would be happy to see some independent and reputable source on this. That blog post is not even relevant, let alone reputable. The "fact sheet" from the Trump State Department (neither reputable nor independent) involves unsourced claims that you haven't even tried to substantiate.

Moving on: SARS 1 was traced to a wet market. SARS 2 was not traceable to the Wuhan (sea food) wet market it was initially thought to have originated in.

Hint: it's not about train stations or even population hubs. Surprisingly, we actually have a pretty good idea how SARS got to the Guangdong wet markets.

This is a false dichotomy. Who said it had to be the wet market or bust? Major transport hubs involve lots of people. There could be people travelling from all sorts of places, by rail or by air. They may be people who got infected and passed on the virus. Given that there are many asymptomatic carriers we simply don't know whether someone carried it into Wuhan after it had been circulating elsewhere in the country.

It seems that the scientists themselves are still considering the wet market:

What can you say now about the market and what you saw?

The market closed on the 31st of December or the 1st of January, and China C.D.C. sent a team in of scientists to try and find out what was going on. It was a very extensive study, swabbing every surface of this place. We knew early on that there were 500 samples collected, and there were many positives, and in that sampling were some animal carcasses, or meat. But there was not really much information publicly about what had been done. So we got all that information. And that, to me, was a real eye-opener.

They’d actually done over 900 swabs in the end, a huge amount of work. They had been through the sewage system. They’d been into the air ventilation shaft to look for bats. They’d caught animals around the market. They’d caught cats, stray cats, rats, they even caught one weasel. They’d sampled snakes. People had live snakes at the market, live turtles, live frogs.

Rabbits were there, rabbit carcasses. A farm with rabbits could have been really critical. There was talk about badgers, and in China, when they say badger, that means ferret badger. It’s a mustelid, related to weasels. Animals were coming into that market that could have carried the coronavirus. They could have been infected by bats somewhere else in China and brought it in. So that’s clue No. 1.

There were 10 stalls that sold wildlife. There were vendors from South China, including Yunnan Province, Guangxi Province and Guangdong Province. Yunnan Province is where the closest relative to SARS-CoV-2 is found in bats. Guangxi and Guangdong are where the pangolins were captured. They had close viruses.

You’ve got animals coming in to the market which are susceptible. Some of these are coming from places where we know the nearest relatives of the virus are found. So there’s the real red flag.

Now the Chinese group did swab those animals, and they were all negative, but it’s just one small group of animals in the freezer that were left behind. We don’t know what else was for sale there. So these two clues are really important.

Link

Anyway, the guy being interviewed suggests a number of possibilities including:

farm-meat being sent to market
human transmission from outside
wildlife farms

And he also raises the possibility of fur-farming, particularly given that mink has been known to be infected.

Another suggestion he raises is raccoon dogs

What is the next step?

For the animals chain, it’s straightforward. The suppliers are known. They know the farm name; they know the owner of the farm. You’ve got to go down to the farm and interview the farmer and the family. You’ve got to test them. You’ve got to test the community. You’ve got to go and look and see if there are any animals left at any farms nearby and see if they’ve got evidence of infection, and see if there is any cross-border movement. If the virus is in those southern border states, it’s possible that there’s been some movement across neighboring countries like Vietnam, Laos or Myanmar. We’re finding more and more related viruses now. There’s one in Japan and one in Cambodia, one in Thailand. For the human side, look for earlier cases, for clusters; look in blood banks for serum, if possible. Anything like this is going to be sensitive in China, and it’s going to take some persuasion and diplomacy and energy for them to do that because, to be honest, looking for the source of this virus within China is not a great, high priority I think for the Chinese government. Anywhere this virus is shown to emerge is a political issue. That’s one of the problems, and that is clear and obvious to anyone who has been looking at this.

Do you have a particular animal that you suspect right now as an intermediate link, more strongly than others?

It’s too up in the air. We don’t know if civets were on sale. We know they are very easily infected. We don’t know what the situation is with the mink farms in China or the other fur farms, like raccoon dogs, even though they’re normally farmed in a different part of China. That needs to be followed up on, too.
But if you were to say which pathway would you put the most weight on, I think the virus emerging either in Southeast Asia or Southern China from bats, getting into a domesticated wildlife farm. I’ve been to many of these, and they often have mixed species — civets, ferret badgers, raccoon dogs. Those animals would be able to get infected from bats.

Either the people that work there get infected and bring it in, or animals are shipped in, live or recently killed, that bring the virus into a market. Once it’s in a market — either Huanan or another one in Wuhan — you’ve got a dense population of people moving through those markets. And it’s going to be a real potential for an amplification.

 

[angrysoba]

The Wuhan Institute of Virology in its present form:In response to SARS a large part of the research was located in Wuhan. I'm not sure what's currently going on at the Beijing facility that also studied SARS at the time.

SARS did not emerge in Wuhan. Why would SARS 2 coincidentally emerge near the lab?

You missed that highlighted bit out as you said the Institute did not exist in 2003.

 

[angrysoba]

See my last post, I'll let you catch up. And it wasn't recent. The source of SARS was discovered more than a decade ago.

More than a decade ago?

What do you think 13 in RaTG13 stands for? It is the year the sample was collected - 2013.

I'm pretty sure your source did not say "share almost all of the genetic make-up of SARS Cov2" or if it did it's not a legit source.

But yeah, why did it happen in Wuhan if it could have happened anywhere?

If you say so...

Link

Here is a BBC write-up of the discovery:

Scientists say coronaviruses related to Sars-CoV-2 may be circulating in bats across many parts of Asia.

They have discovered a virus that is a close match to the virus that causes Covid-19 in bats at a wildlife sanctuary in eastern Thailand.

And they predict that similar coronaviruses may be present in bats across many Asian nations and regions.

The discovery extends the area in which related viruses have been found to a distance of 4,800km (2,983 miles).

And it gives clues to how Covid-19 might have emerged.

The researchers said sampling was limited, but they were confident that coronaviruses "with a high degree of genetic relatedness to Sars-CoV-2 are widely present in bats across many nations and regions in Asia".

The area includes Japan, China and Thailand, the researchers said in a report published in Nature Communications.

...

The virus, named RacCS203, is a close match to the genetic code of Sars-CoV-2 (with 91.5% similarity in their genomes).

It is also closely related to another coronavirus - called RmYN02 - which is found in bats in Yunnan, China (with 93.6% similarity to the genome of Sars-CoV-2).

Link

 

[Skeptic Ginger]

I'm willing to say that WHO scientists know more about this than I -- or most other people -- ever could, and they have concluded that it's very unlikely that covid came from a Wuhan lab. China is a densely populated country in which people move freely from one giant city to another, usually by rail. It might not even have started in Wuhan. Why should it be a surprise that a disease could originate somewhere and travel elsewhere? Coincidences do happen.
https://www.cnn.com/2021/02/14/health/who-mission-china-intl/index.html

Of course coincidences can happen. And sure the source might have been one person or a family bringing it to Wuhan.

But come on, is that a good enough explanation: it is remotely possible?

The problem is the WHO did not come back with an answer to the source of the pandemic. AFAIK, they ruled out the lab based on what the lab personnel told them.

I am not saying it came from a lab accident. I am saying I cannot rule that out at this point.

 

[Skeptic Ginger]

You missed that highlighted bit out as you said the Institute did not exist in 2003.

The point was it wasn't a level 3 or 4 bio-lab when SARS emerged. I'm not sure what point you are trying to make except you thought you had a gotcha or something. And who cares? I don't.

How about discussing the relevant facts.

SARS did not emerge in Wuhan.

SARS did not come directly from the bat caves.

SARS emerged when bats and palm civet cats were housed in crowded, less than sanitary conditions in wet markets around Guangdong.

SARS was not found in wild palm civet cats, that's how we know the civet cats were exposed to the bats for sale in the market.

People who worked in one of the wet markets were the first to get infected.

After the SARS epidemic, the lab in Wuhan was expanded. They essentially built a whole new facility with higher level biosafety specifically to study the family of coronaviruses in bats in order to anticipate and either prevent or prepare for the next SARS-like event.

People who worked in the Wuhan sea food market were not the first to get infected with COVID. There is no identified patient zero who worked around infected pangolins or bats.

China is a huge country with billions of people. That the outbreak began in close proximity to the lab in Wuhan where research into multiple different SARS like viruses were being studied cannot be dismissed as a coincidence until the actual source of COVID is found.

You all can dismiss the possibility. That's fine.

 

[Sherkeu]

More than a decade ago?

What do you think 13 in RaTG13 stands for? It is the year the sample was collected - 2013.

RaGT13 was not the focus of the first SARS in 2002-4, and wasn't published until early in the Covid-19 spread.
It's just from the same cave.

The one particular cave with horseshoe bats seems to have a very diverse and ever-changing assortment of SARS corona viruses that are close to ones that can spill over and infect humans- intermediary or not.

Several reports state that when tested, they can directly infect human cells. Other related viruses around China don't have that. (which doesnt mean those Yunnan cave strains could easily infect live humans...they still need a way in but serology says it has happened to the locals somehow).

I'm not sure why we do not include humans as intermediary hosts on the path- the path back to humans. We do know now we can pass it to cats, dogs, and cattle. Maybe more. Probably more. And then the process could reverse. There is a team of researchers looking into that now.

We need a virologist in here.

eta: found an "easy to read" link discussing bat-human similarities in Yunnan. (For 2002 SARS)
https://www.cidrap.umn.edu/news-per...study-finds-new-clues-about-sars-virus-origin

 

[angrysoba]

The point was it wasn't a level 3 or 4 bio-lab when SARS emerged. I'm not sure what point you are trying to make except you thought you had a gotcha or something. And who cares? I don't.

How about discussing the relevant facts.

SARS did not emerge in Wuhan.

SARS did not come directly from the bat caves.

SARS emerged when bats and palm civet cats were housed in crowded, less than sanitary conditions in wet markets around Guangdong.

SARS was not found in wild palm civet cats, that's how we know the civet cats were exposed to the bats for sale in the market.

People who worked in one of the wet markets were the first to get infected.

After the SARS epidemic, the lab in Wuhan was expanded. They essentially built a whole new facility with higher level biosafety specifically to study the family of coronaviruses in bats in order to anticipate and either prevent or prepare for the next SARS-like event.

People who worked in the Wuhan sea food market were not the first to get infected with COVID. There is no identified patient zero who worked around infected pangolins or bats.

China is a huge country with billions of people. That the outbreak began in close proximity to the lab in Wuhan where research into multiple different SARS like viruses were being studied cannot be dismissed as a coincidence until the actual source of COVID is found.

You all can dismiss the possibility. That's fine.

I'm not dismissing it (see the highlighted below). I want evidence. Besides, I keep asking for you to substantiate a claim you have made (in red), and I would like those to come from someone other than known liars such as Mike Pompeo:

This is not evidence. It's an ac hoc narrative to support a hypothesis which I am not necessarily ruling out (although the WHO scientists who visited Wuhan are ruling it out, so I feel a little arrogant even allowing it to be an option for me), but want to see some actual support for.

Besides, what I really want you to do is post some support for your claim that scientists in Wuhan got sick.

Y

That said, it obviously cannot be completely ruled out, the Virology Institute being located in Wuhan itself obviously raises eyebrows.

 

[angrysoba]

And here it is. Mike Pompeo's op-ed piece in the Wall Street Journal which essentially accuses China generally, and the Wuhan Institute of Virology.

I told you that State Department "factsheet" was written by Mike Pompeo, didn't I!

The Chinese Communist Party is obsessed with viruses. Its army of scientists claim to have discovered almost 2,000 new viruses in a little over a decade. It took the past 200 years for the rest of the world to discover that many. More troubling is the party’s negligence on biosafety. The costs and the risk to world health are enormous, as evidenced by a novel coronavirus that escaped Wuhan. This situation can’t continue. The world must hold the Chinese Communist Party accountable and punish Beijing if it fails to uphold global biosafety standards, including basic transparency requirements.

The most recent example of this malfeasance is playing out around us. The evidence that the virus came from Wuhan is enormous, though largely circumstantial, and most signs point to the Wuhan Institute of Virology, or WIV, as the source of Covid-19. In America, concern about the site is now broad and bipartisan. The Biden administration stated that it has “deep concerns” about the World Health Organization’s investigation into the early days of the pandemic, particularly Beijing’s interference with the investigators’ work.

Here's a juicy allegation:

The Chinese public took note, with several bloggers alleging that WIV’s virus-carrying animals are sold as pets. They may even show up at local wet markets. After the Wuhan outbreak, one since-disappeared blogger asked a WIV researcher to debate the lab’s biosafety practices in public. The offer was ignored.

Hmmm,... random blogger reckons that the BSL-4 sells infected animals as pets? And then "disappears" after offering to debate someone (who?) then "disappears".

"In 2015, WIV’s Dr. Shi Zhengli co-wrote an article titled “A SARS-like Cluster of Circulating Bat Coronaviruses Shows Potential for Human Emergence” in which she admitted that her team had engineered “chimeric” and “hybrid” viruses from horseshoe bats. In a 2019 article titled “Bat Coronavirus in China,” Ms. Shi and her co-authors warned, “It is highly likely that future SARS- or MERS-like coronavirus outbreaks will originate from bats, and there is an increased probability that this will occur in China.” "

Is this supposed to be an indictment? Obviously something like SARS is likely to occur in China. Is pointing this out supposed to be damning somehow?

And in January 2021, the State Department confirmed that people had fallen mysteriously ill at WIV in fall 2019, and that WIV conducts secret bioweapons research with the PLA.

Yeah, could we have some more evidence on that, Mike? I mean, you wrote a fact sheet for the State Department, then write an op-ed saying that you have discovered the State Department has discovered...

Link

 

[Skeptic Ginger]

More than a decade ago?

What do you think 13 in RaTG13 stands for? It is the year the sample was collected - 2013.

I believe you are referring to COVID, not SARS. From the Nature Abstract:

Among the many questions unanswered for the COVID-19 pandemic are the origin of SARS-CoV-2 and the potential role of intermediate animal host(s) in the early animal-to-human transmission. The discovery of RaTG13 bat coronavirus in China suggested a high probability of a bat origin.

SARS OTOH: https://www.cdc.gov/about/history/sars/timeline.htm

April 14 2003: CDC publishes a sequence of the virus believed to be responsible for the global epidemic of SARS. Identifying the genetic sequence of a new virus is important to treatment and prevention efforts. The results came just 12 days after a team of scientists and technicians began working around the clock to grow cells taken from the throat culture of a SARS patient.

That was more than a decade ago.

Jan 2004 anuary 13: CDC issues “Notice of Embargo of Civets.” A SARS-like virus had been isolated from civets (captured in areas of China where the SARS outbreak originated). CDC banned the importation of civets. The civet is a mammal with a catlike body, long legs, a long tail, and a masked face resembling a raccoon or weasel. The ban is currently still in effect.

If you say so...
Link
Here is a BBC write-up of the discovery:
Link

This is what you said:

However, as I posted previously, the types of coronaviruses that share almost all of the genetic make-up of SARS Cov2 are found over wide areas of China, South-East Asia and even in Japan (probably elsewhere as well). We have no reason for thinking that the one that orginated in Yunnan is the one that has emerged as SARS Cov2. There could likely be several areas from which it broke out. ...

This is what the Nature article says:

Although the origin of the virus remains unresolved, our study extended the geographic distribution of genetically diverse SC2r-CoVs from Japan and China to Thailand over a 4800-km range.

So which is it: genetically diverse CoVs or "coronaviruses that share almost all of the genetic make-up of SARS Cov2"?

91% is not "almost all". We share 99% of our genome with chimpanzees.

It's a well established fact there are related viruses in many bat species and especially in horseshoe bats. Of course they are all over the country and beyond. And of course a natural event as opposed to a lab accident is possible. You seem to think I have ruled that out. I haven't. You don't need to go on trying to convince me it could have been a natural event.

Unless you have some evidence that infected pangolins or bats were teeming in the Wuhan area, none of what you are saying changes the significant coincidence COVID emerged near the Wuhan lab.


As far as the Face Saving culture, you're on your own. I am not going to write you a term paper on the subject which is very well known. You don't want to believe it? Fine, don't. Not my problem.

 

[angrysoba]

It's a well established fact there are related viruses in many bat species and especially in horseshoe bats. Of course they are all over the country and beyond. And of course a natural event as opposed to a lab accident is possible. You seem to think I have ruled that out. I haven't. You don't need to go on trying to convince me it could have been a natural event.

Unless you have some evidence that infected pangolins or bats were teeming in the Wuhan area,

What? Nobody is saying that? Those aren't the claims being made by the WHO investigators, for example.

none of what you are saying changes the significant coincidence COVID emerged near the Wuhan lab.

And that coincidence is not going to change any time.

As far as the Face Saving culture, you're on your own. I am not going to write you a term paper on the subject which is very well known. You don't want to believe it? Fine, don't. Not my problem.

I think you are asking the concept of face to do a lot of heavy lifting here. Whatever.

 

[Skeptic Ginger]

...
I'm not sure why we do not include humans as intermediary hosts on the path- the path back to humans. We do know now we can pass it to cats, dogs, and cattle. Maybe more. Probably more. And then the process could reverse. There is a team of researchers looking into that now.

We need a virologist in here.

Not a virologist but I do have expertise in this subject from what I know about influenza species jumps. It's a matter of how close our cells are (respiratory and GI tracks) to the species harboring the pathogen.

These viruses have a particular affinity to certain cells. They can enter the cell easily because of the surface proteins and efficiently reproduce once in the cell.

So for example a bird flu might be adapted to the respiratory cells in a pig but not as close to the human cells it needs to efficiently reproduce in. But as it infects the pig cells it adapts with the result being a closer match to the human cells. That was just an example but we can be infected by both bird and pig flu strains but humans don't typically get infected by equine influenza strains for example.

The H5N1 influenza can infect humans when they have close contact with infected birds. And if that happens one too many times the strain could adapt to human cells in the respiratory track and become a pandemic flu. The molecular structure needed to adapt is thought to be similar to the changes the 1918 flu strain had. By comparing the two and knowledge about which parts of the genome are the parts involved in adapting, it was clear very few mutations could result in the next 1918-like flu event.

CIDRAP: Scientists recreate 1918 flu virus, see parallels with H5N1 Scary stuff.

So it doesn't always have to be an intermediary species involved in the jump.

 

[Skeptic Ginger]

I'm not dismissing it (see the highlighted below). I want evidence. Besides, I keep asking for you to substantiate a claim you have made (in red), and I would like those to come from someone other than known liars such as Mike Pompeo:

Round and around... That evidence could be supplied by the Wuhan lab as they claim they tested the staff and found no evidence of circulating COVID antibodies. AFAIK they did not share the data with the WHO.

 

[lomiller]

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

Yes it’s recombination. The changes to the spike protein that allow it to infect humans came from a recombination event with a Pangolin virus.
https://www.nature.com/articles/s41598-020-78703-6#Tab2

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).

Something else to keep in mind is that RaTG13 is not a direct ancestor to Covid, but in the last year no closer relative has been found. If the direct ancestor to Covid was already in laboratories in 2019 why is so hard to find now?


One possibility as to why the direct ancestor is proving to be so hard to find is that we are looking in the wrong place. Related viruses are found across China, Japan and Southeast Asia. Interestingly Covid-19 neutralizing antibodies have been found in both bats and Pangolins at a wildlife refuge in Thailand.
https://www.nature.com/articles/s41467-021-21240-1

How do you know COVID 19 can't reinfect bats?

The receptor binding doesn’t attach well to bat ACE-2. While it appears Covid-19 can infect many animals, bats are actually somewhat immune. The paper you linked to waved this away as “just models”.

If you aren't aware the Chinese cover things up for political reasons and to 'save face' I recommend you do more reading on the subject.

As I said above, there is good evidence that local officials dragged their feet for several weeks in reporting the outbreak to the central government. How you get from here to “Covid escaped from a lab” I have no idea.

 

[lomiller]

I'm not sure why we do not include humans as intermediary hosts on the path- the path back to humans. We do know now we can pass it to cats, dogs, and cattle. Maybe more. Probably more. And then the process could reverse. There is a team of researchers looking into that now.

Covid-19 enters humans cells by binding to ACE2, but it doesn't bind efficiently to the bat version of ACE2 so it would have a lot of difficulty infecting bats. This effectively rules out the possibility that it's binding mechanism evolved in bats. Conversely the Covid's closest know relative, RaTG13 can't bind efficiently to human ACE2 so neither have much chance to jump directly between species.

Another important factor is that the changes that allow Covid to bind to human ACE2 appear to come from a Pangolin virus Pangolin-CoV-2019 via a recombination event. This event could have occurred in some animal other than a Pangolin, but it must have involved exposure to a Pangolin.

The scenario where the recombination happened in yet another species would require 2 different viruses to jump species and infect the same individual which is less likely than one virus jumping to a Pangolin then recombining with a virus that commonly infects Pangolins.

 

[lomiller]

Round and around... That evidence could be supplied by the Wuhan lab US government as they claim they tested the staff and found no evidence of circulating COVID antibodies there are no aliens at area 51. AFAIK they did not share the data with the WHO. UFO investigators

"They can't be trusted and won't give me the evidence I'm demanding "is not evidence FOR anything. It's a bad argument form and we should not be using it. At best it helps resolve contradictory evidence, but there is no positive evidence for Covid escaping from a lab.

 

[Skeptic Ginger]

... As I said above, there is good evidence that local officials dragged their feet for several weeks in reporting the outbreak to the central government. ...

Why drag their feet at all?

You can refuse to look at the role Chinese culture plays when it comes to scientific research reliability, but it doesn't change the fact it does. I believe that's called ethnocentrism: a tendency to view other ethnic or cultural groups from the perspective of one's own.

I saw it firsthand with SARS. CNN April 2003: China hid SARS patients - report

Beijing authorities have gone to staggering lengths to hide SARS patients from visiting World Health Organization (WHO) inspectors, according to TIME magazine.

At one of the most reputable of the city's hospitals, 31 patients suffering the potentially lethal disease were driven around in ambulances for the duration of the WHO visit, said TIME.

And at a military hospital, 40 SARS patients were said to have been moved to a hotel for the duration of the WHO tour, in an apparent attempt to deceive inspectors about the true extent of the outbreak.

This was well after SARS was spreading in multiple countries and there was no reason by Western cultural standards to hide cases. We even knew about the Guangdong outbreak by that time so hiding cases in Beijing was bizarre from a Western POV.

The Chinese thought it made them look bad in the eyes of the world, or maybe it was in the eyes of their own population. Or maybe it was just the Beijing authorities trying to hide it from the central government. There certainly wasn't any other advantage from hiding these cases from the WHO investigators. It was to serious detriment because they spread SARS further.

The disease first emerged in China's Guangdong Province last November, but health authorities there failed to notify their counterparts internationally until about four months later, according to Dr David Heymann, WHO director of communicable diseases.

But by that time physicians in Guangdong were notifying their international colleagues. I knew about it.

I posted the links upthread. Before the international spread of SARS from the Hong Kong elevator, we heard about a pneumonia of unknown cause that was killing healthcare workers in a Guangdong hospital. That was akin to hearing about ebola killing healthcare workers. An infection spreading to and killing healthcare workers is a rare and alarming event.

My point is, healthcare workers dying from a rapidly spreading pneumonia of unknown origin was no minor thing and initially local authorities tried to cover it up. Why would anyone do that? Was it going to affect tourism dollars? No. Did it mean some new construction project might be halted? No. Did it make sense to the infectious disease experts and researchers in most of the rest of the world? No.

It only makes sense if you understand the Chinese culture of 'saving face'. And lest you think that's an ancient thing, look at the ophthalmologist who was told by authorities to shut up when he tried to raise the alarm about another pneumonia of unknown etiology that was all too frequently fatal.

How you get from here to “Covid escaped from a lab” I have no idea.

I can imagine you don't see how the lab could be the source when you build a straw man like this to argue with.

First, I said I don't know. I am just not ready to rule out the lab.

Second, the point about considering the Wuhan lab people and the WHO may not be reliable is where the 'face saving' comes in. It's why those reports are not absolutely reliable. Reliable? Possibly maybe even probably, but not irrefutable.

 

[Skeptic Ginger]

Covid-19 enters humans cells by binding to ACE2, but it doesn't bind efficiently to the bat version of ACE2 so it would have a lot of difficulty infecting bats. This effectively rules out the possibility that it's binding mechanism evolved in bats. Conversely the Covid's closest know relative, RaTG13 can't bind efficiently to human ACE2 so neither have much chance to jump directly between species.

Another important factor is that the changes that allow Covid to bind to human ACE2 appear to come from a Pangolin virus Pangolin-CoV-2019 via a recombination event. This event could have occurred in some animal other than a Pangolin, but it must have involved exposure to a Pangolin.

The scenario where the recombination happened in yet another species would require 2 different viruses to jump species and infect the same individual which is less likely than one virus jumping to a Pangolin then recombining with a virus that commonly infects Pangolins.

You are relying too much on one thing you heard/read about the COVID 19 receptor site. Important, absolutely. But you've jumped ahead of the evidence that the pangolin was the source of human transmission.

There is evidence some people were infected with a coronavirus directly from bats. Sherkeu posted that evidence.

And this was posted upthread: Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia

However, the immediate animal ancestor or progenitor virus, the equivalent of the >99% identical SARS-CoV sequences identified in civets during the SARS outbreak in 200311, remains elusive for SARS-CoV-2.

IOW it hasn't been found in bats or pangolins yet. I've not seen a single source saying they have definitive evidence the source is [X].


As for recombinant vs genetic drift by mutations, I posted a reference for that as well. Even if it begins with a recombinant event, genetic drift might still have been necessary for the more precise adaptations.

 

[Sherkeu]

I can imagine you don't see how the lab could be the source when you build a straw man like this to argue with.

First, I said I don't know. I am just not ready to rule out the lab.

Second, the point about considering the Wuhan lab people and the WHO may not be reliable is where the 'face saving' comes in. It's why those reports are not absolutely reliable. Reliable? Possibly maybe even probably, but not irrefutable.

The more I read what certain scientists are saying in interviews, and in their papers, the more I am 'reading between the lines' of them being delicate with their working relationships in China.

It's a difficult position. China is an area where risk of pandemic is higher and the global scientists want access to collaborate and to protect the large investments already made (and their jobs too!). But you cannot be too critical or say anything that makes China look culpable or negligent or you get shut out.

Last February the CCP banned publication of anything causing "adverse social impacts" and scientists violating this order would be held accountable. Since then, all papers need approval at the highest level (excepting medical sharing). It's been a big clamp down on open communication.

Joint Prevention and Control Mechanism
(internal doc leaked to AP)

There is a reason the WHO team had such long negotiations about what they could see or have access to. Members of the team were chosen by Beijing. They also had to agree in advance to include China's own theories, such as imported frozen foods, as 'possible'. So they agree. The narrative is controlled. I could be critical of that, but they likely have no choice but to go along. You can either see what they want you to see, or see nothing at all.
(I saw all the monitoring and propaganda first hand while in Shanghai for a science competition in 2019. Even though I knew about it, to experience it was quite eye opening. Luckily, I traveled with friends who are Chinese so I had cultural "interpreters")

That's why I look more favorably at the papers pre-Covid or just at the beginning. Looking to WHO for unbiased information is just not possible in today's climate of science used as political posturing.

 

[lomiller]

There is evidence some people were infected with a coronavirus directly from bats. Sherkeu posted that evidence.

So? Maybe those viruses has a spike structure that could efficiently bind to both human and bat ACE2 receptors. There are also Coronaviruses that don’t bind to ACE2 at all. Neither of these would change the fact that neither Covid nor any known close relative can bind efficiently to both human and bat ACE2 receptors.

And this was posted upthread: Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast AsiaIOW it hasn't been found in bats or pangolins yet. I've not seen a single source saying they have definitive evidence the source is [X].

If it hasn’t been found yet how could it have escaped from a lab?

If Covid’s actual ancestor is circulating in bats and Pangolins in SE Asia rather than Chinese bats that makes it even more likely that it was carried to China by an infected Pangolin and not accidentally released by a lab.

As for recombinant vs genetic drift by mutations, I posted a reference for that as well. Even if it begins with a recombinant event, genetic drift might still have been necessary for the more precise adaptations.

It may be necessary, but this doesn’t mean it MUST be necessary. The Pangolin virus spike binds efficiently to human ACE2 even without further evolution. Newer more virulent strains have evolved as the pandemic has progresses so any required evolution may be occurring right in front of our eyes.

Most importantly how would any of this help the argument that it escaped from a lab? If it needed more evolution it needed it regardless of how the first infections occurred. If it was already highly contagious right after the recombination event it was contagious regardless of how the first infections occurred.

 

[Sherkeu]

Covid-19 enters humans cells by binding to ACE2, but it doesn't bind efficiently to the bat version of ACE2 so it would have a lot of difficulty infecting bats. This effectively rules out the possibility that it's binding mechanism evolved in bats. Conversely the Covid's closest know relative, RaTG13 can't bind efficiently to human ACE2 so neither have much chance to jump directly between species.

Another important factor is that the changes that allow Covid to bind to human ACE2 appear to come from a Pangolin virus Pangolin-CoV-2019 via a recombination event. This event could have occurred in some animal other than a Pangolin, but it must have involved exposure to a Pangolin.

The scenario where the recombination happened in yet another species would require 2 different viruses to jump species and infect the same individual which is less likely than one virus jumping to a Pangolin then recombining with a virus that commonly infects Pangolins.

I've read conflicting things on this. Some assert that the pangolin is just a victim rather than a vector...but I am not knowledgeable enough to compare theories. They have a 2013 bat virus in Yunnan, and an early 2019 pangolin virus from a confiscation in Guangdong that are most similar to the human virus. What happened in late 2019 though remains unknown. That bat virus doesnt infect that pangolin and infected pangolins did not transmit to their human carers over months of close proximity (or so they said).

The lab in Wuhan created chimeras to replicate how it could jump to humans (paper was in 2015). They had animals there with in vivo experiments. Not much is said about that since the pandemic began. I take their word when virologists say they can tell when things are spliced into a genome, and that Covid has no evidence of it.

There are a lot of pieces missing. Might be too late to find them now.

 

[lomiller]

Why drag their feet at all?

You can refuse to look at the role Chinese culture plays when it comes to scientific research reliability, but it doesn't change the fact it does. I believe that's called ethnocentrism: a tendency to view other ethnic or cultural groups from the perspective of one's own.

Since Chinese cultural norms like live animal markets and “traditional medicine” are being called into question because of the Covid outbreak doesn’t it make sense that Chinese researches would try to downplay the role of the Wuhan market? As such I don’t think we can trust any claims that the market or Pangolins held therein were not the source of the virus.

Unlike you, I don’t need jump from "I question the motives of people saying differently" to saying the market must of have been where the virus crossed into humans. I have actual evidence, specifically the genetic connection to the Pangolin virus and Pangolin’s presence at the market. Granted there are other possibility’s but they all involve a more complex series of events. Occam’s razor applies and Pangolins at the Wuhan market is the simplest plausible explanation.

 

[RolandRat]

I haven't looked into this much, but it seems there were reports of the virus earlier in different parts of the world.

"Professor John Watson, a former deputy chief medical officer, said while China remained a “very, very possible source”, reports that the virus was circulating in other parts of the world, notably northern Italy, as early as September and October, warranted further investigation.

“I think that there are all sorts of reasons to do with the way it did start and the outbreak in Wuhan and the various bits of information about the way in which these viruses live in different animal reservoirs that suggest that China is a very, very possible source,” he told BBC One's The Andrew Marr Show.

But he added that China was “by no means necessarily the place where the leap from animals to humans took place and I think we need to ensure that we are looking beyond the borders of China, as well as within China.”

A study released by the National Cancer Institute (INT) in Milan in November showed the new coronavirus was circulating in Italy in September 2019."

https://www.independent.co.uk/news/health/covid-origin-wuhan-who-investigation-china-b1802081.html

Anyone know anymore detail about this?

 

[lomiller]

I've read conflicting things on this. Some assert that the pangolin is just a victim rather than a vector...but I am not knowledgeable enough to compare theories. They have a 2013 bat virus in Yunnan, and an early 2019 pangolin virus from a confiscation in Guangdong that are most similar to the human virus. What happened in late 2019 though remains unknown. That bat virus doesnt infect that pangolin and infected pangolins did not transmit to their human carers over months of close proximity (or so they said).


The lab in Wuhan created chimeras to replicate how it could jump to humans (paper was in 2015). They had animals there with in vivo experiments. Not much is said about that since the pandemic began. I take their word when virologists say they can tell when things are spliced into a genome, and that Covid has no evidence of it.

There are a lot of pieces missing. Might be too late to find them now.

Just to be clear neither Pangolin-CoV-2019 nor the bat virus RaTG13 is a direct ancestor to Covid-19. RaTG13 is the closest relative but not an ancestor. Pangolin-CoV-2019 is even more distantly related but it or a closely related Pangolin virus supplied important genes that give Covid-19 specific features to it’s spike that make if very efficient in infecting humans.

This exchange of genetic material from Pangolin-CoV-2019 to the real Covid-19 direct ancestor is very unlikely to have been deliberate manipulation for 2 reasons:

First, we can’t even find the direct ancestor after a year of intense search, so how would a lab have had it 18 months ago?

Second, while the spike protein in the Pangolin virus is very efficient for infecting humans this wasn’t know prior to seeing Covid itself. Similarly, the bat virus couldn’t infect humans. So essentially the researcher would have to have been splicing together random chunks of random viruses to see if they could make something that infects humans. This isn’t how a research would proceed with something like this they would take parts of viruses already know to infect humans.

Nature, on the other hand does this kind of thing all the time RNA viruses undergo recombination all the time. Most, like Covid, show signs of numerous recombination events. For this to happen either the bat virus would have needed to infect a Pangolin or the Pangolin virus would have needed to infect a bat. Even if the two viruses are not very infectious across species this can still occur on occasion. In this case it looks like the bat virus infected the Pangolin. The resultant virus isn’t very infectious to bats so it would have been facing a dead end if it was stuck inside a bat. Since it was infectious to both Pangolins and humans it could spread within Pangolins until one of them was take to the Wuhan market where it jumped to humans.

It’s possible that both jumped to a third species but this is completely unnecessary and would require 2 unlikely infections simultaneous rather than just one. Also, we now know that Covid-19 neutralizing antibodies can be found in wild bats and Pangolins in SE Asia indicating closely related viruses or Corvid itself was already circulating there.

 

[Skeptic Ginger]

I've read conflicting things on this. Some assert that the pangolin is just a victim rather than a vector...but I am not knowledgeable enough to compare theories. They have a 2013 bat virus in Yunnan, and an early 2019 pangolin virus from a confiscation in Guangdong that are most similar to the human virus. What happened in late 2019 though remains unknown. That bat virus doesnt infect that pangolin and infected pangolins did not transmit to their human carers over months of close proximity (or so they said).

The lab in Wuhan created chimeras to replicate how it could jump to humans (paper was in 2015). They had animals there with in vivo experiments. Not much is said about that since the pandemic began. I take their word when virologists say they can tell when things are spliced into a genome, and that Covid has no evidence of it.

There are a lot of pieces missing. Might be too late to find them now.

This is fascinating.

I saw SARS from a distance but the International Society for Infectious Diseases offered an incredible window. The moderators are top experts in their fields and the contributions are from first hand medical professionals, journals and news reports when relevant. A lot of reports of mysterious clusters of fatalities turn out to be about a toxic exposure so you learn to take some reports of mysterious diseases with a grain of salt. But when it's a real alarm, it doesn't take long before we know it.

This was the first alarm about COVID-19:
UNDIAGNOSED PNEUMONIA - CHINA (HUBEI): REQUEST FOR INFORMATION

Wuhan unexplained pneumonia has been isolated test results will be announced [as soon as available]
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On the evening of [30 Dec 2019], an "urgent notice on the treatment of pneumonia of unknown cause" was issued, which was widely distributed on the Internet by the red-headed document of the Medical Administration and Medical Administration of Wuhan Municipal Health Committee.

On the morning of [31 Dec 2019], China Business News reporter called the official hotline of Wuhan Municipal Health and Health Committee 12320 and learned that the content of the document is true.

It's a whole new world, we didn't have all this social media sharing in 2002-2003. Facebook and Twitter started soon after and when Facebook launched it was for universities. Information was however, readily shared via emails.

This is typical, nothing to see here folks, Chinese hospitals are the best in the world:

The National Health and Health Commission has decided to send an expert group to our province to guide the epidemic disposal on the morning of [31 Dec 2019]. At present, related virus typing, isolation treatment, public opinion control, and terminal disinfection are underway.

On the evening of [30 Dec 2019], an "Urgent Notice on Doing a Good Job in the Treatment of Unknown Cause of Pneumonia" issued by the Wuhan Municipal Health Commission circulated.

Here's a comment from the moderator:

[Having been involved in moderating the SARS-CoV (Severe acute respiratory syndrome - coronavirus) and the MERS-CoV (Middle Eastern Respiratory Syndrome - coronavirus), the type of social media activity that is now surrounding this event, is very reminiscent of the original "rumors" that accompanied the SARS-CoV outbreak. The exception is the transparency of the local government in responding to this currently undiagnosed outbreak. While this report does not contain the tweets, there have been numerous tweets about this as yet undiagnosed outbreak.

Returning to the rumor mill, the discussion of this outbreak (a cluster of 4 or 7 cases) involves an "atypical pneumonia". and now additional information of apparently 27 cases, with 7 severe cases. We do not know if influenza tests were performed, or if tests for the SARS-CoV are underway (but presumably are according to section [2] media report) in addition to other known (or unknown) respiratory viruses. As one of the tweets mentioned, another unusual pneumonia could be associated with infection with the bacteria _Yersinia pestis_ (plague) which has been diagnosed in Inner Mongolia in November 2019, but presumably has already been ruled out. The most recent report refers to the outbreak as a "viral pneumonia", suggesting bacterial agents have been ruled out. But has legionellosis been ruled out? or have viral panels been performed?

Here is the second report on COVID-19, 2 days latter, labeled (1).

UNDIAGNOSED PNEUMONIA - CHINA (HUBEI) (01): WILDLIFE SALES, MARKET CLOSED, REQUEST FOR INFORMATION

Date: 1 Jan 2020
Source: South China Morning Post [edited]
https://www.scmp.com/news/china/pol...seafood-market-linked-mystery-viral-pneumonia


World Health Organisation in touch with Beijing after mystery viral pneumonia outbreak
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The World Health Organisation said it is in ongoing contact with authorities in China over an unidentified outbreak of viral pneumonia in the central city of Wuhan, amid concern it may have been transmitted from animals.

Wuhan health authorities on Tuesday [31 Dec 2019] said 27 people - most of them stallholders at the Huanan Seafood Wholesale Market - had been treated in hospital, with 7 said to be in serious condition. Pathology tests were under way to try and identify the virus, officials said. Hong Kong medical authorities were also on alert.

Wuhan authorities ordered the closure of the market on Wednesday [1 Jan 2020]. Local media said the market sold other animals, including birds, raising concern after the 2002-03 outbreak of severe acute respiratory syndrome (Sars) in China killed several hundred people and is thought to have jumped from animals to humans.

The market is now known to have been a super-spreader event.

We know the civet cat was the source but they are noting the SARS reservoir has not yet been identified:

According to the WHO, the SARS coronavirus is thought to be an animal virus from an as-yet-uncertain animal reservoir, perhaps bats, that spread to other animals and 1st infected humans in Guangdong, near Hong Kong, in late 2002.

Despite the mod saying the local authorities were being transparent, they weren't completely.

Communicated by:
ProMED-mail Rapporteur Kunihiko Iizuka

[There continue to be social media reports on twitter and Weibo (the Chinese social media) on this outbreak without significant news on results of laboratory tests. Most recently there was a report of a suspected case of respiratory illness in Hong Kong in a traveler coming from Wuhan. Follow-up reports state the patient tested negative for SARS and avian influenza.