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Old 20th October 2021, 02:07 AM   #2521
Capsid
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Originally Posted by DetectedMotion View Post
So does anybody here know of any reviewable records of scientific laboratory tests, under a microscope, analyzing and identifying the COVID-19 delta variant (SARS-CoV-2 Delta Variant) virus from isolated samples extracted from a human being?
Use PubMed and put in your search terms. eg https://pubmed.ncbi.nlm.nih.gov/34462756/

Do you mean an electron microscope? You can't see a virus otherwise. You can't identify the variant by looking at it. It is done by sequencing the RNA.
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Old 20th October 2021, 04:11 AM   #2522
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Sorry, missed the earlier post
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Old 20th October 2021, 08:14 AM   #2523
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Originally Posted by angrysoba View Post
Yeah. We’ve been through all of this before....
Re the death threats, interesting again you selectively choose who to believe.
Quote:
According to Vanity Fair, “death threats flooded his inbox” from “prominent scientists,” some of whom Redfield said were once his friends. He added that one of them told him to just “wither and die.”
So he gets a slew of death threats, one colleague he knew told him to “wither and die” and he tells the Vanity reporter he didn't expect that from scientists. Reporters are known to get it wrong. Making it sound like Redfield said he got multiple death threats from scientists then becomes the next news soundbite.

This is such a minor issue here but one easily cherry picked, all the while you don't address the evidence that until recently many of the mainstream scientists avoided the lab origin hypothesis out of peer and other career pressures.


Moving on...
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Old 20th October 2021, 09:16 AM   #2524
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Originally Posted by DetectedMotion View Post
So does anybody here know of any reviewable records of scientific laboratory tests, under a microscope, analyzing and identifying the COVID-19 delta variant (SARS-CoV-2 Delta Variant) virus from isolated samples extracted from a human being?
Not sure what do you want. Viruses are not analyzed under microscope. Also what do you mean by 'isolated samples extracted from a human being' ? Isolated from what ?

Virus variants genealogy and spread can be traced here: https://nextstrain.org/ncov/open/global

Specific genetic changes are best viewed here: https://genome.ucsc.edu/covid19.html

All that is obviously from human samples.
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Old 20th October 2021, 10:44 AM   #2525
DetectedMotion
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Originally Posted by Dr.Sid View Post
Not sure what do you want. Viruses are not analyzed under microscope. Also what do you mean by 'isolated samples extracted from a human being' ? Isolated from what ?

Virus variants genealogy and spread can be traced here: https://nextstrain.org/ncov/open/global

Specific genetic changes are best viewed here: https://genome.ucsc.edu/covid19.html

All that is obviously from human samples.
I should have posed the question in this way: Is there documentation on any Covid 19 virus isolated in a human being regarding each variant and each original isolated. Therefore a showing of the original infection
I'm having a discussion at my work and this is a question some are wanting to know about. I'm hoping to simplify it to where the answer is compelling enough for them to cause further interest in research on their own.
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Old 20th October 2021, 11:58 AM   #2526
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Originally Posted by DetectedMotion View Post
I should have posed the question in this way: Is there documentation on any Covid 19 virus isolated in a human being regarding each variant and each original isolated. Therefore a showing of the original infection
I'm having a discussion at my work and this is a question some are wanting to know about. I'm hoping to simplify it to where the answer is compelling enough for them to cause further interest in research on their own.
It's not like we detect new variant and say 'hey look, this is new'. The virus changes in almost every transmission. We collect viruses over time from all over the world and every sample is different. We can compare the changes and build tree of what's closest to each other, which comes from which.

Most of those changes are insignificant. Some are important. But we can't know right away. We can only tell after several weeks, when the new variant proves itself against older variants. And by that time, the new variant itself is not 1 virus .. it's whole family sharing the important change.

So we learn about the variant by analyzing what has the current variants from new samples in common, then tracing it back to first common ancestor. Then analyzing what changed, and then usually analyzing why it is better.
New variant of concern name with Greek letter can be assigned several months after it was first detected.

Nextstrain site is good for mapping this: https://nextstrain.org/ncov/open/global
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Old 20th October 2021, 12:36 PM   #2527
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Originally Posted by Skeptic Ginger View Post
Everyone you don't agree with is lying and with those who evidence shows are actually lying like Shi and Daszak, you dismiss the evidence. ...
Repeating fantasies does not make Shi into a liar.

An opinion from a "data scientist" in a Vanity Fair article is not "Many scientists, especially virologists" !
Gilles Demaneuf is a data scientist with the Bank of New Zealand in Auckland and one of the DRASTIC group who put out that live bats "fake news" video. The article lists a bit of idiocy from DRASTIC's founders. He had to research lab incidents in China when Wikipedia list them. de Maistre's imaginary notion of the WIV being one lab when anyone who knows about the WIV knows there are multiple labs.
A letter to Lancet from a few scientists does not intimidate scientists into silence. Research into all origins of the virus continued and was published. Anyone who follows the evidence knows that a spillover event is still the most likely origin with a lab leak coming a distant second.

The article omits vital facts about Li Wenliang.
It was the Wuhan CDC who warned hospitals in Wuhan about pneumonia cases of unknown cause.
Li actually warned his medical school classmates (not his colleagues at work) about what he said was SARS and identified as a coronavirus. He was reprimanded as a rumormonger for that SARS outbreak rumor.
Li was "lionized by the Chinese public as a hero and whistleblower", and lionized by the Chinese government as a hero and whistleblower and lionized indirectly by the Chinese Supreme People's Court.
Li was not suppressed by the Chinese government except in the sense of Chinese police procedures of suppressing any news not authorized by the government.
Li was not the only whistleblower. There were 7 others.

The article misrepresents the unclassified cable from diplomats who visited the WIV in 2018.
Reading the whole cable to get the context shows that it was talking about safe operations being limited. It is a limit on the amount of work being done, not the safety of the work. That is not quite the article statement of "threatened the facility’s safe operations".
The summary has "but its current productivity is limited by a shortage of the highly trained technicians and investigators required to safely operate a BSL-4 laboratory and a lack of clarity in related Chinese movement policies and guidelines". IOW in order to do more work the lab will need more personnel and guidance. The implication is that the lab is operating safely with the current staffing level. Page 2 has a "Unclear Guidelines on Virus Access and a Lack of Trained Talent Impede Research" section. If there was a concern about safety that should be in the title. Someone "noted that the new lab has a serious shortage of appropriately trained trained technicians and investigators needed to safely operate this high-containment facility". This is not followed by a discussion of making the lab safe lab but a discussion of how to get trained people.

The Mojiang miners idiocy from DRASTIC comes up. There is a "Blood samples were sent to the Wuhan Institute of Virology, which found that they were positive for SARS antibodies, a later Chinese dissertation documented" lie (from DRASTIC?). Shi and her colleagues found no SARS antibodies in the samples tested in late 2021. Addendum: A pneumonia outbreak associated with a new coronavirus of probable bat origin by 28 authors and Zheng-Li Shi. Published 17 November 2020. This is a June 3, 2021 article!

Last edited by Reality Check; 20th October 2021 at 12:50 PM.
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Old 20th October 2021, 04:01 PM   #2528
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Originally Posted by Skeptic Ginger View Post
Re the death threats, interesting again you selectively choose who to believe.
No, what I do is apply something called "skepticism" to a) propaganda sources (such as right-wing think tanks, science-denial sites, religious media outlets and extreme left-wing outlets) and b) mainstream sources that seem to be making extraordinary claims). You should try it sometime.


Originally Posted by Skeptic Ginger View Post
So he gets a slew of death threats, one colleague he knew told him to “wither and die” and he tells the Vanity reporter he didn't expect that from scientists. Reporters are known to get it wrong. Making it sound like Redfield said he got multiple death threats from scientists then becomes the next news soundbite.
Exactly, in other words you agree with me that he didn't get death threats from fellow scientists. That is what I disagree with. You may point out that he received death threats and no doubt he did - he is a public figure, so unfortunately that goes with the territory, but remember that you were using thie claim he received death threats from fellow scientists as evidence for other scientists not speaking out about the lab leak.

Now you may say, "Oh well the death threats didn't come from fellow scientists but he still got them, so that's why more scientists don't speak out about lab leak." But that would be complete bollocks. Do you have any idea how many death threats that people who think the likelihood of spillover is greater than lab leak get?

Do you think Peter Daszak, Zhengli Shi and Kristian Andersen don't get death threats?

Many of those who say spillover is more likely have had to either suspend their social media accounts or limit those who can reply to them. Angie Rasmussen apparently gets constant death and rape threats.

So when you point to Redfield and say, "Look what happens if you say lab leak" I say, "Yeah, it's nothing compared to getting the QAnon Brigade set on you!"

In fact, look at who is stirring up trouble against scientists who claim spillover. Members of Congress, and ex-president of the United States, podcasters with millions of followers.

Peter Hotez has pointed this out as well:

Quote:
But it did not stop there. Dr. Peter Daszak, just to take one example—the head of the non-profit EcoHealth Alliance—has been routinely hounded by right-wing media as part of their fixation on the (still unresolved) Wuhan Lab Leak hypothesis. GOP Rep. Mike Gallagher has outrageously gone so far as to suggest Daszak may have conspired to block a fair probe of what happened. Scripps Research Institute virologist Kristian Andersen has had to deactivate his Twitter account due to similar aggression.

I’m also personally threatened by emails, phone calls, and on social media for my views on vaccines, including COVID-19 vaccinations. They mostly have far-right and even white nationalist leanings, telling me about impending attacks from “patriots,” some imbued with Nazi imagery. As one colleague eloquently said to me recently in a text: “It’s like a slow moving train coming right for us. We have more lethally armed extremists in the U.S. than anywhere, and GOP members of Congress are whipping them up right now.”

I agree with Dr. Fauci when he says that these personal attacks represent an assault on American science.
Originally Posted by Skeptic Ginger View Post
This is such a minor issue here but one easily cherry picked, all the while you don't address the evidence that until recently many of the mainstream scientists avoided the lab origin hypothesis out of peer and other career pressures.
Well, now is your day in the Sun. So you can stop complaining about it.

Also,

Originally Posted by Skeptic Ginger View Post
So he gets a slew of death threats, one colleague he knew told him to “wither and die” and he tells the Vanity reporter he didn't expect that from scientists. Reporters are known to get it wrong. Making it sound like Redfield said he got multiple death threats from scientists then becomes the next news soundbite.
First of all, don't repeat soundbites then. Second, do you not remember that I made exactly this point to you regarding Zhengli-Shi's claim of fungal infection in the miners. We don't have her exact words: we only have a paraphrased claim that it was fungal infection. It could be that she said something to the effect of "We tested for SARS-like virus and found none so we had to include they died from something else such as a fungal infection". It seems reasonable to me that she could have said what she was able to say as a virologist and speculated further, but the reporter decided to choose a sentence for brevity's sake. She is not a pathologist after all.
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"Evolution and Ethics" T.H. Huxley (1893)
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Old 20th October 2021, 04:03 PM   #2529
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Reviewing some of the out-of-the-lab-ready-to-go evidence:

WSJ Oct 5, 2021; Quay and Muller op ed: Science Closes In on Covid’s Origins
Quote:
Based on experience with SARS-1 in 2003 and MERS in 2012, we know that many people are infected by a host animal long before a coronavirus mutates to the point where it can jump from human to human. An extensive data set from late 2019—more than 9,000 hospital samples—is available of people exhibiting flulike (thus Covid-like) symptoms in China’s Hubei and Shaanxi provinces before the epidemic started. Based on SARS-1 and MERS, the natural zoonotic theory predicts 100 to 400 Covid infections would be found in those samples. The lab-leak hypothesis, of course, predicts zero. If the novel coronavirus were engineered by scientists pursuing gain-of-function research, there would be no instances of community infection until it escaped from the laboratory. The World Health Organization investigation analyzed those stored samples and found zero pre-pandemic infections. This is powerful evidence favoring the lab-leak theory.
This link is from my download file so you'll have to find it by title: "WHO-convened Global Study of Origins of SARS-CoV-2: China Final Report; 14 January-10 February 2021"

From the WHO investigation:
Quote:
Review of Stored Biological Samples Testing
As part of origins of SARS-CoV-2 study, searches for stored respiratory tract, serum or other samples suitable for SARS-CoV-2 laboratory testing were requested. Sub-set of samples were identified and tested from hospitalized patients related to scientific research projects, including patient samples preserved in the biobank of Tongji Hospital, as well as patient samples preserved by the collaborative research institute jointly developed by Wuhan University and Tongji Hospital of Huazhong University of Science and Technology in late 2019. ...

... all laboratory results were negative.

In summary:
No bat source compatible with a Wuhan outbreak and no other proximal animal source found (80,000+ animals including bats were tested). No unusual spikes in pneumonia cases were found in China prior to the Dec cases in Wuhan, and no COVID 19 antibody or viral positive results were found in more than 4,000 body fluid specimens collected and stored in China in 2019.

The op-ed summarizes a number of other points re the lab leak evidence.


Wiki: Richard A Muller
Quote:
Dr Richard A. Muller (born January 6, 1944) is an American physicist and emeritus professor of physics at the University of California, Berkeley. He was also a faculty senior scientist at the Lawrence Berkeley National Laboratory.
And from the Wiki page he's a liberal, not a right-winger. But gee, a PhD in physics, OMG, how dare he have an opinion on COVID's origin.


Discounting sources and not addressing arguments in 3 ... 2 ... 1 ...

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Old 20th October 2021, 04:05 PM   #2530
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By the way, here are two moves right out of the Climate Change Denialist playbook:

1.) Claim that scientists who dissent from the consensus are cowed into silence because they don't want to jeopardize their careers.

2.) Pore through reams of emails and extract the juicy quotes. ("Aha! This looks like they might know something different!") - See University of East Anglia emails thingy.
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"Evolution and Ethics" T.H. Huxley (1893)
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Old 20th October 2021, 04:39 PM   #2531
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Originally Posted by angrysoba View Post
No, what I do is apply something called "skepticism" to a) propaganda sources (such as right-wing think tanks, science-denial sites, religious media outlets and extreme left-wing outlets) and b) mainstream sources that seem to be making extraordinary claims). You should try it sometime.
I did not say the source should be ignored. I said only addressing the source and thereby declaring the evidence moot ignores the evidence.

In addition, I've posted the reason we aren't seeing much from more neutral sources. You've not presented evidence countering that.


Originally Posted by angrysoba View Post
Exactly, in other words you agree with me that he didn't get death threats from fellow scientists. That is what I disagree with. You may point out that he received death threats and no doubt he did - he is a public figure, so unfortunately that goes with the territory, but remember that you were using thie claim he received death threats from fellow scientists as evidence for other scientists not speaking out about the lab leak.
Cherry picking one small thing in my post and making it sound like it's the only thing I said.


Originally Posted by angrysoba View Post
Now you may say, "Oh well the death threats didn't come from fellow scientists but he still got them, so that's why more scientists don't speak out about lab leak." But that would be complete bollocks. Do you have any idea how many death threats that people who think the likelihood of spillover is greater than lab leak get?
Ostracized, peer pressure, career risks, a desire not to have their own GoF research stopped, and the US agencies having a serious issue when funding of the WIV work is scrutinized too closely... That's a lot more than death threats.


Originally Posted by angrysoba View Post
Do you think Peter Daszak, Zhengli Shi and Kristian Andersen don't get death threats?
I'm sure they do.

Originally Posted by angrysoba View Post
Many of those who say spillover is more likely have had to either suspend their social media accounts or limit those who can reply to them. Angie Rasmussen apparently gets constant death and rape threats.

So when you point to Redfield and say, "Look what happens if you say lab leak" I say, "Yeah, it's nothing compared to getting the QAnon Brigade set on you!"

In fact, look at who is stirring up trouble against scientists who claim spillover. Members of Congress, and ex-president of the United States, podcasters with millions of followers.

Peter Hotez has pointed this out as well:
Are they getting peer pressure, being ostracized professionally, does that position threaten their careers?

Of course now that it has come out Daszak has been putting his thumb on the scale, that he has a serious conflict of interest he has yet to admit to and that he and EcoHealth have a lot of data he is refusing to disclose, Daszak is getting peer pressure, being ostracized professionally, and his funding has been threatened.


Originally Posted by angrysoba View Post
First of all, don't repeat soundbites then. Second, do you not remember that I made exactly this point to you regarding Zhengli-Shi's claim of fungal infection in the miners. We don't have her exact words: we only have a paraphrased claim that it was fungal infection. It could be that she said something to the effect of "We tested for SARS-like virus and found none so we had to include they died from something else such as a fungal infection". It seems reasonable to me that she could have said what she was able to say as a virologist and speculated further, but the reporter decided to choose a sentence for brevity's sake. She is not a pathologist after all.
Your analogy sucks but I suspect you know that. Shi's exact words?

Here's the paragraph from the SciAm interview:
Quote:
“The mine shaft stunk like hell,” says Shi, who, like her colleagues, went in wearing a protective mask and clothing. “Bat guano, covered in fungus, littered the cave.” Although the fungus turned out to be the pathogen that had sickened the miners, she says it would have been only a matter of time before they caught the coronaviruses if the mine had not been promptly shut.
There is nothing vague there which can be construed to fit your speculative version. And my repeating the sound bite is not the issue. You cherry picking that one thing and ignoring the rest is the issue.

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Old 20th October 2021, 04:45 PM   #2532
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Look at that quote again. Shi’s words are paraphrased, not quoted, to say that the fungus killed the miners. Again, she is not a pathologist so I have no reason to think she made some conclusive autopsy on the miners, only that she did not find any evidence of coronavirus from tested samples.
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"Evolution and Ethics" T.H. Huxley (1893)
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Old 20th October 2021, 04:48 PM   #2533
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You can accuse me of cherry picking if you like but I am merely pointing out that you are fashioning a narrative for yourself and bolting down the components of it on every retelling. It seems to me that there is a lot speculation which you insist has been confirmed.
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"Evolution and Ethics" T.H. Huxley (1893)
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Old 20th October 2021, 06:33 PM   #2534
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Originally Posted by angrysoba View Post
By the way, here are two moves right out of the Climate Change Denialist playbook:

1.) Claim that scientists who dissent from the consensus are cowed into silence because they don't want to jeopardize their careers.

2.) Pore through reams of emails and extract the juicy quotes. ("Aha! This looks like they might know something different!") - See University of East Anglia emails thingy.
And here you are again trying to drag this evidence based discussion into the CT forum. Is this reference to "juicy quotes" a continuation of ignoring the evidence and instead only address one cherry picked bit from my post?


It might be an issue if said repression of the lab leak hypothesis wasn't so well documented.

Attempts to make the lab leak look like a CT make heavy use of "scientists say", "researchers say", "virologists say" and so on.

I've seen 2 recent op-eds claiming this very thing.

Covid-19 lab leak theory highly unlikely, scientists say
Quote:
according to a team of global scientists.
Note they are still claiming the Wuhan Seafood market was the source of the first cases when that was ruled out well over a year ago.
Quote:
possibly other markets
Which have never been identified and never connected directly to any of the first cases.


And the other one:
Why many scientists say it’s unlikely that SARS-CoV-2 originated from a “lab leak”

Sept 2021 and they are still repeating this lie:
Quote:
In fact, early in the pandemic, a group of prominent researchers dismissed lab-origin notions as “conspiracy theories” in a letter in The Lancet.
That letter along with Daszak have been shown to be demonstrably tainted after an email came to light where Daszak tells colleagues not to let it get out that Daszak wrote the letter.

Emails show scientists discussed masking their involvement in key journal letter on Covid origins
Quote:
Daszak drafted the statement and circulated it to other scientists to sign. But the emails reveal that Daszak and two other EcoHealth-affiliated scientists thought they should not sign the statement so as to mask their involvement in it. Leaving their names off the statement would give it “some distance from us and therefore doesn’t work in a counterproductive way,” Daszak wrote. ...

The two scientists Daszak wrote to about the need to make the paper appear independent of EcoHealth, are coronavirus experts Ralph Baric and Linfa Wang.

In the emails, Baric agreed with Daszak’s suggestion not to sign The Lancet statement, writing “Otherwise it looks self-serving, and we lose impact.”
Let's list some of the more blatant lies trying to mislead opinion on the lab leak hypothesis:
Referring to the seafood market as the source when it was not connected to the first cases.

Assert there was another wet market associated with the first case and then repeating it when there is no supporting evidence.

Shi's claim the Yunnan miners died of a fungal infection.

Daszak's dishonest manipulation using the Lancet letter he wrote.

Daszak's claim there were lots of spillover events involving coronaviruses and bats when his entire paper only speculated this was a possibility. The actual evidence looking at CoV antibodies in people living near the Yunnan caves where the bats live found actual spillover events were incredibly rare.
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Old 20th October 2021, 06:36 PM   #2535
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Originally Posted by angrysoba View Post
You can accuse me of cherry picking if you like but I am merely pointing out that you are fashioning a narrative for yourself and bolting down the components of it on every retelling. It seems to me that there is a lot speculation which you insist has been confirmed.
You didn't address your cherry picking. Or did I miss it? Should I repeat the problem?

"Ostracized, peer pressure, career risks, a desire not to have their own GoF research stopped, and the US agencies having a serious issue when funding of the WIV work is scrutinized too closely... That's a lot more than death threats."
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Old 20th October 2021, 06:40 PM   #2536
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Originally Posted by angrysoba View Post
Look at that quote again. Shi’s words are paraphrased, not quoted, to say that the fungus killed the miners. Again, she is not a pathologist so I have no reason to think she made some conclusive autopsy on the miners, only that she did not find any evidence of coronavirus from tested samples.
That's quite an apology for Shi's claim that the miners died of a fungal infection.

But let's take a step back, are you agreeing they did not die of a fungal infection? Wasn't Shi's claim supposed to supersede the master's and doctorate theses which concluded the evidence pointed to a viral infection and more specifically a CoV?
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Old 20th October 2021, 07:00 PM   #2537
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Originally Posted by Skeptic Ginger View Post
You didn't address your cherry picking. Or did I miss it? Should I repeat the problem?

"Ostracized, peer pressure, career risks, a desire not to have their own GoF research stopped, and the US agencies having a serious issue when funding of the WIV work is scrutinized too closely... That's a lot more than death threats."
This is just singing from the climate change denier playbook.
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"Evolution and Ethics" T.H. Huxley (1893)
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Old 20th October 2021, 07:05 PM   #2538
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Originally Posted by Skeptic Ginger View Post
That's quite an apology for Shi's claim that the miners died of a fungal infection.

But let's take a step back, are you agreeing they did not die of a fungal infection? Wasn't Shi's claim supposed to supersede the master's and doctorate theses which concluded the evidence pointed to a viral infection and more specifically a CoV?
No, what I am saying is that given her role in testing samples, the most she can say with any degree of confidence is that the samples did not test positive for coronavirus.

We don't know the confidence with which she suggested they died of fungus. She may have said it was probable that they did, etc... and why not?

However you are claiming that she defo said it was fungus and you claim that she knew it was not fungus and you claim that they died of a spillover of SARS, and you claim that she and Daszak found the virus, covered up the spillover, lied (for no apparent gain) that it was fungus, secretly engineered a secret virus into SARS-CoV2.

For me, your claim is the extraordinary one and based on very cynical assumptions of motivations and it is cobbled together from some paraphrasing of her words in a single article.

To support this, you gleefully put forward all kinds of wacky news sources like the Epoch Times as confirmation.
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"Evolution and Ethics" T.H. Huxley (1893)
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Old 20th October 2021, 08:04 PM   #2539
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Originally Posted by lomiller View Post
Other than being significantly more developed now what do you *think* has changed? The current regime is simpler a continuation of the one that has ruled China or decades.

If you are so worried about China don't you think it's worth investing in the critical thinking skills needed to figure out what they are really up to? I don't trust China so I'm willing to believe anything anyone says about it isn't exactly a good way to protect yourself, it just opens you up for manipulation.
What do I think has changed? I live in Hong Kong, mate, so I can see exactly what has changed in the 14 years that I have lived here.

Anyone who thinks the current CCP regime is a simple continuation of that under Deng is willfully blind and naďve. Deng opened up China to the west, fully embraced capitalism, opened up the financial markets and systems, and allowed western money to poor into China, which enabled them to raise millions out of poverty, generate a huge middle class and smaller number of extremely rich, and become the worlds de facto manufacturer.

Under Xi, they have gone the other way and there is a new cultural revolution on the way. The CCP has closed their borders both figuratively to outside investment and physically to non-Chinese, they have cracked down on education, on property giants, on tech giants. Not to mention the crackdown in HK, and their current military threats to Taiwan, the military expansion in the south china sea, clashes of "coastguard" vessels with Philippine and Vietnamese fishing boats etc.

HK still has a restriction of 4 people being allowed to meet in public, despite there being no local Covid cases for months. There have been no local elections for 2 years, since the government supporters got trounced last time. Under the new security law it is now a crime to "foster hatred against the government"; and that can be interpreted as loosely as it sounds. Since that law was applied, the HK government have pretty much given up pretending they are anything other than controlled by the CCP; they have no independent power or policy now.

Chinese state newspapers push the theory to their citizens that Covid comes from the US, and have recently openly accused the US of an act of biological warfare against China.

They are now planning for redistribution of wealth, a universal income and a return to actual communism.

Their stated aim is and has always been stability at all costs throughout China, as the primary goal is the continuation of the CCP. Anything that could cause instability is rooted out, hammered down, or disappeared. If there isn't a current law for it, the catch all "picking quarrels and provoking trouble" is used. Good luck getting a trial at all if that happens.

The CCP feel themselves strong enough now that they frankly don't care what the west thinks, and will act largely according to their desires. Their internal market is strong enough at the moment to support the economy, and their exports have grown during covid.

Their only concern is strength and internal stability. They have always played down the fact that the first cases started in China, but are absolutely terrified about the lab leak theory, as it would cause a big problem for internal stability and be something big enough that they feel the whole world could turn against them, not just the west. They would do anything, literally anything, to stop that theory in its tracks. Hence they deleted databases and restricted access when the WHO came calling, then flatly denied they had done those things.

Because China under the CCP is all these things, do I therefore think that their citizens are evil moustache twirling Fu Manchu caricatures, thus Covid must have started in a lab? Does that mean everything China does is untrustworthy?

No, of course not. I myself largely lean towards the natural spillover theory, but don't rule the lab leak out. In fact, much like the WHO!

My whole point all along is simply that you cannot treat China under Xi like some western country, and assume that "oh they wouldn't do that", or think that scientists like Shi are playing under the same rules as scientists in another country, because, through no fault of their own, they are not. If (and it is still an if) there is something the Chinese state does not want to get out, it will not get out. This is not a conspiracy, it is a fact.
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Old 20th October 2021, 09:07 PM   #2540
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Funny how the Lancet has changed its tune to embrace a CT.

Voice of Healthcare, Sept 2021: Covid origins probe: The Lancet does U-turn over lab leak theory
Quote:
The international team of health experts, in the open letter, make an appeal for "objective, open, and transparent scientific debate about the origin of SARS-CoV-2".

Scientists "need to evaluate all hypotheses on a rational basis, and to weigh their likelihood based on facts and evidence, devoid of speculation concerning possible political impacts", the authors wrote. ...

... it was revealed earlier that Peter Daszak -- a British scientist and president of the US-based non-profit EcoHealth Alliance that has a direct connection with China -- had secretly orchestrated the now-infamous letter. The firm has also funded research at the Wuhan Institute of Virology (WIV).
The Daszak letter said:
Quote:
"We stand together to strongly condemn conspiracy theories suggesting that Covid-19 does not have a natural origin", they said, in a statement that "imparted a silencing effect on the wider scientific debate".
Like I said ...

But independent scientists struck back with a letter of their own, one that wasn't mired in deceit:
Quote:
However, "there is no direct support for the natural origin of SARS-CoV-2, and a laboratory-related accident is plausible", the authors stated. ...

"For a leading medical journal like Lancet to agree to finally open its doors to a letter from scientists highlighting the ongoing uncertain origins of Covid-19, indicates how far we have come in 18 months in requesting an open scientific debate on the topic, but also indicates just how far we still have to go," he added.


Lancet Sept 17, 2021: An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2
Quote:
On July 5, 2021, a Correspondence was published in The Lancet called “Science, not speculation, is essential to determine how SARS-CoV-2 reached humans”.1 The letter recapitulates the arguments of an earlier letter (published in February, 2020) by the same authors,2 which claimed overwhelming support for the hypothesis that the novel coronavirus causing the COVID-19 pandemic originated in wildlife. The authors associated any alternative view with conspiracy theories by stating: “We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin”. The statement has imparted a silencing effect on the wider scientific debate, including among science journalists.3
There is little to no evidence for a spillover:
Quote:
There is so far no scientifically validated evidence that directly supports a natural origin. Among the references cited in the two letters by Calisher and colleagues,1, 2 all but one simply show that SARS-CoV-2 is phylogenetically related to other betacoronaviruses. The fact that the causative agent of COVID-19 descends from a natural virus is widely accepted, but this does not explain how it came to infect humans. The question of the proximal origin of SARS-CoV-2—ie, the final virus and host before passage to humans—was expressly addressed in only one highly cited opinion piece, which supports the natural origin hypothesis,4 but suffers from a logical fallacy:5
The logical fallacies are described in the letter.
Quote:
Although considerable evidence supports the natural origins of other outbreaks (eg, Nipah, MERS, and the 2002–04 SARS outbreak) direct evidence for a natural origin for SARS-CoV-2 is missing. After 19 months of investigations, the proximal progenitor of SARS-CoV-2 is still lacking. Neither the host pathway from bats to humans, nor the geographical route from Yunnan (where the viruses most closely related to SARS-CoV-2 have been sampled) to Wuhan (where the pandemic emerged) have been identified. More than 80 000 samples collected from Chinese wildlife sites and animal farms all proved negative.13
The letter goes on to describe all the evidence and possible mechanisms for a lab origin. In the end they state that there is no compelling evidence to choose between either origin hypotheses.
Quote:
Contrary to the first letter published in The Lancet by Calisher and colleagues,2 we do not think that scientists should promote “unity” (“We support the call from the Director-General of WHO to promote scientific evidence and unity over misinformation and conjecture”). As shown above, research-related hypotheses are not misinformation and conjecture. More importantly, science embraces alternative hypotheses, contradictory arguments, verification, refutability, and controversy. Departing from this principle risks establishing dogmas, abandoning the essence of science, and, even worse, paving the way for conspiracy theories. Instead, the scientific community should bring this debate to a place where it belongs: the columns of scientific journals.31, 32
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Old 20th October 2021, 09:20 PM   #2541
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More Lancet mea culpa:

BMJ Oct 2021: Covid-19: Lancet investigation into origin of pandemic shuts down over bias risk
Quote:
The work of a task force commissioned by the Lancet into the origins of covid-19 has folded after concerns about the conflicts of interest of one its members and his ties through a non-profit organisation to the Wuhan Institute of Virology.

Task force chair Jeffrey Sachs, economics professor at Columbia University in New York, told the Wall Street Journal that he had shut down the scientist led investigation into how the covid-19 pandemic started because of concerns about its links to the EcoHealth Alliance, a non-profit organisation run by task force member Peter Daszak.1 ...

The decision came as evidence continued to accumulate that Daszak had not always been forthright about his research and his financial ties to the Wuhan Institute of Virology. Daszak now faces increased scrutiny from scientists, the media, and members of US Congress. ...

Daszak’s story began falling apart last November when the non-profit group US Right to Know published emails gathered through a freedom of information request that showed he had orchestrated the Lancet statement without disclosing that he was funding Shi Zhengli through grants from the National Institutes of Health (NIH). ...

That same month [b]the Lancet posted an addendum to the February 2020 statement,6 /b]which had previously read, “We declare no competing interests.” The half page addendum discusses EcoHealth Alliance’s funding of researchers in China and studies involving recombinant bat viruses. Daszak also resigned that month from the Lancet task force.
But wait, there's more:
Quote:
further information emerged questioning the veracity of several other statements made by Daszak. After suing the NIH to gain access to Daszak’s grants, the US media organisation the Intercept released details of several of Daszak’s NIH grants and grant applications, including one that seemed to involve gain-of-function research by creating chimeric SARS viruses. ...

a week after the Intercept’s story a group of online investigators called DRASTIC (Decentralized Radical Autonomous Search Team Investigating Covid-19) published leaked documents that included a grant application that Daszak had submitted to the US Department of Defense in 2018. In that document Daszak proposed creating chimeric SARS viruses. The department declined to fund Daszak’s grant, adding that if it were funded in the future the chimeric research would require a risk mitigation plan for gain-of-function research.
Guess that was a grant proposal for GoF research after all.

That the NIH grant was denied doesn't preclude the WIV obtaining funding through the Chinese government or some other of Daszak's fungible donations.
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Old 20th October 2021, 09:26 PM   #2542
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And more re the media being conned:

BMJ: The covid-19 lab leak hypothesis: did the media fall victim to a misinformation campaign?

The evidence says, why yes, yes they did.
Quote:
The theory that SARS-CoV-2 may have originated in a lab was considered a debunked conspiracy theory, but some experts are revisiting it amid calls for a new, more thorough investigation. Paul Thacker explains the dramatic U turn and the role of contemporary science journalism ...

Scientists and reporters contacted by The BMJ say that objective consideration of covid-19’s origins went awry early in the pandemic, as researchers who were funded to study viruses with pandemic potential launched a campaign labelling the lab leak hypothesis as a “conspiracy theory.”

This should piss people off in this thread debate, not encourage even more doubling down calling the lab leak hypotheses a CT.
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Old 20th October 2021, 09:37 PM   #2543
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Originally Posted by Skeptic Ginger View Post
Reviewing some of the out-of-the-lab-ready-to-go evidence:

WSJ Oct 5, 2021; Quay and Muller op ed: Science Closes In on Covid’s Origins
Some obvious ignorance quoted from the Richard Muller and Steven Quay op-ed in the WSJ.
That "extensive data set from late 2019—more than 9,000 hospital samples" just shows there were no COVID-19 infections in the samples in late 2019 in Hubei and Shaanxi provinces. That is powerful evidence that COVID-19 originated after that "late 2019" probably from animals or less likely from a lab leak.. This is really simple:
  • A spillover event after the samples were collected predicts no infections.
  • A spillover event before the samples were collected predicts infections.
  • A lab leak after the samples were collected predicts no infections.
  • A lab leak before the samples were collected predicts infections.
Wiki: Richard A Muller shows that he is a 77 year old, retired physicist. Anyone writing "This is powerful evidence favoring the lab-leak theory." is ignorant of or ignoring basic biology. No matter what the origin of COVID-19 is, the virus or antibodies would be in the samples only if that origin was before the samples were taken. Both origins are supported by the evidence. What the evidence does show is that COVID-19 originated after late 2019.

People with sense will discount an obviously ignorant opinion piece in a financial journal by a retired physicist and a physician who publishes with the DRASTIC clowns (Gilles Demaneuf and DRASTIC Team)

Last edited by Reality Check; 20th October 2021 at 09:39 PM.
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Old 20th October 2021, 10:02 PM   #2544
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Originally Posted by Skeptic Ginger View Post
Here's the paragraph from the SciAm interview:
It is clear you are are still unable to see what are Shi's words in that quote and which are the reporter's.
Quote:
“The mine shaft stunk like hell,” says Shi, who, like her colleagues, went in wearing a protective mask and clothing. “Bat guano, covered in fungus, littered the cave.” Although the fungus turned out to be the pathogen that had sickened the miners, she says it would have been only a matter of time before they caught the coronaviruses if the mine had not been promptly shut.
Shi's actual words are in quotes. The reporters version of what else Shi said in their words are not. It is possible that "Although the fungus turned out to be the pathogen that had sickened the miners" are purely from the reporter. In any case
  • The fungal infection claim is not an actual quote from Shi.
  • If Shi said that the miners became ill from fungal infection, Shi was telling the truth.
    There is no evidence that they had a viral infection. Their symptoms did not differentiate between fungal and viral pneumonia. Shi and her colleagues ruled out 3 viral infections.
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Old 20th October 2021, 10:11 PM   #2545
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Originally Posted by Skeptic Ginger View Post
Funny how the Lancet has changed its tune to embrace a CT.

Voice of Healthcare, Sept 2021: Covid origins probe: The Lancet does U-turn over lab leak theory


The Daszak letter said:
Like I said ...

But independent scientists struck back with a letter of their own, one that wasn't mired in deceit:




Lancet Sept 17, 2021: An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2


There is little to no evidence for a spillover:The logical fallacies are described in the letter.

The letter goes on to describe all the evidence and possible mechanisms for a lab origin. In the end they state that there is no compelling evidence to choose between either origin hypotheses.
Originally Posted by Skeptic Ginger View Post
More Lancet mea culpa:

BMJ Oct 2021: Covid-19: Lancet investigation into origin of pandemic shuts down over bias risk

But wait, there's more:
Guess that was a grant proposal for GoF research after all.

That the NIH grant was denied doesn't preclude the WIV obtaining funding through the Chinese government or some other of Daszak's fungible donations.
Originally Posted by Skeptic Ginger View Post
And more re the media being conned:

BMJ: The covid-19 lab leak hypothesis: did the media fall victim to a misinformation campaign?

The evidence says, why yes, yes they did.



This should piss people off in this thread debate, not encourage even more doubling down calling the lab leak hypotheses a CT.
This is just heavy editorializing with your claims that the Lancet etc... are doing mea culpas, etc...

What you are talking about is just that they published letters in their letter pages from Lab Leak proponents and going, "HA ha!" But of course, it merely undercuts your claim that none dare speak out because of the influence of the dastardly Peter Darth Vader Daszak.

In fact, you then say that he had GoF funding not authorized so how it boosts your claim that everyone says spillover to get funding is some weird pretzel logic that I cannot untangle.
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"Evolution and Ethics" T.H. Huxley (1893)
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Old 20th October 2021, 10:37 PM   #2546
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Question Has anyone seen any quote "claiming there were no in vitro CoV cultures at the WIV"

Originally Posted by Skeptic Ginger View Post
Let's list some of the more blatant lies trying to mislead opinion on the lab leak hypothesis:
A repeated fantasy of blatant lies.
  • There may be outdated or less knowledgeable sourced still claiming that the seafood market was the connected to the first cases. This does not mislead
    about the lab leak hypostasis. WUIV people would eat seafood! If that market were a source.
  • What looks like a "another wet market associated with the first case " fantasy.
  • Shi's claim the Yunnan miners died of a fungal infection is valid.
    Their symptoms were compatible with fungal pneumonia and viral pneumonia. Blood samples were tested and 3 viruses including a bat virus or antibodies were not found. The probable cause of death is fungal infection.
    Then there is your "incredibly rare" infection rate below !
    If spillover events are "incredibly rare" then how did 6 miners get infected?
    Were there hundreds of miners in the cave working for a year?
    1 September 2021 onward: Repeating fantasies does not make Shi into a liar.
  • A "Daszak's dishonest manipulation using the Lancet letter he wrote" lie. It was an open letter to the Lancet containing the authors option. An open letter to a journal is statements that they hope other people would agree with
    Unfortunate language but that is not dishonest.
    Daszak should have made his association with the WIV clear which was fixed later.
  • No evidence of "Daszak's claim there were lots of spillover events involving coronaviruses and bats".
    We have evidence of 7 such spillover events in the last 50 years (Bat-borne virus diversity, spillover and emergence). Extend this to say 100,000 years with adjustments for population and "lots" would be justified.
    23 September 2021: Daszak's preprint and paper do not disagree.
    Daszak was a coauthor on a preprint that modeled interactions with bats and came to a potential number of ~400,000 people infected a year.
    Daszak was a coauthor on a paper looking at CoV antibodies in people living near the Yunnan caves where the bats live found found a number that is compatible with Daszak's preprint (150,000 infections per year).
    Highlighting of "incredibly rare" is a lie when that is not what the paper says. The paper just says "The low seroprevalence observed in this study suggests that bat coronavirus spillover is a rare event."
Has anyone seen any any quote "claiming there were no in vitro CoV cultures at the WIV" from Shi?
Sounds like just a unfounded assertion from Skeptic Ginger or maybe rubbish from DRASTIC. It is well known that the WIV isolated and grew 3 bat CoV. Shi would know that!

Last edited by Reality Check; 20th October 2021 at 10:56 PM.
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Old 20th October 2021, 11:29 PM   #2547
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Originally Posted by angrysoba View Post
This is just heavy editorializing with your claims that the Lancet etc... are doing mea culpas, etc...

What you are talking about is just that they published letters in their letter pages from Lab Leak proponents and going, "HA ha!" But of course, it merely undercuts your claim that none dare speak out because of the influence of the dastardly Peter Darth Vader Daszak.

In fact, you then say that he had GoF funding not authorized so how it boosts your claim that everyone says spillover to get funding is some weird pretzel logic that I cannot untangle.
This post makes no sense in relation to the evidence posted. You are just ignoring anything/everything that doesn't confirm your bias, that or you have no desire to actually be serious.


It's unfortunate you are not willing to/interested in actually discussing the evidence.

Last edited by Skeptic Ginger; 20th October 2021 at 11:37 PM.
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Old 21st October 2021, 12:31 AM   #2548
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Originally Posted by Skeptic Ginger View Post
This post makes no sense in relation to the evidence posted. You are just ignoring anything/everything that doesn't confirm your bias, that or you have no desire to actually be serious.


It's unfortunate you are not willing to/interested in actually discussing the evidence.
I'm not really sure what "evidence" you want me to discuss. Most of what you posted is long on insinuation and speculation and short on evidence.
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"Evolution and Ethics" T.H. Huxley (1893)
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Old 21st October 2021, 12:39 AM   #2549
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Originally Posted by Dr.Sid View Post
It's not like we detect new variant and say 'hey look, this is new'. The virus changes in almost every transmission. We collect viruses over time from all over the world and every sample is different. We can compare the changes and build tree of what's closest to each other, which comes from which.
Ok I see how the comparison is done when changes occur.
What I'm more interested in finding out is how the virus sample itself was isolated and tested after discovery/or given to be tested to provide the proof and therefore documented.
I was looking through the CDC site to possibly find this, but it seems as though the CDC had no actual virus..

https://www.fda.gov/media/134922/downloadhttps://www.fda.gov/media/134922/download
On page 40 of Performance Characteristics it reads as follows:
Since no
quantified virus isolates of the 2019-nCoV were available for CDC use at the time the test was developed
and this study conducted
, assays designed for detection of the 2019-nCoV RNA were tested with
characterized stocks of in vitro transcribed full length RNA (N gene; GenBank accession: MN908947.2) of
known titer (RNA copies/µL) spiked into a diluent consisting of a suspension of human A549 cells and
viral transport medium (VTM) to mimic clinical specimen.

The hilited section above indicates they had no virus isolates when the test was developed and when the study was conducted.

Last edited by DetectedMotion; 21st October 2021 at 12:42 AM.
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Old 21st October 2021, 01:26 AM   #2550
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Originally Posted by DetectedMotion View Post
Ok I see how the comparison is done when changes occur.
What I'm more interested in finding out is how the virus sample itself was isolated and tested after discovery/or given to be tested to provide the proof and therefore documented.
I was looking through the CDC site to possibly find this, but it seems as though the CDC had no actual virus..

https://www.fda.gov/media/134922/downloadhttps://www.fda.gov/media/134922/download
On page 40 of Performance Characteristics it reads as follows:
Since no
quantified virus isolates of the 2019-nCoV were available for CDC use at the time the test was developed
and this study conducted
, assays designed for detection of the 2019-nCoV RNA were tested with
characterized stocks of in vitro transcribed full length RNA (N gene; GenBank accession: MN908947.2) of
known titer (RNA copies/µL) spiked into a diluent consisting of a suspension of human A549 cells and
viral transport medium (VTM) to mimic clinical specimen.

The hilited section above indicates they had no virus isolates when the test was developed and when the study was conducted.
Fortunately, the virus was isolated from the first cases and the sequence was determined and deposited in the database. From that sequence, it is possible to design primers and probes for the RT-PCR assay and the assay performance was checked using cell culture-derived RNA (see above). Again the full-length RNA was produced from the published sequence. The assay can be developed using synthetically produced RNA/DNA without the need of the virus but you need the sequence.

Last edited by Capsid; 21st October 2021 at 01:28 AM.
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Old 21st October 2021, 12:56 PM   #2551
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Originally Posted by Capsid View Post
Fortunately, the virus was isolated from the first cases and the sequence was determined and deposited in the database. From that sequence, it is possible to design primers and probes for the RT-PCR assay and the assay performance was checked using cell culture-derived RNA (see above). Again the full-length RNA was produced from the published sequence. The assay can be developed using synthetically produced RNA/DNA without the need of the virus but you need the sequence.
I have been watching for more corroboration or challenging the results of Quay et al's analysis.

And I've been looking to see if anything in the Bangladesh specimens Daszak or EcoHealth collected has any unique markers also found in the Nipah virus sequences of the COVID 19 analyses.

Isolation and Full-Genome Characterization of Nipah Viruses from Bats, Bangladesh
Quote:
Affiliations ... EcoHealth Alliance, New York, New York, USA (Ariful Islam, P. Daszak, J.H. Epstein); ...

We report isolation of NiVs from P. medius bats in Bangladesh. We performed full-genome characterization of these viruses by using enrichment-based next-generation sequencing (NGS)....

During January 2011–April 2014, we collected 2,749 bat samples from various ongoing projects in the region. We collected samples nondestructively from individual bats as described (7) and collected environmental urine samples from underneath roosts by using polyethylene sheets. ...

Samples were tested at the CSIRO Australian Animal Health Laboratory under BioSafety Level 4 containment. ...

For virus isolation from PCR-positive samples, we prepared Vero cells in 96-well plates in Eagle minimum essential medium (EMEM) ... Virus stocks were amplified in Vero cells, and supernatants were harvested ...

Full-length genome sequences were obtained from 10 bat NiV isolates. We constructed a phylogenetic tree (Figure 2) that showed all bat isolates had nearly identical genome sequences; there was 99.9% conservation among all 10 genomes characterized (Table). The virus isolated in Sylhet during January 2013 was nearly identical to all other isolates obtained in 2013 in Raipur, which is ≈350 km from Sylhet, suggesting that NiV homogeneity might be supported by bat movements connecting disparate bat colonies (10).
Results were recorded in GenBank.



The thing about using the gene sequences on file is it rules out Quay et al finding the genetic sequences upon re-examining the specimens directly.

Right now the issues are:

Did they really find Nipah sequences in the data? That should be easy to confirm or refute. And the finding of contamination is significant. Were it only the odd things like grass pollen or whatever Quay said in the interview, one could explain that as probable contamination in collecting and transporting the specimens. But where Nipah virus contamination occurred if it did, had to have been within the WIV walls, but not necessarily in the BSL4 lab.

I am reminded of one of the first hospital searches for COVID contamination and it was found everywhere from the floors to the supply rooms. IOW anywhere healthcare workers tracked it on their shoes and where contaminated air flowed (few if any of these viral particles proved to be complete or infectious). That's completely different of course because they were dealing with patients who were shedding a large amount of virus. But it does suggest an improper ventilation system in the WIV labs could have spread contamination all over the labs including to the COVID specimens. And that need not have been viable Nipah virus so one would not see detection of the problem via an outbreak.



One question needed to be asked is where was the COVID genome sequencing done?

Lancet
The nine samples analyzed were from the first recognized patients from the Huanan Seafood market cluster.
Quote:
Five of the patients (WH19001, WH19002, WH19004, WH19008, and YS8011) had samples collected by the Chinese Center for Disease Control and Prevention (CDC) ... Four of the patients (WH01, WH02, WH03, and WH04) had samples collected by BGI (Beijing, China) ... All collected samples were sent to BGI for sequencing.
BGI is a private company with offices in China and elsewhere. They must have their own lab(s) in Beijing so there is not necessarily a connection here to the WIV though there is one to the CCDC.

It shouldn't be that hard to compare the sequences Quay et al looked at with this cluster. According to the Quay report: Nipah virus vector sequences in COVID-19 patient samples sequenced by the Wuhan Institute of Virology
Quote:
We report the detection of Nipah virus in an infectious clone format, a BSL4-level pathogen and CDC-designated Bioterrorism Agent, in raw RNA-Seq sequencing reads deposited by the Wuhan Institute of Virology (WIV) produced from five December 2019 patients infected with SARS-CoV-2.
Not sure what to make of "in an infectious clone format".

At a minimum one should be able to compare those 5 sequences with either the other 4 or 9 sequences in the Lancet depending on which 5 specimens Quay is talking about.

And while the Lancet article says BGI Beijing, this is from the company's website:
Quote:
The company is headquartered in Shenzhen, China. It has branches and medical laboratories in major domestic cities such as Beijing, Tianjin, Wuhan, Shanghai, Guangzhou, and Hong Kong. ....
I'll have to keep looking.



Interesting finding:
Quote:
The eight complete genomes were nearly identical across the whole genome, with sequence identity above 99·98%, indicative of a very recent emergence into the human population (figure 1A). The largest nucleotide difference was four mutations. Notably, the sequence identity between the two virus genomes from the same patient (WH19001, from bronchoalveolar lavage fluid, and WH19005, from cell culture) was more than 99·99%, with 100% identity at the amino acid level. In addition, the partial genomes from samples WH02 and WH19002 also had nearly 100% identity to the complete genomes across the aligned gene regions.
IIRC these were all from lineage B. Note there are references to lineage A, B and C which are not the same as the A and B lineages noted in the first COVID specimens. It gets very confusing when these same labels differ in different articles.



Other interesting comments:
Quote:
First, the outbreak was first reported in late December, 2019, when most bat species in Wuhan are hibernating. Second, no bats were sold or found at the Huanan seafood market, whereas various non-aquatic animals (including mammals) were available for purchase.
They suggest an intermediate species which we know has not been found.

And one patient had not visited the market:
Quote:
Eight of the patients had visited the Huanan seafood market before the onset of illness, and one patient (WH04) did not visit the market but stayed in a hotel near the market between Dec 23 and Dec 27, 2019 (table)


The other question of course is, are the Quay et al conclusions correct that these sequences were evidence of the Nipah virus being adapted in the lab? I expect much more pushback on these conclusions.


Guess I need to go back through these reports: Feb 2021: Vector sequences in early WIV SRA sequencing data of SARS-CoV-2 inform on a potential large-scale security breach at the beginning of the COVID-19 pandemic

Feb 2020: A pneumonia outbreak associated with a new coronavirus of probable bat origin

Maybe could have saved myself some time.


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Old 21st October 2021, 01:00 PM   #2552
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Originally Posted by DetectedMotion View Post
.... I was looking through the CDC site to possibly find this, but it seems as though the CDC had no actual virus..

https://www.fda.gov/media/134922/downloadhttps://www.fda.gov/media/134922/download
On page 40 of Performance Characteristics it reads as follows:
Since no quantified virus isolates of the 2019-nCoV were available for CDC use at the time the test was developed and this study conducted, assays designed for detection of the 2019-nCoV RNA were tested with characterized stocks of in vitro transcribed full length RNA (N gene; GenBank accession: MN908947.2) of known titer (RNA copies/µL) spiked into a diluent consisting of a suspension of human A549 cells and viral transport medium (VTM) to mimic clinical specimen.

The hilited section above indicates they had no virus isolates when the test was developed and when the study was conducted.
That's completely different from the specimens from the first COVID patients so I'm not sure what you are saying.

And remember China has its own CDC. I use the acronym CCDC to designate the Chinese CDC.

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Old 21st October 2021, 04:01 PM   #2553
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Well Yuri Deigin and Steven Quay are both pretty active on Twitter and elsewhere. I suppose we could contact them directly to find out more about what they presume happen.

I think it WOULD be interesting if we think that the sequencing was done at a BSL that was inappropriate for Nipah (which is BSL-4) but had some contamination from Nipah.

That said, I truly don’t understand what is being claimed here.
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Old 21st October 2021, 06:45 PM   #2554
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Originally Posted by Skeptic Ginger View Post
One question needed to be asked is where was the COVID genome sequencing done?

Lancet
Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding is irrelevant to the question. This was testing done when the outbreak was almost 2 months old. There is no connection to the WIV.
  • BGI having labs in Wuhan does not say that this analysis was done in Wuhan.
  • We know that the virus has "a very recent emergence into the human population", e.g. the first known case is in early December 2019.
  • Patient WH04 reported a fever on Dec 27, 2019.
    It is not a surprise that they had not visited the Huanan seafood market before becoming ill, when COVID-19 is infectious. They "stayed in a hotel near the market between Dec 23 and Dec 27, 2019". That is 4 days of exposure to a carrier who had visited the market. for example, think about where the hotel got its seafood.

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Old 21st October 2021, 07:15 PM   #2555
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Originally Posted by Skeptic Ginger View Post
I have been watching for more corroboration or challenging the results of Quay et al's analysis.
Nipah virus vector sequences in COVID-19 patient samples sequenced by the Wuhan Institute of Virology is a preprint submitted on 19 Sep 2021.
Quote:
COVID-19 e-print
Important: e-prints posted on arXiv are not peer-reviewed by arXiv; they should not be relied upon without context to guide clinical practice or health-related behavior and should not be reported in news media as established information without consulting multiple experts in the field.
What is bad about this preprint
  • The abstract sounds like previous "COVID-19 was genetically engineered" nonsense with "encapsulated in synthetic vectors".
    Later there is "Here we review the recovery of a partial infectious clone of a Bangladesh strain of Nipah virus".
  • Preprints usually state where they have been submitted, accepted or published. A month and that preprint has not been submitted, accepted or published.
  • Authors with no appropriate affiliation or credentials.
Nipah virus "normally circulates among some fruit bats". Other bats species carrying the virus not unexpected. Shi and 28 colleagues tested for the miner samples for Nipah virus, presumably based on that expectation.
19 October 2021: Shi and 28 colleagues published that miner blood samples were tested (no coronavirus or antibodies)

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Old 21st October 2021, 10:09 PM   #2556
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This is interesting and I can't find much in the way of followup. I also looked for viral co-infections with COVID and didn't see anything else mentioning Nipah or viruses in that family.

There was a simultaneous outbreak of the zoonotic Nipah henipavirus inWuhan - 4 out of 5 patients have the virus in Jinyintan Hospital, along withSARS-Cov2, in their metagenome - which seems to have resolved by itself
Quote:
The metagenome also shows the co-infection with Nipah henipavirus virus in 4 out of 5 patients. The sequences are in SI:Nipah.fa - 167 reads in all.One can almost assemble the full genome (about 18kbps) from it. It seems to have originated fromBangladesh, though I have not done the phylogeny. Most reads are 100% identical, but some are (97% -145/150).
It does look like the 5 early patients who had genome sequencing at the WIV were from the seafood market cluster.

I'm not sure how to reconcile those 5 specimens with 9 noted in the above Lancet citation:
... nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan.

Perhaps the specimens were analyzed at a different time or in a different lab.


From the Quay et al paper:
Quote:
Here we document the presence of Nipah virus (NiV) sequences, Banglisash strain, interpreted as likely for assembly of a NiV infectious clone, found in raw sequencing reads by the Wuhan Institute of Virology (WIV) from five patients infected with SARS-CoV-2 sampled by the Wuhan Jin Yin-Tan Hospital at the beginning of the COVID-19 outbreak (Zhou et al. 2020). The five patients experienced COVID-19 illness onset between 12/12/2019 and 23/12/2019 and were admitted to intensive care between 20/12/2019 and 29/12/2019 with all BALF (bronchoalveolar lavage fluid) sampling conducted on the 30/12/2019 and the 10/1/2020.

4 of 5 or 5 of 5 also doesn't match up exactly. But they are talking about the same patients and specimens:
Quote:
These patient samples have been previously reported to contain reads from several other viruses: Influenza A, Spodoptera frugiperda rhabdovirus and Nipah. Previous authors have interpreted the presence of these virus sequences as indicative of co-infections of the patients in question by these pathogens or laboratory contamination. However, our analysis shows that NiV genes are encapsulated in synthetic vectors, which we infer was for assembly of a NiV infectious clone.
There was no corroboration any of the patients had co-infection with Nipah. And it seems like the "lab contamination" hypothesis wasn't pursued but there it is right there in plain sight.

So there were genetic sequences from Nipah and no reason for the sequences to be there. That much corroborates Quay et al.

The interpretation that the Nipah virus segments had signs of being manipulated remains to be corroborated, of course. But why was evidence of Nipah there at all?


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Old 22nd October 2021, 01:05 AM   #2557
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Originally Posted by Skeptic Ginger View Post
This is interesting and I can't find much in the way of followup. I also looked for viral co-infections with COVID and didn't see anything else mentioning Nipah or viruses in that family.

There was a simultaneous outbreak of the zoonotic Nipah henipavirus inWuhan - 4 out of 5 patients have the virus in Jinyintan Hospital, along withSARS-Cov2, in their metagenome - which seems to have resolved by itself


It does look like the 5 early patients who had genome sequencing at the WIV were from the seafood market cluster.

I'm not sure how to reconcile those 5 specimens with 9 noted in the above Lancet citation:
... nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan.

Perhaps the specimens were analyzed at a different time or in a different lab.


From the Quay et al paper:



4 of 5 or 5 of 5 also doesn't match up exactly. But they are talking about the same patients and specimens:

There was no corroboration any of the patients had co-infection with Nipah. And it seems like the "lab contamination" hypothesis wasn't pursued but there it is right there in plain sight.

So there were genetic sequences from Nipah and no reason for the sequences to be there. That much corroborates Quay et al.

The interpretation that the Nipah virus segments had signs of being manipulated remains to be corroborated, of course. But why was evidence of Nipah there at all?

I'm confused. Is this Nipah virus or Henipahvirus? The two are not necessarily the same. The assay could easily confuse the two.
Sequencing does not need to be done in BSL-4, once the RNA is extracted (within a safety cabinet) it can be handled at BSL-2.
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Old 22nd October 2021, 01:13 AM   #2558
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Originally Posted by Skeptic Ginger View Post
That's completely different from the specimens from the first COVID patients so I'm not sure what you are saying.

And remember China has its own CDC. I use the acronym CCDC to designate the Chinese CDC.
What I'm looking for is documentation of the original virus to substantiate it's actual existence proving this virus is exactly what they say it is because there are legal challenges being made recently in courts of law. Challenges that dispute the PCR testing on the one hand that determines some people as testing positive although they are listed "Asymptomatic". Since these people have no symptoms at all, how could it be proven they are actually sick?
Either man-made or mammal, but no actual documentation to prove that it is a "Novel" virus. I have one person who tried to find documentation of the actual virus to prove it exists: This person tried to obtain this very same information by requesting it through the Freedom Of Information Act in his state of Illinois "All records of scientific laboratory tests, analyzing and identifying the COVID-19 delta variant virus from isolate samples extracted from a human being".
The state sent him a letter back 6 weeks later that reads "after conducting a search, the Governors Office has located no records responsive to your request".

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Old 22nd October 2021, 01:37 AM   #2559
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Originally Posted by DetectedMotion View Post
What I'm looking for is documentation of the original virus to substantiate it's actual existence proving this virus is exactly what they say it is because there are legal challenges being made recently in courts of law. Challenges that dispute the PCR testing on the one hand that determines some people as testing positive although they are listed "Asymptomatic". Since these people have no symptoms at all, how could it be proven they are actually sick?
Either man-made or mammal, but no actual documentation to prove that it is a "Novel" virus. I have one person who tried to find documentation of the actual virus to prove it exists: This person tried to obtain this very same information by requesting it through the Freedom Of Information Act in his state of Illinois "All records of scientific laboratory tests, analyzing and identifying the COVID-19 delta variant virus from isolate samples extracted from a human being".
The state sent him a letter back 6 weeks later that reads "after conducting a search, the Governors Office has located no records responsive to your request".
Original publications
https://www.nature.com/articles/s41586-020-2008-3
https://www.nature.com/articles/s41586-020-2012-7
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Old 22nd October 2021, 02:51 AM   #2560
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Originally Posted by Capsid View Post
I'm confused. Is this Nipah virus or Henipahvirus? The two are not necessarily the same. The assay could easily confuse the two.
Sequencing does not need to be done in BSL-4, once the RNA is extracted (within a safety cabinet) it can be handled at BSL-2.
Looking it up (because I didn't know), Nipah is also called Nipah henipahvirus even though there is a separate henipahvirus group.

Here are the Wiki pages for each:
Henipavirus is a genus of negative-strand RNA viruses in the family Paramyxoviridae, order Mononegavirales containing five species.[1][2]

Nipah virus, scientific name Nipah henipavirus, is a bat-borne virus that causes Nipah virus infection in humans and other animals, a disease with a high mortality rate.

It would appear Nipah virus is what both Sandeep Chakraborty (the first analysis) and Quay et al are referring to.

I didn't see the details of which lab within the WIV the initial COVID specimens were analyzed in. That short letter is the only mention I found so far.

The hospital the patients were in corroborates which patients the specimens came from. Interesting in that your first link notes 7 specimens:
Quote:
Samples from seven patients with severe pneumonia (six of whom are sellers or deliverymen from the seafood market), who were admitted to the intensive care unit of Wuhan Jin Yin-Tan Hospital at the beginning of the outbreak, were sent to the laboratory at the Wuhan Institute of Virology (WIV) for the diagnosis of the causative pathogen
The letter notes the same hospital:
Quote:
Jinyintan hospital
It seems possible the different number of specimens reflect an initial batch followed by subsequent additional specimens being analyzed.


It still appears there was a lot of contamination in at least one of the WIV labs. It wasn't just Nipah that Quay et al identified in the early COVID specimens.


This is from the 2012 search of bat specimens and needs to be sorted out as well. I'll have to go back and look at why they suspected and then ruled out this rat virus when COVID first emerged.
CDC Novel Henipa-like Virus, Mojiang Paramyxovirus, in Rats, China, 2012
Quote:
To the Editor: The genus Henipavirus (family Paramyxoviridae) contains 3 established species (Hendra virus, Nipah virus, and Cedar virus) and 19 newly identified species, including 1full-length sequenced virus, Bat Paramyxovirus Eidhel/GH-M74a/GHA/2009 (1,2). The zoonotic pathogens Hendra virus and Nipah virus have been associated with lethal neurologic and respiratory diseases in humans, horses, and pigs (3–5). The known natural reservoirs of henipaviruses are fruit bats (1,3); these viruses have not been reported in other wild animals. We report on a novel henipa-like virus, Mojiang paramyxovirus (MojV), in rats (Rattus flavipectus) in China. ...

Half a year later [after the miners became ill], we investigated the presence of novel zoonotic pathogens in natural hosts in this cave. ...

On the basis of the nonredundant protein alignment results, we identified 38 sequence reads that were classified as Henipavirus spp. However, the sequences shared low nucleotide and amino acid identities with known henipaviruses.

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