Origins of Covid

[Planigale]

Originally Posted by Skeptic Ginger

Now where was I, oh yeah, coronavirus cultures at the WIV.

The above discussion about recovering viable coronavirus from bat feces is well documented but it's also a useless sidetrack. What matters is that despite Dr Shi claiming they had no viral cultures at the WIV, it was a lie.

We documented the evidence they did indeed have not only SARS-like coronavirus cultures at the WIV, they were doing gain of function research on those cultures. What do you think Shi wanted human adapted mice from Dr Baric for? Shi also learned reverse engineering of coronaviruses from working in Baric's lab. One just needs to look at papers published in 2019 and earlier by Shi and Daszak et al.

And Daszak in his own words in the interview at the Nipah virus conference just before he was aware the pandemic had begun (posted up thread multiple times) said specifically that coronaviruses were easily manipulated in the lab.


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

Note this was about SARS1 not SARS2. Shi and her colleagues had tracked down the reservoir of SARS1 in horseshoe bats in a cave in Yunnan.


Table
From 2011 - 2015 feces and anal swabs (because that's where the coronaviruses are found) were collected from bat caves in Yunnan, China.
This was not simply the genomes. They cultured the coronaviruses and used serial passages on the cultured virus.

Note they used the SARS backbone. Baric used the HIV backbone.
DNA fragments were inserted... gee, no GoF research here, move along.

[Mel Brooks Frankenstein movie voice]It's alive, it's alive![/]

And so on and so on.

This was at the WIV, not at the lab at the UNC. [post split here to encourage people not to skim it.]

For clarity Rs3367 and RsSHC014 were SARSrCoV identified by PCR and WGS and never cultured, there was no viable virus isolated from fecal sampling. WIV1 and WIV16 are the first and second live viable viruses cultured from bat fecal samples.
https://www.nature.com/articles/nature12711

From your reference
https://journals.plos.org/plospathog...l.ppat.1006698

Quote:

A total of 602 alimentary specimens (anal swabs or feces) were collected and tested for the presence of CoVs by a Pan-CoV RT-PCR targeting the 440-nt RdRp fragment that is conserved among all known α- and β-CoVs [20]. In total, 84 samples tested positive for CoVs.
...
To understand the genetic diversity of these bat SARSr-CoVs, the most variable region of the SARSr-CoV S gene, corresponding to the receptor-binding domain (RBD) of SARS-CoV, were amplified and sequenced. Due to low viral load in some samples, RBD sequences were successfully amplified only from 49 samples.
....
Based on the diversity of RBD sequences, 11 novel SARSr-CoV strains named by abbreviation of bat species and sample ID (Rs4081, Rs4084, Rs4231, Rs4237, Rs4247, Rs4255, Rs4874, Rs7327, Rs9401, Rf4092 and As6526) were selected for full-length genomic sequencing based on sample abundance, genotype of RBD as well as sampling time.

All thses viruses exist essentially ony as Whole Genome Sequences (WGS) on a database. None of the above viruses were in the form of live viable culturable viruses. But they were trying to isolate live virus and they did so only once, this is the third occasion globally when a live SARS related coronavirus has been isolated from a bat. This is the third of the three isolates in 15 years of trying.

Quote:

In the current study, we successfully cultured an additional novel SARSr-CoV Rs4874 from a single fecal sample using an optimized protocol and Vero E6 cells [17]. Its S protein shared 99.9% aa sequence identity with that of previously isolated WIV16 and it was identical to WIV16 in RBD.

They then compared the new viable virus with the two previously isolated viable viruses.

Quote:

To assess whether the three novel SARSr-CoVs can use human ACE2 as a cellular entry receptor, we conducted virus infectivity studies using HeLa cells with or without the expression of human ACE2. All viruses replicated efficiently in the human ACE2-expressing cells. The results were further confirmed by quantification of viral RNA using real-time RT-PCR

This paper does not report gain of function research. It does not utilise recombinant mice. They used the S proteins from the three novel strains on a SARS back bone so that the only variable was the S protein, and the effect of the variations in the S protein could be compared with SARS. This is not gain of function research.

Prior to December 2019 there would habe been no reason not to announce the isolation of viable virus. This paper reports the third viable SARSr CoV to be cultured. None of these three can be turned into SARS-CoV-2 by serial passage or gain of function techniques.

[Planigale]

Originally Posted by Skeptic Ginger

Now where was I, oh yeah, coronavirus cultures at the WIV.

The above discussion about recovering viable coronavirus from bat feces is well documented but it's also a useless sidetrack. What matters is that despite Dr Shi claiming they had no viral cultures at the WIV, it was a lie.

Can you reference a source for a quote from Dr Shi saying that there were no (corona) viral cultures at the WIV?

[Planigale]

Originally Posted by Skeptic Ginger

The following has been posted already. My apologies to people keeping up in the thread. It is a long, well worth reading discussion of events that preceded the COVID pandemic.

MIT Tech Review: PANDEMIC TECHNOLOGY PROJECT
Inside the risky bat-virus engineering that links America to Wuhan - China emulated US techniques to construct novel coronaviruses in unsafe conditions


So unless people think this MIT author is a CT believer, ...

Oh dear, am I data dumping again. It's so hard not to. I and others have done so many literature reviews for this thread. Sigh, all that work and here we are again having to repeat what is already in the thread to newcomers to the conversation who so triumphantly believe they know it all.




There was a mutually beneficial trade between Baric and Shi.
Shi et al assisted nature in producing recombinant versions of SARSr CoVs. That's how one does GoF research in the lab.

Angrysoba posted rebuttals to these research papers. I don't recall what the objections were. Some were reasonable (that have been countered), some not so much like dismissing everything out of hand that Quay, Chan and a few others had to say. I'll let AS remind us.


Baric was extremely careful, the WIV, not so much:


Shi worked at BSL2, not even BSL3 let alone BSL4, which BTW was also plagued by a shortage of expertise and other problems described in a US diplomatic cable. And coronaviruses were recovered from sewage runoff from the WIV. Again links are posted up thread and I'm not going to hunt them down. Anyone who wants to, feel free.

Moving on:



Then we get to Rand Paul and his fixation on Fauci who also lied (or in his mind used a pedantic argument) when he claimed the US did not fund any GoF research at the WIV. That's another waste of time sidetrack that only serves to discredit actual supportable facts. The NIH did admit they funded GoF research at the WIV (documented up thread).

Who cares? I don't, not at this point. There is plenty of blame to go around. One thing that does matter: you cannot do GoF research without live cultures.

If there had been a trail of a bat spillover into humans in Wuhan one might argue it was a natural spillover, not a lab leak. Bats were not a popular item for sale in Wuhan wet markets. And now we have the spillover proponents in a tizzy because raccoon dogs were around when COVID-19 was. No bats though.

We are back to a coincidence that is about as likely as a meteorite hitting my house. First one needs human adapted or a virus very closely related to SARS CoV2 to be circulating in bats in Yunnan. That has not been found. Then a raccoon dog needs to get infected with that virus. That could happen in the wild or it could happen in an animal farm that raccoon dogs and bats are in contact with each other. Said related virus has yet to be found circulating in raccoon dogs anywhere.

Now you have to multiply the probability one or more of those raccoon dogs made it to the Wuhan wet market without a single person in contact with the animals—trappers, farmers, transporters—getting infected until an exposure at the wet market. And that virus has to die out in the raccoon dogs and/or in the bats because again, there were no COVID infections until Wuhan. And that was searched for in a number of different ways (again, sources posted up thread).

Multiply that probability by the odds the person infected in the wet market was a super spreader. Or maybe the first person infected spread the virus more silently in Wuhan until it made its way back to the wet market super spreader. ??? But then how does this explain the dog DNA/virus RNA recovery in one stall at the market?

This chain of events has plot holes, lots of them. And Worobey ignored them.


Daszak was excited about GoF research with coronaviruses. He was sure it would lead to a universal vaccine before a deadly virus spread.
And why not? That could mean millions more in grants that the EchoHealth Alliance controlled. And he'd be a hero.



The evidence is in their published papers before Dec 2019. They can't take those back or hide them from the internet.


These were clearly viable PPPs, not some segments whose genomes were analyzed.


There's a further discussion in the paper that is well worth reading.

From your reference (a popular review and not a scientific review).

Quote:

Baric was a legend in the field, but no matter how many safety precautions are taken, there is always a chance that a never-before-seen virus can escape and trigger an outbreak. Baric felt that the extreme measures he took in the lab minimized the risk.

Scary nonsense, by definition gain of function research is done on known viruses so a never-before-seen virus would not exist to escape.

Quote:

By taking thousands of samples from guano, fecal swabs, and bat tissue, and searching those samples for genetic sequences similar to SARS, Shi’s team began to discover many closely related viruses. In a cave in Yunnan Province in 2011 or 2012, they discovered the two closest, which they named WIV1 and SHC014.

Shi managed to culture WIV1 in her lab from a fecal sample and show that it could directly infect human cells, proving that SARS-like viruses ready to leap straight from bats to humans already lurked in the natural world. This showed, Daszak and Shi argued, that bat coronaviruses were a “substantial global threat.” Scientists, they said, needed to find them, and study them, before they found us.

Many of the other viruses couldn’t be grown, but Baric’s system provided a way to rapidly test their spikes by engineering them into similar viruses. When the chimera he made using SHC014 proved able to infect human cells in a dish, Daszak told the press that these revelations should “move this virus from a candidate emerging pathogen to a clear and present danger.”

Note how your reference specifies that the screening was done by PCR, and that many (most) of the viruses could not be grown. Only WIV 1 was grown. That the viruses could not be grown does not mean that the virus is not a potential human pathogen (nor does it mean if it can be grown it is a potential human pathogen). What was done was test the spike protein from non-culturable bat origin coronaviruses to see if they could be or become human pathogens by testing whether the spike protein would bind to human cells. This is not gain of function research. The virus used as the back bone was a low virulence virus, virulence is more than the spike protein. Swapping the spike protein wasn't going to make the virus more virulent.

Quote:

The genetic code of SARS-CoV-2 does not resemble that of any virus the WIV was known to be culturing in its lab.

This is the key point. There was no virus in the lab that could be turned into SARS-CoV-2 by gain of function nor serial passage. So all the discussion about gain of function work or biosafety levels is irrelevant. If there was no source virus it could not be manipulated and it could not escape.

[Planigale]

Originally Posted by Skeptic Ginger

I didn't accuse you of lying. I accused you of not reading what has already been posted in the thread. And no, why would I accept your citation interpretation when you ignore what's in your own citation about failures due to using the wrong culture media?

Do you really think that all the virologists who have looked for culturable coronaviruses from bats just used the 'wrong culture media' and if they had simply used a different one lots of viruses would have been cultured? All the samples would have been put through for culture on a variety of cell lines. Despite this only three have grown over 15 years.

Originally Posted by Skeptic Ginger

And you think Shi and Daszak didn't want to coverup their role in the COVID pandemic? Of course they did.

I think this is putting the cart before the horse. You have assumed they are guilty, therefore because they are guilty they would have lied, therefore you disbelieve the evidence they are innocent.

Originally Posted by Skeptic Ginger

Shi has had the option of putting the coronavirus genome library back online but she has failed to do so. And that includes her not sharing that database with a limited number of researchers who have asked her to. One thing Shi isn't is stupid.

I am not alone calling Daszak and Shi out on their lies. Understanding how the Chinese government secrecy works is not some CT. It's just a fact, like face saving.

You can not have it both ways. Either Shi is closely supervised by Chinese government officials in which case she would not have the option of putting the WIV genome database on-line or she is free to say and do as she wants.

[Skeptic Ginger]

Your denial is mind-boggling.

As for Shi saying there were no live cultures at the WIV, look it up. I don't have any obligation to cite a source when that is already in the thread.


ETA: Maybe someone else can help you out here. A live culture is a live culture no matter how many fragments of a genome are mentioned elsewhere a paper. Maybe if I simplify it.

Evidence of viral replication is not evidence of PCR amplification of genetic fragments.

"we successfully cultured", "All viruses replicated efficiently", and "Determination of virus infectivity by immunofluorescence assay" all say viruses were being grown at the WIV.

They weren't growing the tiddlywinks virus.

[The Atheist]

Originally Posted by jt512

So, again, when faced with an argument you cannot counter, you just descend into nonsense.

Bye, again.

You should step back and re-read your posts some time. You are so far from making a valid argument it's downright hilarious.
______________________________

On a side note, I see my theory that the lab leak involved the scientists all deliberately heading for the wet market is looking good.

[Skeptic Ginger]

Originally Posted by Planigale

Do you really think that all the virologists who have looked for culturable coronaviruses from bats just used the 'wrong culture media' and if they had simply used a different one lots of viruses would have been cultured? All the samples would have been put through for culture on a variety of cell lines. Despite this only three have grown over 15 years.

That's a straw man. The reference was to that paper and that paper alone. Do you think no one isolated the SARS1-related viruses from civet cats? Think no one isolated the virus that infected the 3 miners who died in Yunnan?

What about all the coronaviruses we know about that cause mild infection in people? No one could culture those? And the coronavirus that infects pigs, do we only know about these because someone identified the genomes but never replicated the viruses first?

What is your problem with common sense?

Originally Posted by Planigale

I think this is putting the cart before the horse. You have assumed they are guilty, therefore because they are guilty they would have lied, therefore you disbelieve the evidence they are innocent.

Well, yeah! I also posted evidence they lied.

Originally Posted by Planigale

You can not have it both ways. Either Shi is closely supervised by Chinese government officials in which case she would not have the option of putting the WIV genome database on-line or she is free to say and do as she wants.

How is that two ways? It's an 'AND' not an 'OR'. Shi cannot speak freely. Her government minders are indeed almost certainly blocking her from sharing that genome database.

Not sharing the database that was online and accessible until mid-Sept, 2019 would be something Shi would do under duress.

What we don't know (a lab leak hypothesis plot hole) is what moved the government to take the database offline that early. What did they know about that hiding the genome database became important? Maybe the virus leaked from the CCDC lab that was under Dr Gao. While we are all looking at the WIV maybe something else happened earlier.

And by earlier I don't mean there was a wet market exposure in Sept 2019. No super spreader event occurred until Dec.

[Skeptic Ginger]

Originally Posted by The Atheist

You should step back and re-read your posts some time. You are so far from making a valid argument it's downright hilarious.

TA, lomiller posts frequently inaccurate and unsupported scientific conclusions. Maybe you should read more of his posts.

I've cited multiple sources that viable (aka infectious) coronavirus is shed in bat guano. Do you have some evidence it is not?

______________________________

Originally Posted by The Atheist

On a side note, I see my theory that the lab leak involved the scientists all deliberately heading for the wet market is looking good.

That sarcasm belongs in the CT subforum.

[The Atheist]

Originally Posted by Skeptic Ginger

TA, lomiller posts frequently inaccurate and unsupported scientific conclusions. Maybe you should read more of his posts.

I think you missed the exchange I was referring to, because science had nothing to do with it.

[Skeptic Ginger]

Originally Posted by The Atheist

I think you missed the exchange I was referring to, because science had nothing to do with it.

But it was nonsense. The argument started with an attempt to discredit the fact the pandemic started very close to several labs that were studying coronaviruses. That is significant.

That there are other labs in China doesn't negate the improbable coincidence near the WIV is where the pandemic started.

And it doesn't negate that argument (of all the gin joints) to say there are wet markets all over China.

Lomiller did descend into nonsense when he said, "if there were no Earth."

I admit I don't know what "that annoying tiger thing" is. Was that important to your sarcasm?