Origins of Covid

[angrysoba]

Peter Daszak is talking here to MSNBC about origins of Covid-19 and the report that is to come out.

I don't claim to be good at spotting anyone being shifty or lying, etc... but he comes across as pretty genuine to me and explains why he thinks it is likely to have originated from the wildlife farms, and why it is unlikely to have emerged from a lab:

https://www.msnbc.com/ayman-mohyeldi...s-108171333677

[lomiller]

Originally Posted by Skeptic Ginger

You ignoring evidence cited in this thread doesn't make your position true. I'm not saying [whatever you think], I am telling you what we have found sources refuting and ruling out your hypothesis.

No you haven’t and repeating yourself isn’t changing that. See below for more detail, but I’ve already addressed any legitimate source you have linked, and you have not provided any counterargument.

Originally Posted by Skeptic Ginger

Review of findings appear today (July 28, 2020) in Nature Microbiology.Evolutionary origins of SARS-CoV-2 identified

I’ve already addressed the actual paper the article is discussing. It’s:
-Outdated and contradicted by more recent work
-Doesn’t address genetic similarities with Pangolin virus spike structures. Evolution can result in similar physical structures but the chances of something evolving to become more similar at a genetic level is astronomically small.
-Doesn’t address how such a structure could have evolved in species that isn’t susceptible to SARS-CoV-2. The jump from bats to humans requires the virus to be able to infect BOTH animals, Covid can’t do this. (it could be the paper predates the research showing the Covid-19 spike can’t bind efficnetly too bat ACE2 receptors.)
-The specific genetic sequence from Pangolin viruses has been identified within the Covid spike structure proving the suspected recombination event with Pangolin virus did in fact occur.

Originally Posted by Skeptic Ginger

The NEXT coronavirus pandemic? Bats in China are carrying other viruses that may infect humans

Not an actual paper and it doesn’t even support your assertions. The Chinese scientist it’s interviewing speculates that Pangolins imported from SE Asia as the source of the initial outbreak. (Did you not tell us that we were not supposed to trust Chinese scientists because they are into “face saving”) The primary point of the article is that there is potential for Corona viruses to jump from Chinese Horseshoe bats to humans, something that has been know since the SARS outbreak at least.

Originally Posted by Skeptic Ginger

MattRidley blog: THE BATS BEHIND THE PANDEMICSo much for the bat soup myth.

An outdated blog post written by Matt Ridley, who is a right wing journalist and climate change denier with no particular qualifications to speak on virology.

The quote you provided was discussing SARS rather than Covid. Unlike SARS, RaTG13 can’t infect people readily nor can Covid infect bats readily, which speaks strongly against the possibility of a direct jump.

While he is correct in saying RaTG13 was (and still is) the closest known relative of SARS-CoV-2, he ignores the fact that Covid spike is genetically more similar to the one found in the Pangolin viruses. He is not correct in saying the Pangolin virus was originally thought to be the closest Covid Relative, this was never the case. Because the spike, but only the spike was more closely related to the Pangolin virus it was thought to have been a product of recombination. As I showed in previous posts, this has been confirmed and the specific genetic sequence involved has been identified.

Originally Posted by Skeptic Ginger

Useful relevant science: the bats behind the Covid-19 pandemic

Do you really think a climate change denial site like polarbearsceince is going to do any better when it comes to Covid? In any case all they do is quote Ridley from the previous blog so there is nothing to discuss.

[lomiller]

Originally Posted by angrysoba

Daszak (note the spelling!) and the WHO investigation has been discredited?

Discredited by whom?

The links to climate denier websites would suggest it's the same people who claim Michael Mann is "discredited"

Originally Posted by angrysoba

Lolmiller claims Covid-19 comes from bat soup? Or is this a strawman?

I'm arguing that it's very unlikely to come directly from bats at all, due to the inefficient binding to bat ACE2. Covid may have descended from a bat virus it can't circulate in bats and would have needed an intermediary which is highly likely to be a Pangolin.

So year. More made up than it is strawman, but either way it has nothing to do with anything I have written.

[Skeptic Ginger]

In all that did you find evidence pangolins specifically were sold at the market?

Did you provide evidence the first infections actually were at the market?

I'm trying to simplify this in order to facilitate a discussion.

[lomiller]

Originally Posted by Skeptic Ginger

In all that did you find evidence pangolins specifically were sold at the market?

It's been alluded to in many papers and media reports and I have been given no reason to doubt that it is in fact the case.

Originally Posted by Skeptic Ginger

Did you provide evidence the first infections actually were at the market?

While a some early cases had no obvious link to the market, most did. The most likely explanation for this is that the crossover to humans occurred there.

There are other possible scenarios like the crossover occurring at a different market and spreading to the fish market from there, but these are lower probability. If new data comes along that favors some other scenario I'll certainly consider it, but as of right now this is the most plausible scenario.

[Skeptic Ginger]

Re Daszak sounds credible...

RCP: How the COVID-19 Censors Killed the Truth

Quote:

It's in everybody's interest to understand exactly where it came from and how it started, but efforts at investigation have been stymied from the start. Among those eager to suppress dissent on this topic are: the Chinese government, U.S. media outlets, the Big Tech platforms and scientists with a financial or reputational stake in the outcome of any investigation....

... Dr. Peter Daszak, the sole U.S. citizen on the WHO investigative team, is a close associate of China's premier bat-based coronavirus researcher and was a key figure in directing American taxpayer funds to the Wuhan Institute of Virology. Daszak even organized a public relations campaign in early 2020 to paint the lab leak hypothesis as a "conspiracy" before any thorough investigation had been conducted. His spokesperson later said the goal was to protect the lab's scientists, but ultimately the beneficiary was Beijing and its preferred narrative.

How is that not a conflict of interest?


WHO COVID-19 Investigation Is Tainted by Conflict of Interest, Says AHF

Quote:

The alleged conflict of interest stems from the connection one of the investigators, a British zoologist and EcoHealth Alliance President Dr. Peter Daszak has with the Wuhan Institute of Virology (WIV). According to The Wall Street Journal, Dr. Daszak has worked closely with a leading virologist at WIV, Dr. Shi Zhengli on the study of bat viruses, which from 2014, was in part funded by US government grants. The institute is located just a few miles away from the wet market where Chinese authorities say SARS-CoV-2 first emerged.

“For the WHO [World Health Organization] investigation in Wuhan to stand up to scientific scrutiny, neutrality is a must,” said AHF President Michael Weinstein. “Dr. Daszak has a clear-cut conflict of interest that should’ve disqualified him from participation on the WHO team.

Chinese authorities say it started in the wet market, earliest cases had no exposure or connection to the market.


Politico: In 2018, Diplomats Warned of Risky Coronavirus Experiments in a Wuhan Lab. No One Listened. - After seeing a risky lab, they wrote a cable warning to Washington. But it was ignored.

Quote:

These researchers, the American officials learned, had found a population of bats from caves in Yunnan province that gave them insight into how SARS coronaviruses originated and spread. The researchers boasted that they may have found the cave where the original SARS coronavirus originated. But all the U.S. diplomats cared about was that these scientists had discovered three new viruses that had a unique characteristic: they contained a "spike protein” that was particularly good at grabbing on to a specific receptor in human lung cells known as an ACE2 receptor. That means the viruses were potentially very dangerous for humans—and that these viruses were now in a lab with which they, the U.S. diplomats, were largely unfamiliar....

In total, the [US] embassy sent three teams of experts in late 2017 and early 2018 to meet with the WIV scientists, among them Shi Zhengli, often referred to as the “bat woman” because of her extensive experience studying coronaviruses found in bats.

When they sat down with the scientists at the WIV, the American diplomats were shocked by what they heard. The Chinese researchers told them they didn’t have enough properly trained technicians to safely operate their BSL-4 lab. The Wuhan scientists were asking for more support to get the lab up to top standards.

The diplomats wrote two cables to Washington reporting on their visits to the Wuhan lab. More should be done to help the lab meet top safety standards, they said, and they urged Washington to get on it. They also warned that the WIV researchers had found new bat coronaviruses could easily infect human cells, and which used the same cellular route that had been used by the original SARS coronavirus....

Of course Trump would not have wanted to send funds to China.

[lomiller]

Originally Posted by Skeptic Ginger

Re Daszak sounds credible...

RCP: How the COVID-19 Censors Killed the Truth
How is that not a conflict of interest?


WHO COVID-19 Investigation Is Tainted by Conflict of Interest, Says AHF
Chinese authorities say it started in the wet market, earliest cases had no exposure or connection to the market.

I'm at a loss as to what expertise the AIDS Healthcare Foundation would have on bat viruses in China.

the motivation for Realclearpolitics is a little easier to understand given their support for far right causes. I'm still not going to trust their opinion on, well anything.

[Sherkeu]

Originally Posted by lomiller

It's been alluded to in many papers and media reports and I have been given no reason to doubt that it is in fact the case.



While a some early cases had no obvious link to the market, most did. The most likely explanation for this is that the crossover to humans occurred there.

There are other possible scenarios like the crossover occurring at a different market and spreading to the fish market from there, but these are lower probability. If new data comes along that favors some other scenario I'll certainly consider it, but as of right now this is the most plausible scenario.

The wet market is an incidental cluster, not the origin of anything.
Scientists know now that Sars-COV-2 was circulating globally back in November- before anyone at the market was sick (which was Dec 8). Samples from the Dec 2019 patients in China, with no connection to the market, already showed divergent strains.

Even China's CDC states the market was not the origin.

[angrysoba]

Originally Posted by Sherkeu

The wet market is an incidental cluster, not the origin of anything.
Scientists know now that Sars-COV-2 was circulating globally back in November- before anyone at the market was sick (which was Dec 8). Samples from the Dec 2019 patients in China, with no connection to the market, already showed divergent strains.

Even China's CDC states the market was not the origin.

Circulating globally by November? If that’s the case then that is a massive hole in the WIV lab release theory isn’t it given that the major claim for it coming from the lab is that it started in Wuhan.

Are you now saying we have no evidence it started in Wuhan?

[Skeptic Ginger]

Originally Posted by lomiller

I'm at a loss as to what expertise the AIDS Healthcare Foundation would have on bat viruses in China.

Their assertion had to do with Daszak's conflict of interest. You don't need a PhD in virology to recognize a conflict of interest in a WHO investigation team.

Quote:

AIDS Healthcare Foundation (AHF), the largest global AIDS organization, currently provides medical care and/or services to over 1.5 million clients in 45 countries worldwide in the US, Africa, Latin America/Caribbean, the Asia/Pacific Region and Europe.

Originally Posted by lomiller

the motivation for Realclearpolitics is a little easier to understand given their support for far right causes. I'm still not going to trust their opinion on, well anything.

There are a dozen reports of Daszak's conflict of interest. You don't like the ones I cited, pick some others.

Are there any sources defending Daszak's untainted credibility? No, there isn't.

[The Atheist]

Originally Posted by Sherkeu

Scientists know now that Sars-COV-2 was circulating globally back in November- before anyone at the market was sick (which was Dec 8).

False.

This thread really ought to be in the conspiracy section - what idiot posted it in science?

[Skeptic Ginger]

Originally Posted by lomiller

It's been alluded to in many papers and media reports and I have been given no reason to doubt that it is in fact the case.

I'm not sure how reliable "alluded to" is supposed to be.

It's been denied and didn't show up on a list of animals sold in the market, with the caveat that they might want to hide the sale of illegal meat.

Before pangolins were being considered, they did not show up as openly for sale at the market.

Jan 2020: Bizarre Wuhan Wet Market Menu Shows Over 100 Wild Animals Sold As Food, Link With Virus Unclear

One could "allude to" it was one of those animals on the list.

Originally Posted by lomiller

While a some early cases had no obvious link to the market, most did. The most likely explanation for this is that the crossover to humans occurred there.

There are other possible scenarios like the crossover occurring at a different market and spreading to the fish market from there, but these are lower probability. If new data comes along that favors some other scenario I'll certainly consider it, but as of right now this is the most plausible scenario.

This is all well and good but that's not how an epidemiological investigation works. You don't start out with your preconceived conclusion and go from there. Peter Daszak openly asserted it was not from the lab before he went on the WHO team investigation as well.

[Sherkeu]

Perhaps I can clarify on 'global' for Mr. Atheist in case my post was misinterpreted.
Samples from late 2019 blood, swabs, and even sewage samples in several geographical areas around the globe, including USA west coast, Italy, Spain and France, show antibodies or segments of the SARS-COV-2 genome itself.

Perhaps the conclusions of those tests are wrong and someone might want to contribute their own knowledge here.

Members of the WHO team have put the origin anywhere from late summer to early November.

[RecoveringYuppy]

Originally Posted by Sherkeu

Perhaps I can clarify on 'global' for Mr. Atheist in case my post was misinterpreted.
Samples from late 2019 blood, swabs, and even sewage samples in several geographical areas around the globe, including USA west coast, Italy, Spain and France, show antibodies or segments of the SARS-COV-2 genome itself.

Perhaps the conclusions of those tests are wrong and someone might want to contribute their own knowledge here.

Members of the WHO team have put the origin anywhere from late summer to early November.

Citation required.

[Skeptic Ginger]

Originally Posted by angrysoba

Circulating globally by November? If that’s the case then that is a massive hole in the WIV lab release theory isn’t it given that the major claim for it coming from the lab is that it started in Wuhan.

Are you now saying we have no evidence it started in Wuhan?

No it isn't and no there is no evidence of another origin source. However, one always has to consider that possibility until the source is pinned down.



Jaime Metzl interview (also interviewed in the podcast)

Quote:

JAMIE METZL: I wouldn't necessarily categorize it that way. Some people have talked about genetically engineered virus versus non genetically engineered. By that would mean using the tools of genome editing, like CRISPR. Then there are other tools to actually manipulate, using genome editing tools, a virus. Then the second possibility is there is just a really dangerous virus that maybe exists in a remote cave somewhere and it exists in one of these labs. So without any kind of manipulation, that leaks. A third possibility is that there is this dangerous, naturally occurring pathogen and then experiments are done on that virus in the lab. Some people are starting to hear about this so-called gain of function research. Like with dogs, you understand that you now have a dog. But the dog's ancestors were wolves. And how did wolves become dogs? It wasn't through genome editing. It was through selective breeding. Essentially, gain of function research is selective breeding. You select for qualities in a virus, it could be the ability to replicate rapidly or infect human cells. ...

JAMIE METZL: Let's look at these four options. One would be a series of animal to animal jumps. Zoonotic jump through intermediate hosts is the technical terms. Basically, it means bat to pangolin or civet or cat, to human. That would be a very likely possibility. That's what happened with the first SARS. But in the first SARS, there was actually evidence that turned up. Here we are more than one year after the beginning of the pandemic and there is absolutely no evidence for that. It could be. There are lots of scientists who think that's what happened. It's a very real possibility.
Frozen food hypothesis. I think it's extremely unlikely. Absolutely no evidence. It's kind of a ridiculous hypothesis. ...

Quote:

That leads us to the possibility of an accidental lab leak. Here would be my best case for why I think this is the most likely option.

You all can read his detailed case or ignore it.

Quote:

... That doesn't mean genetically engineered, but it means pushed in the direction of being highly contagious and transmissible for humans.

MICHAEL MORELL: What would be the purpose of such research?

JAMIE METZL: Gain of function research is very controversial in the scientific world and in the United States and elsewhere.

Daszak's conflict of interest:

Quote:

There was a huge debate about that. So much so that after some very controversial research came out in 2014, the Obama administration established a moratorium on U.S. government funding for gain of function research. There was a grant, however, that had already been provided to an organization called the Eco Health Alliance. They passed some of that money to the Wuhan Institute of Virology for this research. ...

Back to the lab hypothesis:

Quote:

Jaime Metzl: [he summarizes the above about the research]...but then we need to look at what China did in the earliest days of the pandemic until now. In the earliest days of the pandemic, China prevented World Health inspectors from coming to Wuhan for nearly a month. They immediately started taking down databases that had previously been accessible to the public. They immediately started silencing people who may have been able to provide invaluable evidence to the world about the origins of COVID-19. As a matter of fact, the only reason that we had the sequenced genome of the SARS-COV-2 virus as early as we did is that there was a Chinese scientist who went rogue and paid the consequences for sharing that information.

That last one is not a reference to the Ophthalmologist whistle blower who later died. I hadn't known it was an ask forgiveness, not permission leak (the genome data).

So far I only found a paywalled source on that initial sharing of the genome. But it is consistent with Metzl's interview.

Chinese laboratory that first shared coronavirus genome with world ordered to close for ‘rectification’, hindering its Covid-19 research

Quote:

No reason was given for the closure of Shanghai facility, which released information about the virus ahead of authorities

I'm going to come back to this but I found another rabbit hole to go down.

[Sherkeu]

Originally Posted by RecoveringYuppy

Citation required.

Italy:
Evidence of SARS-CoV-2 RNA in an Oropharyngeal Swab Specimen, Milan, Italy, Early December 2019
https://wwwnc.cdc.gov/eid/article/27/2/20-4632_article

Summary article:
https://www.ncbi.nlm.nih.gov/researc...ation/33176598

Quote:

This study shows an unexpected very early circulation of SARS-CoV-2 among asymptomatic individuals in Italy several months before the first patient was identified, and clarifies the onset and spread of the coronavirus disease 2019 (COVID-19) pandemic. Finding SARS-CoV-2 antibodies in asymptomatic people before the COVID-19 outbreak in Italy may reshape the history of pandemic.

France:
Evidence of early circulation of SARS-CoV-2 in France: findings from the population-based “CONSTANCES” cohort
https://link.springer.com/article/10...54-020-00716-2

https://presse.inserm.fr/en/was-sars...er-2019/42169/

Quote:

Their findings: SARS-CoV-2 antibodies were detected in 353 participants (3.9%). The proportion of positive participants had increased from 1.9% in November and 1.3% in December to 5.0% in January, 5.2% in February, and 6.7% in the first half of March. Neutralizing antibodies were detected in 44 participants,

U.S.
Coronavirus Was In U.S. Weeks Earlier Than Previously Known, Study Says
https://www.npr.org/sections/coronav...own-study-says

Quote:

This discovery adds to evidence that the virus was quietly spreading around the world before health officials and the public were aware, disrupting previous thinking of how the illness first emerged and how it has since evolved. It also shows the virus's presence in U.S. communities likely didn't start with the first case identified case in January.

and China:

Covid-19 Was Spreading in China Before First Confirmed Cases, Fresh Evidence Suggests
https://www.wsj.com/articles/covid-1...ts-11613730600

Quote:

New evidence from China is affirming what epidemiologists have long suspected: The coronavirus likely began spreading unnoticed around the Wuhan area in November 2019, before it exploded in multiple different locations throughout the city in December.

In examining 13 genetic sequences of the virus from December, Chinese authorities found similar sequences among those linked to the market, but slight differences in those of people without any link to it, according to the WHO investigators. The two sets likely began to diverge between mid-November and early December, but could possibly indicate infections as far back as September, said Marion Koopmans, a Dutch virologist on the WHO team.

[Skeptic Ginger]

Going down another rabbit hole:

Quote:

By comparing the two dozen genomes, scientists can address the “when did this start” question. The 24 available samples, including from Thailand and Shenzhen as well as Wuhan, show “very limited genetic variation,” Rambaut concluded on an online discussion forum where virologists have been sharing data and analyses. “This is indicative of a relatively recent common ancestor for all these viruses.”

Given what’s known about the pace at which viral genomes mutate, if nCoV had been circulating in humans since significantly before the first case was reported on Dec. 8, the 24 genomes would differ more. Applying ballpark rates of viral evolution, Rambaut estimates that the Adam (or Eve) virus from which all others are descended first appeared no earlier than Oct. 30, 2019, and no later than Nov. 29....

The genome sequences suggest that was a one-time-only jump. “The genomes [from the 24 samples] are very uniform,” Andersen said. “If there had been multiple introductions,” including from many different animals, “there would be more genomic diversity. This was a single introduction.”

Quay refers to this lack of diversity in the first couple of cases for which he found essentially 2 clades.

[Skeptic Ginger]

Originally Posted by Sherkeu

Italy:
Evidence of SARS-CoV-2 RNA in an Oropharyngeal Swab Specimen, Milan, Italy, Early December 2019
https://wwwnc.cdc.gov/eid/article/27/2/20-4632_article

Summary article:
https://www.ncbi.nlm.nih.gov/researc...ation/33176598

France:
Evidence of early circulation of SARS-CoV-2 in France: findings from the population-based “CONSTANCES” cohort
https://link.springer.com/article/10...54-020-00716-2

https://presse.inserm.fr/en/was-sars...er-2019/42169/

We'll have to see how those antibody tests pan out. But the relatedness of the Wuhan strains pretty much pin down the origin in Wuhan.

Originally Posted by Sherkeu

U.S.
Coronavirus Was In U.S. Weeks Earlier Than Previously Known, Study Says
https://www.npr.org/sections/coronav...own-study-says

This was also revealed when genetic tracks showed outbreaks from the single patient in Everett (north of Seattle) and the military base in CA where passengers from the infected ship spread out from. And the cases in NY had an EU origin that festered quite a while before it was recognized.

Originally Posted by Sherkeu

and China:

Covid-19 Was Spreading in China Before First Confirmed Cases, Fresh Evidence Suggests
https://www.wsj.com/articles/covid-1...ts-11613730600

Quote:

In examining 13 genetic sequences of the virus from December, Chinese authorities found similar sequences among those linked to the market, but slight differences in those of people without any link to it, according to the WHO investigators. The two sets likely began to diverge between mid-November and early December,

That is interesting.

So the market cluster is closely related but the cases not connected to the market are not closely related to the market cluster.

It comes back to Quay's analysis of the mass transit line #2.

COVID-19 Origin and Spread Linked to PLA Hospital and Wuhan Metro System Line 2 by Physician-Scientist Dr. Steven Quay

I'm not sure why we haven't seen a better genetic map yet the same way we have one for human migrations out of Africa. It looks like the data is all there waiting for someone to put it together. It's only a matter of a little more time.

[Sherkeu]

Originally Posted by Skeptic Ginger

That is interesting.

So the market cluster is closely related but the cases not connected to the market are not closely related to the market cluster.

It doesn't mean they aren't closely related, just that the differences are enough to put some point of divergence between them. They have some way of calculating (or rather estimating) how long it takes to mutate.
From earlier reports I have read it seems that viruses can be many decades past divergence are still considered very similar. (eta: of course in this sars-cov-2 case it would be a short time period)

I agree that the data is there (somewhere) to get closer to knowing. Unfortunately, not many people are allowed access to the crucial early patient data or other early samples. That is one of the things WHO asked for last month but were denied. A report is supposedly due out this week.

[angrysoba]

Originally Posted by Sherkeu

Italy:
Evidence of SARS-CoV-2 RNA in an Oropharyngeal Swab Specimen, Milan, Italy, Early December 2019
https://wwwnc.cdc.gov/eid/article/27/2/20-4632_article

Summary article:
https://www.ncbi.nlm.nih.gov/researc...ation/33176598



France:
Evidence of early circulation of SARS-CoV-2 in France: findings from the population-based “CONSTANCES” cohort
https://link.springer.com/article/10...54-020-00716-2

https://presse.inserm.fr/en/was-sars...er-2019/42169/




U.S.
Coronavirus Was In U.S. Weeks Earlier Than Previously Known, Study Says
https://www.npr.org/sections/coronav...own-study-says



and China:

Covid-19 Was Spreading in China Before First Confirmed Cases, Fresh Evidence Suggests
https://www.wsj.com/articles/covid-1...ts-11613730600

Originally Posted by Skeptic Ginger

We'll have to see how those antibody tests pan out. But the relatedness of the Wuhan strains pretty much pin down the origin in Wuhan.


This was also revealed when genetic tracks showed outbreaks from the single patient in Everett (north of Seattle) and the military base in CA where passengers from the infected ship spread out from. And the cases in NY had an EU origin that festered quite a while before it was recognized.


That is interesting.

So the market cluster is closely related but the cases not connected to the market are not closely related to the market cluster.

It comes back to Quay's analysis of the mass transit line #2.

COVID-19 Origin and Spread Linked to PLA Hospital and Wuhan Metro System Line 2 by Physician-Scientist Dr. Steven Quay

I'm not sure why we haven't seen a better genetic map yet the same way we have one for human migrations out of Africa. It looks like the data is all there waiting for someone to put it together. It's only a matter of a little more time.

Originally Posted by Sherkeu

It doesn't mean they aren't closely related, just that the differences are enough to put some point of divergence between them. They have some way of calculating (or rather estimating) how long it takes to mutate.
From earlier reports I have read it seems that viruses can be many decades past divergence are still considered very similar. (eta: of course in this sars-cov-2 case it would be a short time period)

I agree that the data is there (somewhere) to get closer to knowing. Unfortunately, not many people are allowed access to the crucial early patient data or other early samples. That is one of the things WHO asked for last month but were denied. A report is supposedly due out this week.

Yes, a report is due soon, by the WHO investigative team.

I think once it comes out, maybe it will give more of a clearer picture of why they see a wildlife link as being far more likely than a lab leak.

In fact, the suggestions of early spread both elsewhere in China and abroad are some of the things that reduce the lab leak hypothesis.

China in fact have said they wanted more investigations to take place abroad, particularly in Europe (which is something that other commentators have pooh-poohed as China trying to absolve itself of responsibility etc...).

Daszak and others in the WHO team have said they wanted to see testing along the routes of the wildlife trade, suggesting that people in some of the wildlife farms may have been infected by Covid-19 and been unaware of it.

Maybe there will be maps of the genetic sequences as well.

I think we will just have to wait and see.

[angrysoba]

So, Vincent and Amy did get a question:

"Where did the virus come from? WIV?"

Their answer is no...

https://youtu.be/ydYwVis9zvE?t=1100

ETA: Another from the same person:

"Is it possible it started in bats. Was taken to WIB where they did gain of funciton serial passage research?"

Vincent's answer: "no. You can make up anything..."

https://youtu.be/ydYwVis9zvE?t=3120

Next: "Frozen food is being named as a source of origin in Wuhan being pushed by Dyzak [sic]... is that a joke? How much does the CCP pay him and how serious is frozen food as a vector?"

https://youtu.be/ydYwVis9zvE?t=3405

Vincent's Answer: "I don't think frozen food is a source. I think there is no evidence for that."

[RecoveringYuppy]

Originally Posted by Sherkeu

Scientists know now that Sars-COV-2 was circulating globally back in November

This isn't accurate. There are now known very few isolated cases from November, not "circulating globally". Which isn't inconsistent with what has been known for a long time about the expected time of origin for Covid.

[lomiller]

Originally Posted by Skeptic Ginger

This is all well and good but that's not how an epidemiological investigation works. You don't start out with your preconceived conclusion and go from there. Peter Daszak openly asserted it was not from the lab before he went on the WHO team investigation as well.

It's not a "preconceived idea" it's an educated assessment based on the fact that in the initial stages of it's exponential growth curve the highest number of cases are most likely to be centred on the place it's been reproducing the longest.

If evidence comes forward in favor of some other local I'll certainly consider it and I fully support WHO investigators looking for other plausible locals. Such searches are important, because the harder we for other locals without finding evidence, the more likely it becomes that the fish market was indeed where the crossover occurred. If we consider the weight of the evidence NOW, however ,it favors the fish market as the location of initial transmission.

[Skeptic Ginger]

Originally Posted by Sherkeu

It doesn't mean they aren't closely related, just that the differences are enough to put some point of divergence between them. They have some way of calculating (or rather estimating) how long it takes to mutate.
From earlier reports I have read it seems that viruses can be many decades past divergence are still considered very similar. (eta: of course in this sars-cov-2 case it would be a short time period)

I agree that the data is there (somewhere) to get closer to knowing. Unfortunately, not many people are allowed access to the crucial early patient data or other early samples. That is one of the things WHO asked for last month but were denied. A report is supposedly due out this week.

I knew my adjectives were going to cause trouble. Sorry about that.

It's tracing clades and seeing a mutation in one that all the subsequent virus that follows will have that mutation. But the strains not connected to the market don't have that 'marker'.

I wouldn't put too much credence in the final WHO report if it is going to blame a wet market exposure to a pangolin.

I notice there is now mention of other wet markets in Wuhan that could have been the place of the initial jump. The problem remains, there are people not connected to any wet market. If one is going to claim maybe it was a different market to confirm one's bias, one still needs to demonstrate the pathway, not just say well it could have been.

Or we can just look at 'could have been we don't know', that's fine. But to say that and then definitively rule out the lab because we are told it wasn't them is not fine.

[Skeptic Ginger]

Originally Posted by angrysoba

Yes, a report is due soon, by the WHO investigative team.

I think once it comes out, maybe it will give more of a clearer picture of why they see a wildlife link as being far more likely than a lab leak.

In fact, the suggestions of early spread both elsewhere in China and abroad are some of the things that reduce the lab leak hypothesis.

China in fact have said they wanted more investigations to take place abroad, particularly in Europe (which is something that other commentators have pooh-poohed as China trying to absolve itself of responsibility etc...).

Daszak and others in the WHO team have said they wanted to see testing along the routes of the wildlife trade, suggesting that people in some of the wildlife farms may have been infected by Covid-19 and been unaware of it.

Maybe there will be maps of the genetic sequences as well.

I think we will just have to wait and see.

Wishful thinking.

The preliminary report simply denied the lab leak without evidence. Daszak denied it was the lab before the team even left. The head of the team said the lab was not ruled out. Now Daszak has some "new information" from China about wildlife farms.

I believe Daszak even suggested if China shut down the many-dollar wildlife farming industry that is the smoking gun. He said the same about the market. China shut the market that means they had evidence it was.

How is it there is new evidence that the team didn't have after their trip to investigate. Gee, no one believed us when we ruled the lab out without evidence. Better come up with some.

BTW regarding the smoking gun of China closing the wildlife industry down, they also scrubbed a lot of stuff from the lab.

[Skeptic Ginger]

Originally Posted by angrysoba

So, Vincent and Amy did get a question:

"Where did the virus come from? WIV?"

Their answer is no...

https://youtu.be/ydYwVis9zvE?t=1100

ETA: Another from the same person:

"Is it possible it started in bats. Was taken to WIB where they did gain of funciton serial passage research?"

Vincent's answer: "no. You can make up anything..."

https://youtu.be/ydYwVis9zvE?t=3120

Next: "Frozen food is being named as a source of origin in Wuhan being pushed by Dyzak [sic]... is that a joke? How much does the CCP pay him and how serious is frozen food as a vector?"

https://youtu.be/ydYwVis9zvE?t=3405

Vincent's Answer: "I don't think frozen food is a source. I think there is no evidence for that."

I don't know who Vincent and Amy are but the denial any such research was going on at the lab has been repeated. The evidence: researchers at the lab said so.

I and Sherku have posted evidence to the contrary including papers on their research before COVID 19 emerged meaning before they (the Chinese government) scrubbed the information off the web.

And we posted evidence how the Gain of Function research on live cultures in the WIV led to a SARS-like coronavirus from the horseshoe bats being able to infect human cells.

There was also evidence they may have had live bats there.

[angrysoba]

Originally Posted by Skeptic Ginger

Wishful thinking.

The preliminary report simply denied the lab leak without evidence. Daszak denied it was the lab before the team even left. The head of the team said the lab was not ruled out. Now Daszak has some "new information" from China about wildlife farms.

I believe Daszak even suggested if China shut down the many-dollar wildlife farming industry that is the smoking gun. He said the same about the market. China shut the market that means they had evidence it was.

How is it there is new evidence that the team didn't have after their trip to investigate. Gee, no one believed us when we ruled the lab out without evidence. Better come up with some.

BTW regarding the smoking gun of China closing the wildlife industry down, they also scrubbed a lot of stuff from the lab.

Let's see what the initial report from the WHO said in March 2020:

Quote:

What have we learned from the investigations of the first known human COVID-19 cases?
As soon as the first cases of COVID-19 were reported in late December 2019, investigations were conducted to understand the
epidemiology of COVID-19 and the original source of the outbreak. A large proportion of the initial cases in late December 2019
and early January 2020 had a direct link to the Huanan Wholesale Seafood Market in Wuhan City, where seafood, wild, and farmed
animal species were sold. Many of the initial patients were either stall owners, market employees, or regular visitors to this market.
Environmental samples taken from this market in December 2019 tested positive for SARS-CoV-2, further suggesting that the
market in Wuhan City was the source of this outbreak or played a role in the initial amplification of the outbreak. The market was
closed on 1 January 2020 and was cleaned and disinfected. The virus could have been introduced into the human population from
an animal source in the market or an infected human could have introduced the virus to the market and the virus may have then been
amplified in the market environment.
Origin of SARS-CoV-2
-2-
Subsequent investigations into the first human cases have determined that they had onset of symptoms around 1 December 2019.
However, these cases had no direct link to the Huanan Wholesale Seafood Market and they may therefore have been infected in
November through contact with earlier undetected cases (incubation time between date of exposure and date of symptom onset can
be up to 14 days). Additional studies are ongoing to as whether unrecognized infections in humans may have happened as early as
mid-November 2019

LINK

So unlike some of the very definitive statements being made by lab-leak theorists, the WHO report simply said the market had an important role (may have been the source OR may have been an amplifier). This is pretty much where the WHO still are, and yet their statements are being read as though they have been deliberately crafted to be deceptive.

I think some of the lab-leak theorists could do with being a little more nuanced in their theorizing and less definitive and categorical otherwise it becomes very confusing.

I keep assuming that some of the things that Skeptic Ginger and Sherkeu are saying are demonstrated facts but more often than not they turn out to be mere suspicions or they are repeating speculation as though it had been confidently asserted by qualified specialists. Often, it may be speculation or the assertions have been made by non-specialists, sometimes involving politicized statements by mostly right-wing figures.

[The Atheist]

Originally Posted by angrysoba

Often, it may be speculation or the assertions have been made by non-specialists, sometimes involving politicized statements by mostly right-wing figures.

True, and more than a little ironic.

[Skeptic Ginger]

Originally Posted by angrysoba

Let's see what the initial report from the WHO said in March 2020:

LINK

So unlike some of the very definitive statements being made by lab-leak theorists, the WHO report simply said the market had an important role (may have been the source OR may have been an amplifier).

We know from the evidence it is the latter. That is specific genetic markers, not someone's hypothesis.

Originally Posted by angrysoba

This is pretty much where the WHO still are, and yet their statements are being read as though they have been deliberately crafted to be deceptive.

If you would have listened to the podcast you posted you would know this is not the case. Other than Daszak's conflict of interest the limitation in the WHO investigation has to do with the political position the WHO needs to maintain with China (as with many larger countries) and the unwillingness because of that to challenge the evidence China did not allow the team access to.

Originally Posted by angrysoba

I think some of the lab-leak theorists could do with being a little more nuanced in their theorizing and less definitive and categorical otherwise it becomes very confusing.

I keep assuming that some of the things that Skeptic Ginger and Sherkeu are saying are demonstrated facts but more often than not they turn out to be mere suspicions or they are repeating speculation as though it had been confidently asserted by qualified specialists. Often, it may be speculation or the assertions have been made by non-specialists, sometimes involving politicized statements by mostly right-wing figures.

Care to argue the specifics rather than this general handwaving away claim?

Originally Posted by The Atheist

True, and more than a little ironic.

You got the ironic part right.

[angrysoba]

Originally Posted by Skeptic Ginger

We know from the evidence it is the latter. That is specific genetic markers, not someone's hypothesis.


If you would have listened to the podcast you posted you would know this is not the case. Other than Daszak's conflict of interest the limitation in the WHO investigation has to do with the political position the WHO needs to maintain with China (as with many larger countries) and the unwillingness because of that to challenge the evidence China did not allow the team access to.


Care to argue the specifics rather than this general handwaving away claim?

You got the ironic part right.

If you mean the Rogan clip and his talk with Jamie Metzl I did listen to it.

I get it, you keep repeating the conflict of interest that Daszak has. I get it already!

[Skeptic Ginger]

Originally Posted by angrysoba

Let's see what the initial report from the WHO said in March 2020:
LINK
...

Getting back to this link to the WHO statement, I'm not sure what your point is. You have so much highlighted it was hard to tell.

Did you see the date on that FAQ on the Origin of SARS-CoV-2? March 2020.

Know when the investigative team went to China? Jan 2021.

So you might want to consider all of that open-mindedness the WHO had back in March and compare it to what they had to say after their visit.

NPR: WHO Team Reconstructs Origins Of Coronavirus Outbreak In Wuhan - February 16, 2021

Quote:

NPR's Steve Inskeep speaks to Marion Koopmans, ...

KOOPMANS: So the first cases that were detected were linked to the market, but it's clear that - so now there's a bigger list of cases that are confirmed. And it's clear that not everyone is linked to the market., China, to investigate the beginning of the COVID-19 outbreak. ...

The market has been one of those spreading events, but there also was circulation outside of - or aside from the market.

If you weren't looking at a 10 month old document you wouldn't have to question whether or not the market was the initial start.

She goes on:

Quote:

But even if you then have a case that has not linked to the market, because of this stealth mechanism of spread, it can still be linked somehow - but because someone picked up an infection from another person that was at the market.

But now we have genetic evidence there is not a direct link from the market to the other patients. (See Sherkeu's last 2 posts.)

Quote:

KOOPMANS: Yeah, yeah, yeah. Sure. So from everything that we've looked at and we've also visited three labs in (unintelligible) and also three labs that work on these viruses. From that, we have not been able to find any credible link there.

INSKEEP: How open and transparent were the Chinese once they let you in?

KOOPMANS: Of course, this is a topic and a mission that is - there are sensitivities around it, if only for the - there's, of course, big political tensions that are around it. And that's something you cannot completely avoid in a situation like this. But once we got out of our quarantine, got into the face-to-face meetings, I think we've managed to get into real good scientific exchange with stiff discussions here and there because to start from different backgrounds and different views. But I tell everyone, wait and - read the report, and let's discuss then. But I think we managed to get a good outcome of this meeting. I think it was, in that sense, quite successful. ...

KOOPMANS: Not really. So if you say, did the Chinese colleagues hand over the complete raw data files? No, they did not. But then again, I did not expect that in a mission like this. So we've seen a lot of information. We've been given a lot of information.

IOW, no they didn't give us free access but we think we got good interviews.

You think you see definitive evidence in that interview the lab was ruled out?

[angrysoba]

Originally Posted by angrysoba

Let's see what the initial report from the WHO said in March 2020:

Originally Posted by Skeptic Ginger

Did you see the date on that FAQ on the Origin of SARS-CoV-2? March 2020.

[angrysoba]

Originally Posted by Skeptic Ginger

You think you see definitive evidence in that interview the lab was ruled out?

The WHO haven't definitively ruled it out. Not even Peter Daszak when asked in that video I posted a couple of days ago definitively ruled it out.

They said it was unlikely.

[angrysoba]

Originally Posted by Skeptic Ginger

She goes on:But now we have genetic evidence there is not a direct link from the market to the other patients. (See Sherkeu's last 2 posts.)

I don't get it.

Sherkeu's posts arguing that it wasn't the Wuhan wet market have been claiming that the virus had been circulating in Europe and other places.

Well, that's one way to dispose of the wet market theory if you absolutely must, but then it also massively reduces the evidence that it came from the WIV, doesn't it.

Instead of "Huh! Bit of a coincidence that the market was right next to the WIV!" it becomes, "Oh, you mean Wuhan may not even have been the epicenter!"

Sorry, at this point, I don't even understand what the lab leak theory is even suppposed to be:

Is it:

"Right off the bat" (a bit infected a worker who left with it?)
"Gain of function" (the scientists altered it in a lab themselves through manipulation and then left with it).
"Out the sewage pipes"
"Sold to the market"
"Somebody got it in Wuhan Institute of Virology from a bat then did gain of function on it, went skiing in Italy, spread it around Europe, then came back to China, went up and down on the subway etc..."

Or how about this...

"Someone went to Yunnan, picked up the bat, took it with them to Wuhan, released it from the third floor of the building. It had the Covid-19, but then the workers also did gain of function to make it more susceptible to human transmission, and now they are looking for that particular bat colony in Yunnan, but they are trying to stop others finding out what they already know about it..."

Or something like that....?

[Skeptic Ginger]

Originally Posted by Sherkeu

Italy:
Evidence of SARS-CoV-2 RNA in an Oropharyngeal Swab Specimen, Milan, Italy, Early December 2019
https://wwwnc.cdc.gov/eid/article/27/2/20-4632_article

Summary article:
https://www.ncbi.nlm.nih.gov/researc...ation/33176598
...

I'll come back to the other countries when I have time. I think we are getting closer to a map going back to the beginning.

The CDC data in your first link is consistent with the phylogenic tree in my link but the second one showing antibodies earlier is not.

The first two cases of 2019‐nCoV in Italy: Where they come from?

Quote:

The Bayesian phylogenetic reconstruction showed that 2019‐2020 nCoV firstly introduced in Wuhan on 25 November 2019, started epidemic transmission reaching many countries worldwide, including Europe and Italy where the two strains isolated dated back 19 January 2020, the same that the Chinese tourists arrived in Italy. Strains isolated outside China were intermixed with strains isolated in China as evidence of likely imported cases in Rome, Italy, and Europe, as well. In conclusion, this report suggests that further spread of 2019‐nCoV epidemic was supported by human mobility and that quarantine of suspected or diagnosed cases is useful to prevent further transmission.

When one is looking at antibodies in serum from specimens collected for other reasons (one study looked at blood from blood bank donors) and your link looking at serum from cancer screening, my first question is why didn't they perform the most obvious control tests: test serum stored a year or more ago?

It's not likely that you'd find antibodies from COVID 19 in these stored serums because they represent a fraction of the population. There would have had to have been COVID 19 circulating widely for a small sample to contain them.

Well here's one study that did just that, looked at serum stored well before the COVID pandemic:

Pre-existing coronavirus antibodies could protect against new COVID-19 strains

Quote:

The researchers made this discovery while developing highly sensitive antibody tests for COVID-19. To see how well their assay tests were performing, they compared the blood of patients with COVID-19 to patients who had not had the disease. They found that some people who had not been exposed to SARS-CoV-2 had antibodies in their blood which would recognise the virus. To confirm their findings, they analysed over 300 blood samples collected before the pandemic, between 2011 and 2018.

Nearly all samples had antibodies that reacted with common cold coronaviruses. However, a small fraction of adult donors, about one in 20, also had antibodies that cross-reacted with SARS-CoV-2 and this was not dependent on recent infection with a common cold coronavirus.

So the evidence COVID 19 was in Italy in Dec 2019 is strong. The evidence from blood tests showing antibodies sooner than Oct 2019 is weak at best.

[Skeptic Ginger]

Originally Posted by angrysoba

I don't get it.

Sherkeu's posts arguing that it wasn't the Wuhan wet market have been claiming that the virus had been circulating in Europe and other places.

Well, that's one way to dispose of the wet market theory if you absolutely must, but then it also massively reduces the evidence that it came from the WIV, doesn't it.
[snip]

Or something like that....?

You are not looking carefully at the data, you are looking at the headlines and a couple paragraphs. See my post above where I looked at the kind of tests done and the reliability of that testing.

Look at this phylogenic tree from my link to get an idea how one traces genomes.

[angrysoba]

Originally Posted by Skeptic Ginger

You are not looking carefully at the data, you are looking at the headlines and a couple paragraphs. See my post above where I looked at the kind of tests done and the reliability of that testing.

Look at this phylogenic tree from my link to get an idea how one traces genomes.

So where on that tree are the ones that were "circulating globally" in November (or late summer)?

If that's the claim, then what use is that tree?

[Skeptic Ginger]

Originally Posted by angrysoba

So where on that tree are the ones that were "circulating globally" in November (or late summer)?

If that's the claim, then what use is that tree?

You seem to want "globally" to mean all over the world. The first case was in late Oct or early Nov in Wuhan based on genetic mapping using the rate of mutation as a clock.

By Dec (and maybe as early as late Nov), cases started spreading around China and nearby countries, to Europe, the US and those cruise ships.

That is globally.

A phylogenic tree will show where cases began and where they went.

[Skeptic Ginger]

Look at the phylogenic tree. Cases went from Wuhan to the US before they went from Wuhan to Italy. They also spread to France, Germany and Australia in separate pathways. It's pretty clear from that data that all roads lead back to Wuhan.

[angrysoba]

Originally Posted by Skeptic Ginger

You seem to want "globally" to mean all over the world.

Stop that!

This is getting tiresome when you start making up things that I "seem" to be saying when I have not said anything remotely similar to what you say I "seem" to be saying.

As far as I understand, Wuhan is the location of the emergence of Covid-19.

Do you agree with that? Yes or No.

Now, there is a question about whether or not the wet market had a role in the emergence, isn't there? Yes or No.

Now, one reason some people think otherwise is because some early victims had no connection to the wet market, right? Yes or No.

If that's the case, then we might look elsewhere for the emergence, right? Yes or No.

If the earliest case is December 8th apparently from someone who never visited the market, then this gives rise to doubts about it emerging in the wet market, right? Yes or No.

So how do we explain it? At this point eyes turn to another place in Wuhan... the Wuhan Institute of Virology! Hmmmm...they are doing bat research there with cultures of SARSr...

But then...Sherkeu is saying oh yeah and there may have been cases abroad, in France, Italy, the US as far back as November....

But wait...wait...wait... how does that square with the escaped from the WIV theory?



To be honest, that is what I would expect China to want you to believe! Hey maybe it didn't start in Wuhan at all...etc...Maybe not even in China!!

Obviously this is not what I think, but where does this "circulating globally" theory however you define it help the case that it came from the WIV? What is the connection?