Recent Article on the Evolution of a Theory of Covid Origins

[jedishrfu]

https://theintercept.com/2023/01/19/covid-origin-nih-emails/

As Covid-19 was spreading fear and spurring lockdowns across the United States in early 2020, the scientific journal Nature Medicine published a paper on March 17 titled “The Proximal Origin of SARS-CoV-2.” Written by five renowned academic scientists, it played an important early role in shaping the debate about a fiercely controversial topic: the origin of the virus that has killed millions since it emerged in Wuhan, China, in late 2019. Did it spill from animals to humans in nature, on a farm, in a market? Or did it leak from a lab like the Wuhan Institute of Virology, a leading center of coronavirus research in China? Drawing on “comparative analysis of genomic data,” the paper’s authors wrote that “our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated construct.” Toward the end of the paper, they added, “we do not believe that any type of laboratory-based scenario is plausible” in explaining the origin of the virus. Instead, the scientists strongly favored a natural origin, arguing that the virus likely spilled from bats into humans, possibly by way of an intermediate animal host.

 

[pinball1970]

https://theintercept.com/2023/01/19/covid-origin-nih-emails/

Similar from John Hopkins last August.
Wuhan market. Bats, pangolin and civets have been cited but Raccoon dogs are mentioned which I have not heard before as an intermediary.

https://publichealth.jhu.edu/2022/origins-of-sars-cov-2

 

[.Scott]

Thanks for posting the link.
I had not realized that unredacted material on this research had become available.

The Wuhan Institute of Virology existed well before SARS-1. But based on the timing, it was SARS-1 that inspired the addition of a Biosafety Level 4 lab at that site. Given the suspected origins in Guangdong Province of SARS-1, positioning a BSL-4 lab in a similar environment in Wuhan has always seemed to make great sense to me. I have never been tempted to describe the proximity of the Wuhan BSL-4 lab to the SARS-2 home as "coincidental".

 

[bob012345]

“we do not believe that any type of laboratory-based scenario is plausible” in explaining the origin of the virus. Instead, the scientists strongly favored a natural origin, arguing that the virus likely spilled from bats into humans, possibly by way of an intermediate animal host."

By origin of the virus do they also mean origin of the release of the virus? Does that include possible scenarios involving natural samples stored and accidentally released by some form of accidental contamination from the lab?

 

[jedishrfu]

No when they say natural its in contrast to engineered in a lab.

 

[.Scott]

By origin of the virus do they also mean origin of the release of the virus? Does that include possible scenarios involving natural samples stored and accidentally released by some form of accidental contamination from the lab?

The proof of the pudding is in the eating.
The virulence of a virus can only be measured after it is "released".

In the case of a naturally developed virus, it can only develop while it is being passed from host to host.
So "natural samples stored" would be either samples already in the human population or samples in another population - say bats - with unknown human virulence.

That second scenario is unlikely because there are so many other more direct ways of communicating a virus from bats to human than collection by a lab followed by the accidental release - presumably to a lab worker or to the person doing the collection. This is why the discovery of a very similar virus in the pangolin was so convincing. At that point, they not only had historic data of this method of bat-to-human transmission, but had something very recent and tied very closely to SARS-2.

 

[Dark Star]

“While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal7 and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding7,11.”

“ Thus, the high-affinity binding of the SARS-CoV-2 spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise.”

“ This is strong evidence that SARS-CoV-2 is not the product of purposeful manipulation.”

https://www.nature.com/articles/s41591-020-0820-9#rightslink The proximal origin of SARS-CoV-2

I am having trouble understanding the above.

1. What is the first quote saying? It seems to be comparing computational analysis to actually reality.

2. Another optimal binding solution? Optimal relative to what?

3. Is this evidence, strong evidence? Why is this considered strong?

 

[TeethWhitener]

“While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal7 and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding7,11.”

“ Thus, the high-affinity binding of the SARS-CoV-2 spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise.”

“ This is strong evidence that SARS-CoV-2 is not the product of purposeful manipulation.”

https://www.nature.com/articles/s41591-020-0820-9#rightslink The proximal origin of SARS-CoV-2

I am having trouble understanding the above.

1. What is the first quote saying? It seems to be comparing computational analysis to actually reality.

2. Another optimal binding solution? Optimal relative to what?

3. Is this evidence, strong evidence? Why is this considered strong?

The point is that if someone were to purposely design a protein to bind to the ACE2 receptor using our best computational models, they likely wouldn’t choose the structure of the spike protein found in SARS-CoV-2, because our models predict that it doesn’t bind very well with the ACE2 receptor.

Edit: Therefore it’s reasonable to conclude that the SARS-CoV-2 protein wasn’t purposely designed to bind to ACE2 (thus suggesting a natural origin for SARS-CoV-2).

 

[Dark Star]

"In silico comparison of SARS-Cov-2 spike protein - ACE2 binding affinities across species and implications for virus origin"

https://www.nature.com/articles/s41598-021-92388-5

"These findings show that the earliest known SARS-CoV-2 isolates were surprisingly well adapted to bind strongly to human ACE2, helping explain its efficient human to human respiratory transmission."

"Conspicuously, we found that the binding of the SARS-CoV-2 S protein was higher for human ACE2 than any other species we tested."

This study, which I find to be very credible, contradicts your "doesn't bind very well" statement.

 

[TeethWhitener]

This study, which I find to be very credible, contradicts your "doesn't bind very well" statement.

The first study refers to “absolute” binding strength of spike protein to human ACE2 vs various mutated forms of spike (ACE2 constant, spike variable). The second study refers to comparison of spike binding to human ACE2 vs other animal ACE2 (spike constant, ACE2 variable). Both studies acknowledge that the binding event happens with high affinity regardless of spike mutation or ACE2 origin species.

“Doesn’t bind well” was sloppy language on my part. The ultimate arbiter is the actual value of $K_d$ from experiment or binding free energy from MD simulations. Note that the first study cites a handful of other studies for its conclusions.

 

[artis]

I would say there's no need to argue over how good the spike binds to ACE2 , I'd say very good given the ease at which Covid, especially the latter versions managed to transmit themselves.

One other simple proof that I know that proves this is that while there were mask mandates in almost any public place I did not contract any regular "winter virus" or the flu , nor did most of those I know.
Sure enough this isn't scientific proof, but my argument would be that due to the much lower virulence of those typical viruses they just couldn't get through the masks most of the time to reach a concentration high enough to cause symptoms.
Covid on the other hand did manage to get through at the same time while the other viruses were "radio silent".

 

[pinball1970]

I would say there's no need to argue over how good the spike binds to ACE2 , I'd say very good given the ease at which Covid, especially the latter versions managed to transmit themselves.

One other simple proof that I know that proves this is that while there were mask mandates in almost any public place I did not contract any regular "winter virus" or the flu , nor did most of those I know.
Sure enough this isn't scientific proof, but my argument would be that due to the much lower virulence of those typical viruses they just couldn't get through the masks most of the time to reach a concentration high enough to cause symptoms.
Covid on the other hand did manage to get through at the same time while the other viruses were "radio silent".

People got infected with Covid 19 and other respiratory viruses just in much lower numbers during lockdown. In the UK at least.
Masks was just one measure in 2020, isolation and social distancing when people met which also had restrictions in terms of numbers were others.

 

[artis]

https://edition.cnn.com/2023/02/28/politics/wray-fbi-covid-origins-lab-china/index.html

FBI Director Christopher Wray on Tuesday acknowledged that the bureau believes the Covid-19 pandemic was likely the result of a lab accident in Wuhan, China.

“You’re talking about a potential leak from a Chinese government-controlled lab that killed millions of Americans,” Wray said of the coronavirus, “and that’s precisely what that capability was designed for.”


Wray said that most details of the FBI’s investigation remain classified, and that it has been difficult to work with the Chinese government on investigating the pandemic’s origin.


“I will just make the observation that the Chinese government, it seems to me, has been doing its best to try to thwart and obfuscate the work here,” the bureau director said. “The work that our US government and close foreign partners are doing. And that’s unfortunate for everybody.”

I myself have had a long held suspicion which grows as time goes that this virus is either a human made error or a deliberate plot by whoever (time will only tell maybe).

People with more knowledge can correct me but from a simple evolutionary viewpoint it would be very unlikely for a virus to both jump species as well as immediately be very fit to interact with the new species at the same time without prior "training".

The ACE2 receptors are similar for chimps and humans but chimps aren't anywhere close the source of this virus , the source is considered bats and some intermediary animal but they don't have ace2 receptors that are just as well suited for spike as those of chimps and humans.

And quite frankly the fact which even China admits that Wuhan lab did research on coronaviruses including the closest sibling to Covid , the RATG 13, it's one hell of a "coincidence" for Covid to emerge in the same city that has a biolab that does research including gain of function within the very virus group this virus is from.

There was a time when opinion like this was considered conspiratorial and banned but I hope not anymore.
At the same time I don't think we will know the truth if it indeed was a lab accident, because we would need a very brave whistle blower to step forth but knowing China even that won't help much as I'm sure their intelligence apparatus has already erased from existence any proof (including humans) that exist or existed to to give any proof.
It wouldn't be "below them" to do that given their regime history of murdering people like flies, especially when they knew what was at stake if such information became known.
So the prospect of a cover up if it was a lab leak is very real.

 

[pinball1970]

https://edition.cnn.com/2023/02/28/politics/wray-fbi-covid-origins-lab-china/index.html

I myself have had a long held suspicion which grows as time goes that this virus is either a human made error or a deliberate plot by whoever (time will only tell maybe).

People with more knowledge can correct me but from a simple evolutionary viewpoint it would be very unlikely for a virus to both jump species as well as immediately be very fit to interact with the new species at the same time without prior "training".

The ACE2 receptors are similar for chimps and humans but chimps aren't anywhere close the source of this virus , the source is considered bats and some intermediary animal but they don't have ace2 receptors that are just as well suited for spike as those of chimps and humans.

And quite frankly the fact which even China admits that Wuhan lab did research on coronaviruses including the closest sibling to Covid , the RATG 13, it's one hell of a "coincidence" for Covid to emerge in the same city that has a biolab that does research including gain of function within the very virus group this virus is from.

There was a time when opinion like this was considered conspiratorial and banned but I hope not anymore.
At the same time I don't think we will know the truth if it indeed was a lab accident, because we would need a very brave whistle blower to step forth but knowing China even that won't help much as I'm sure their intelligence apparatus has already erased from existence any proof (including humans) that exist or existed to to give any proof.
It wouldn't be "below them" to do that given their regime history of murdering people like flies, especially when they knew what was at stake if such information became known.
So the prospect of a cover up if it was a lab leak is very real.

The science community appeared to favour "from nature" in 2022
https://www.science.org/content/article/evidence-suggests-pandemic-came-nature-not-lab-panel-says

Also this from 2021
https://www.forbes.com/sites/starts...asnt-leaked-from-a-wuhan-lab/?sh=68d389025585

Best read all sides keep an open mind and follow what the science publications tell us. @Laroxe has posted on Covid recently and will have deeper insight.

Given the current climate the comments could have been more politically rather scientifically motivated.

 

[berkeman]

There was a time when opinion like this was considered conspiratorial and banned but I hope not anymore.

It still is here, so please don't go there in this thread or it will be shut down.

In the version of the CNN article that I read yesterday, it said there was general agreement that the lab release (if that's how it happened) was not intentional. Let's keep it at that for now, at least in this thread. Thanks.

 

[jim mcnamara]

Let's stick to Science. For example RNA viruses have a huge "randomizing" event - the newly minted viruses on average have ~10% mutation rate This is why ferrets, deer, and other wild animals are now infected with COVID. The list is large. See CDC this microsite on the topic.
https://www.cdc.gov/widgets/microsi...ataid=404908&chashOptMode=out#!/detail/405242

Zoonosis:
FWIW Covid can spillover from humans to other species like ferrets, and then move back again to another human, then to deer.... ad nauseam. This is why the site listed above warns about human->livestock spillovers.

 

[BillTre]

from a simple evolutionary viewpoint it would be very unlikely for a virus to both jump species as well as immediately be very fit to interact with the new species at the same time without prior "training".

This was never really the argument as I understand it.
There is no reason to think that these events happened "immediately". Sounds like a straw-man argument.

 

[Dark Star]

This may be of some interest

https://www.nature.com/articles/s41591-020-0820-9 Kristian G. Anderson et. al. The proximal origin of SARS-CoV-2

"While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal7 and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding7,11."

IF YOU HAVE NOT READ THE SOURCES HERE YOU SHOULD. WELL DONE AND INTERESTING

7. https://journals.asm.org/doi/10.1128/JVI.00127-20 Ralph S. Baric et. al. 17 March 2020 Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus
11. https://journals.asm.org/doi/10.1128/JVI.02041-07 Ralph Baric et. al. 1 March 2008 Mechanisms of Zoonotic Severe Acute Respiratory Syndrome Coronavirus Host Range Expansion in Human Airway Epithelium

 

[atyy]

Some people criticize the Proximal Origin paper by Andersen and colleagues for prematurely dismissing the possibility of a lab leak. However, while the paper argued that genetic manipulation to introduce specific sequence changes were extremely unlikely, it left the door open to other lab leak scenarios. In fact I cited the paper on PF to support not prematurely dismissing a lab leak. Since then, evidence has accumulated against a lab leak, and evidence points strongly towards the animal trade associated with Huanan market in Wuhan.

https://www.physicsforums.com/threads/coronaviruses-in-malayan-pangolins.987501/post-6328114

 

[artis]

"While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal7 and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding7,11."

And it shouldn't be ideal, why would it? One would only assume that if one was set from the start to create a certain type of virus parts of which interact with certain cells in certain ways.

There are other avenues I think how this could have happened. What if you take a virus that exists in nature and study it without manipulating it. Let it interact with different cell cultures etc to see whether it poses a risk of adapting to them and become infectious to the very organisms having those cells, would this not run the chance of that virus mutating and becoming more fit for the very cell type that it interacts with?

Not to make any conclusions but to the best of my understanding one can give a particular virus a selected environment and thereby providing the ground for the virus to build itself.
In nature the virus couldn't do that or would have a very small chance of doing that because the right conditions are rarely met.It's like that fruit fly experiment one forum member gave me here while we were discussing evolution/biology , IIRC, you take a single species of fly that easily mate and you separate them where each of the two groups has a different environment/food and after a while they can't produce offspring anymore even though they started as single species.
Forgot the exact experiment but the idea I think holds, you can take a virus and artificially make it evolve by supplying the right circumstances.
Such a virus if looked at genetically wouldn't differ, I think, from one that came by randomly from nature, it's just that in nature the chances of it interacting with humans for example, are far far lower.

If this was the avenue how it came about it would answer the questions of why the spike protein isn't perfect in it;'s binding capability according to a computational model, because evolution irrespective of whether completely random/natural or artificially supported/accelerated doesn't know how to make perfect mechanisms ,. just make them good enough to survive and Covid managed to do that from the get go,

I think this is what most of the experts who think the lab leak is a possibility think, they don't think that someone essentially wrote the virus as if it was a code, rather that there were certain biological experiments taking place to see the potential danger of such corona viruses found in Asia.

 

[BillTre]

In nature the virus couldn't do that or would have a very small chance of doing that because the right conditions are rarely met.

Yet your explanations posit similar events happening in much smaller populations (making the random recombinations or other mutations less likely) as those that could occur in the wild.
The only selection needed in either case is reproductive success in a different cell. Not too difficult in a world full of viruses that have no real respect for their host's species boundaries.

It's like that fruit fly experiment one forum member gave me here while we were discussing evolution/biology , IIRC, you take a single species of fly that easily mate and you separate them where each of the two groups has a different environment/food and after a while they can't produce offspring anymore even though they started as single species.

I don't recall ever hearing about this experiment.
There are other examples, but speciation in animals is not very relevant to viruses.

 

[atyy]

There are other avenues I think how this could have happened. What if you take a virus that exists in nature and study it without manipulating it. Let it interact with different cell cultures etc to see whether it poses a risk of adapting to them and become infectious to the very organisms having those cells, would this not run the chance of that virus mutating and becoming more fit for the very cell type that it interacts with?

Andersen and colleagues discussed in their "Proximal Origin" paper how SARS2 features like the receptor binding domain (RBD) and the furin cleavage site (polybasic cleavage site) might have arisen through selection by passage in cell culture. They believed these scenarios unlikely, but left the door open to them. https://www.nature.com/articles/s41591-020-0820-9

Evidence since the publication of Proximal Origin in April 2020 makes any lab leak (including the leak of a natural virus, or a virus selected by passage) extremely unlikely.

By Jan 2020 the Wuhan Institute of Virology (WIV) submitted to Nature the full sequence of RaTG13, likely their closest virus to SARS2 in context, & too far to be the direct source of SARS2 at 96% similarity. By July 2020 WIV confirmed RaTG13 as their closest virus, and reported other data making a lab leak improbable. Multiple lines of evidence corroborate that.
https://www.nature.com/articles/s41586-020-2012-7
https://www.science.org/pb-assets/PDF/News PDFs/Shi Zhengli Q&A-1630433861.pdf

Before the pandemic, WIV submitted & published many papers, accompanied by submissions of SARS-related sequences in international databases. As expected, partial sequences of RaTG13 are in these submissions. Their database submissions include many novel SARS-related sequences in 2018 & 2019, but there is no sign of SARS2. They could not have known to make public these SARS-related sequences, while specifically hiding SARS2. So it's improbable that SARS2 was in the WIV catalog in mid-2018.
https://www.nature.com/articles/s41467-020-17687-3

https://ncbi.nlm.nih.gov/nucleotide/MH615898.1
https://www.ncbi.nlm.nih.gov/nuccore/MH615843

The WIV coronavirus lab hosted Wang Linfa, a professor in Singapore, around 15 Jan 2020, shortly before the WIV submitted their RaTG13 paper. This means they had compared SARS2 against their catalog by the time of Wang Linfa's visit, and would have known of any leak from their catalog by then, even if all infections of WIV staff had been asymptomatic.

The WIV coronavirus lab mixed with Wang Linfa and took him to a restaurant, behavior that is not easily consistent with them knowing of any leak from their catalog. The New York Times published a picture of Wang Linfa and members of the WIV coronavirus lab, including Shi Zhengli, the lab head, at an Wuhan restaurant on 15 Jan 2020. So it's improbable that WIV had SARS2 in its catalog before the pandemic.
https://www.science.org/content/art...bats-now-hes-working-uncover-origins-covid-19
https://www.nytimes.com/2021/06/14/world/asia/china-covid-wuhan-lab-leak.html

Danielle Anderson was at the WIV till Nov 2019, and heard of nothing unusual while she was there. WIV staff including Shi Zhengli attended a conference in Singapore around 9 Dec 2019. These are not consistent with any sizeable WIV outbreak from Nov 2019 - mid-Jan 2020, and are easily consistent with no WIV outbreak.
https://www.bloomberg.com/news/feat...a-lab-scientist-at-wuhan-institute-speaks-out
https://nipah2019.miceapps.com/client/sites/page/503/1389

Many early cases were linked to the market as suggested from the earliest reports. Worobey et al (2022) added that unlinked cases clustered around the market like the linked cases, and that positive market environment samples were collected near live animal stalls.
https://www.science.org/doi/10.1126/science.abp8715

Epidemiology suggests SARS2 Lineages A & B arose from separate introductions into people, with Lineage B introduced first. In contrast a lab leak is more easily consistent with Lineage A having been introduced first, because Lineage A is likely evolutionarily older given other CoVs.
https://www.science.org/doi/10.1126/science.abp8337
https://academic.oup.com/nsr/article/8/8/nwab073/6287578

 

[artis]

It seems @atyy you have followed this topic quite a bit ?

Either way, without trying to draw any conclusions which quite frankly I can't, it is very possible that indeed "low hygiene" within a crowded meat market was a breeding ground for evolution.

I would just advise to keep one thing in mind and that is that China just like the former USSR has a policy where all major research centers and factories/businesses have two facades. One is the public/official with the official story and the other one is the classified/secret one where the companies/research centers are carrying out work for the government/military.
There are books out there detailing how this happened in the former USSR. Ussr was rather successful at eradicating major diseases and vaccinating their population but they were also successful at testing many of those diseases for bio weapons applications.
Without going into much detail
https://en.wikipedia.org/wiki/Soviet_biological_weapons_program

They even tried to weaponize smallpox of all things.
One can also google the term biopreparat - worlds largest ever agency for development of biological weapons.
From what I've read within the USSR there were scientists who had to work dual careers, they were only given grants and research funds for their civilian work if they agreed to "help out" the government, sometimes this dual work happened in the same building/research center, where the "dayjob" was located at one side and the secretive work at another wing of the building.It might just be that in case of Covid it;'s all just a bad coincidence where random events came together in a way that is just perfect for a conspiracy (major virus from a city with a biolab etc etc) but as things currently stand one shouldn't forget that other avenues are possible.

If indeed WIV had a second job (which is rather likely) which wasn't civil science related then one shouldn't expect they would give out the details of it in "nature.com" or make a preprint of it in "arxiv" and post a picture next to it with Shi Zhengli and their staff.
I hope that much we can all agree on.

 

[artis]

Heres a US Department of State factsheet from a year ago.

https://2017-2021.state.gov/fact-sheet-activity-at-the-wuhan-institute-of-virology/index.html

Just some highlights from the link

For more than a year, the Chinese Communist Party (CCP) has systematically prevented a transparent and thorough investigation of the COVID-19 pandemic’s origin, choosing instead to devote enormous resources to deceit and disinformation

The virus could have emerged naturally from human contact with infected animals, spreading in a pattern consistent with a natural epidemic. Alternatively, a laboratory accident could resemble a natural outbreak if the initial exposure included only a few individuals and was compounded by asymptomatic infection.

The U.S. government has reason to believe that several researchers inside the WIV became sick in autumn 2019, before the first identified case of the outbreak, with symptoms consistent with both COVID-19 and common seasonal illnesses. This raises questions about the credibility of WIV senior researcher Shi Zhengli’s public claim that there was “zero infection” among the WIV’s staff and students of SARS-CoV-2 or SARS-related viruses.

Accidental infections in labs have caused several previous virus outbreaks in China and elsewhere, including a 2004 SARS outbreak in Beijing that infected nine people, killing one.

The CCP has prevented independent journalists, investigators, and global health authorities from interviewing researchers at the WIV, including those who were ill in the fall of 2019.

By Jan 2020 the Wuhan Institute of Virology (WIV) submitted to Nature the full sequence of RaTG13, likely their closest virus to SARS2 in context, & too far to be the direct source of SARS2 at 96% similarity. By July 2020 WIV confirmed RaTG13 as their closest virus, and reported other data making a lab leak improbable. Multiple lines of evidence corroborate that.

But some evidence goes against that
https://2017-2021.state.gov/fact-sheet-activity-at-the-wuhan-institute-of-virology/index.html

• Starting in at least 2016 – and with no indication of a stop prior to the COVID-19 outbreak – WIV researchers conducted experiments involving RaTG13, the bat coronavirus identified by the WIV in January 2020 as its closest sample to SARS-CoV-2 (96.2% similar). The WIV became a focal point for international coronavirus research after the 2003 SARS outbreak and has since studied animals including mice, bats, and pangolins.
• The WIV has a published record of conducting “gain-of-function” research to engineer chimeric viruses. But the WIV has not been transparent or consistent about its record of studying viruses most similar to the COVID-19 virus, including “RaTG13,” which it sampled from a cave in Yunnan Province in 2013 after several miners died of SARS-like illness.

WIV altered and then removed online records of its work with RaTG13 and other viruses.

So essentially it has studied the closest virus to Covid - the RaTG 13 and all the animals that are also officially thought to have been the intermediaries in the jump to humans.

Here is the recent info that came out assessing Covid origins, it has a more favorable view to the natural origin story. From the National Intelligence Council.

https://www.dni.gov/files/ODNI/documents/assessments/Declassified-Assessment-on-COVID-19-Origins.pdf

Though it also contains conclusions like these

Some genetic engineering techniques may make
genetically modified viruses indistinguishable from
natural viruses, according to academic journal
articles. For instance, a 2017 dissertation by a
WIV student showed that reverse genetic cloning
techniques—which are standard techniques used in
advanced molecular laboratories—left no trace of
genetic modification of SARS-like coronaviruses

Although one thing hasn't changed throughout these documents and that is this

China’s cooperation most likely would be needed to reach a conclusive assessment of the origins of COVID-19.
Beijing, however, continues to hinder the global investigation, resist sharing information, and blame other
countries, including the United States. These actions reflect, in part, China’s government’s own uncertainty about
where an investigation could lead as well as its frustration the international community is using the issue to exert
political pressure on China.

I happen to agree on this, that if China was so sure they have "clean hands" with respect to this, then why not once and for all do everything you can to assure the world that millions of deaths and countless more ruined lives is not the fault of your negligence?

Danielle Anderson was at the WIV till Nov 2019, and heard of nothing unusual while she was there. WIV staff including Shi Zhengli attended a conference in Singapore around 9 Dec 2019. These are not consistent with any sizeable WIV outbreak from Nov 2019 - mid-Jan 2020, and are easily consistent with no WIV outbreak.
https://www.bloomberg.com/news/feat...a-lab-scientist-at-wuhan-institute-speaks-out

I'm sorry if this comes across as a joke, but the title of that link from Bloomberg literally says this

The Last—And Only—Foreign Scientist in the Wuhan Lab Speaks Out​

And even if something unusual was going on within WIV, do you really think the staff there would first inform "the last and only foreign scientist" among them?

Though to your defense the last link I posted also says this

Early in the pandemic, the WIV identified that a
new virus was responsible for the outbreak in
Wuhan. It is therefore assessed that WIV
researchers pivoted to COVID-19-related work to
address the outbreak and characterize the virus.
These activities suggest that WIV personnel were
unaware of the existence of SARS-CoV-2 until the
outbreak was underway

Anyway at this point I guess it's futile to try to "get to the bottom" of this because it has no bottom, too much information and the blame game is too large from all involved sides to definitively claim who is right and who lies.

 

[Dark Star]

Evidence since the publication of Proximal Origin in April 2020 makes any lab leak (including the leak of a natural virus, or a virus selected by passage) extremely unlikely.

"Extremely unlikely"? You quote a lot of material. I would appreciate you focusing in on the exact information that you found that made a lab leak "extremely unlikely". If you could quote the statements within the articles and then via sequential analysis show how you arrived at "extremely unlikely" one could have more assurance that the conclusion was justified.

 

[artis]

"Extremely unlikely"? You quote a lot of material. I would appreciate you focusing in on the exact information that you found that made a lab leak "extremely unlikely". If you could quote the statements within the articles and then via sequential analysis show how you arrived at "extremely unlikely" one could have more assurance that the conclusion was justified.

I think at this point it's just everybody taking their favorite side in the absence of clear evidence.

Here is an article from Nytimes from the end of 2021, a really good read,
https://www.nytimes.com/2021/11/23/magazine/covid-lab-leak.html

 

[atyy]

https://zenodo.org/record/7754299#.ZBjpby8w30o
Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control

Alexander Crits-Christoph, Karthik Gangavarapu, Jonathan E. Pekar, Niema Moshiri, Reema Singh, Joshua I. Levy, Stephen A. Goldstein, Marc A. Suchard, Saskia Popescu, David L. Robertson, Philippe Lemey, Joel O. Wertheim, Robert F. Garry, Angela L. Rasmussen, Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut, Michael Worobey, Florence Débarre

This a report about genetic material in environmental samples from Huanan market: "We find that the RNA and/or DNA sequence reads from susceptible animals are at the highest frequency in wildlife stalls in the southwest corner of the market. This quadrant of the market is where most SARS-CoV-2 environmental RNA was detected, and live mammals were being sold. For multiple samples, mitochondrial nucleic acids from susceptible, or potentially susceptible, animals, including raccoon dogs, were significantly more abundant than human mitochondrial nucleic acids"

 

[PeroK]

https://zenodo.org/record/7754299#.ZBjpby8w30o
Genetic evidence of susceptible wildlife in SARS-CoV-2 positive samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and interpretation of data released by the Chinese Center for Disease Control

The animals at the seafood market must have come from the wild somewhere. I don't believe it could have originated at the market.

Is there evidence of the virus's evolution in the wild?

The CCP controls everything that is published in China. One problem with having no independent media or government scrutiny is that there is no way to tell how much has been fabricated or suppressed.

It's bad enough in countries with a free press and opposition to the incumbent government.

 

[artis]

The animals at the seafood market must have come from the wild somewhere. I don't believe it could have originated at the market.

A good point I believe, because if we assume animal origin (instead of human) then the virus had to be within one of the animals there and then jump to humans. Just a tiny problem... no such exact virus existed in nature as far as we know before the pandemic, only close ones like the RatG -13 so a close virus like this had to evolve and then jump species from the wildlife in the market.
I would assume for a busy market the rotation of any one animal there is rather high. So let's say in came a infected animal with a virus that is as close to Covid as we know , again like the Ratg-13 , that animal then had to not only spread that virus to other animals around there but all of the infected animals had to stay there long enough so that the virus within either one of them mutates to eventually reach the right mutation that allowed the easy jump and quick spread into humans.

Every time one (or all) of the potentially sick animals there were bought, then brought home and cooked or eaten the necessary step for evolution was removed. Because before the necessary evolutionary steps whatever virus the animal had wasn't contagious to humans, apparently.

So it seems to me that if Covid was to originate at the market it wasn't enough for a sick animal to be taken there, it as well as the other animals infected had to stay there long enough for the virus to change and then jump species eventually.The other option of course is that Covid already evolved in the wild and then simply at some point someone came in contact with it and it happened in or around the market.
This has an even lesser chance because how spread out animals are in the wild VS in a market.

Is there evidence of the virus's evolution in the wild?

I personally am not aware of any specific evidence, maybe some others can comment on that.

The CCP controls everything that is published in China. One problem with having no independent media or government scrutiny is that there is no way to tell how much has been fabricated or suppressed.

And this is where the "buck stops" because the way I see it , current evidence only says that there is Covid genetic material found within the market.
But that genetic material had more than one way of getting there. Two immediate examples come to mind.
1) It evolved there from another wild virus within one of the animals
2) It was brought there by an infected human who visited the market

If indeed a safety breach happened within the lab and the person who took the virus out was asymptomatic , that person then could have easily transferred the virus to any one location in the city.

And we know now that Covid spread from humans back to animals (wild deer) so it seems if it got there from humans then it could have spread to the Wuhan wet market animals in a reverse way , namely , humans - animals.So how do we know whether the animals there became infected first or whether "patient zero" spilled the virus in the market which then got the animals infected.
As far as I'm aware , anyone who is susceptible to the spike protein entry can become infected with the virus.
It seems to me those animals instead of being the source could have easily been the "victims" that got infected from another source and we now can't tell the difference can we?

 

[pinball1970]

The animals at the seafood market must have come from the wild somewhere. I don't believe it could have originated at the market.

Is there evidence of the virus's evolution in the wild?

They do not have a clear evolutionary pathway for Ebola either, emerged in the mid 70s has a well known reservoir now but in terms why then? From which species? What mechanism?
Like Covid a few candidates but not clear.

I have been looking at a few papers on origins of certain diseases to get an insight. Measles was one, theme appears to be where there is a change in societal behaviour.
Either extending into areas closer to wild animals then living, farming, markets and consumption.
This on measles
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838858/

I posted a possible evolutionary mechanism from a paper 12 months ago, I will try and find it
Suffice to say it is very complex, involving multiple species and dozens of variants so finding the most evolutionary parsimonious family tree (it was more like a bush) will be a challenge for the geneticists and molecular biologists.

 

[PeroK]

They do not have a clear evolutionary pathway for Ebola either, emerged in the mid 70s has a well known reservoir now but in terms why then? From which species? What mechanism?
Like Covid a few candidates but not clear.

Here's a spurious argument. Can you spot the mistake?

There are almost 40,000 wet markets in China. If it came from a wet market, there is only a remote chance that it would have come from Wuhan, where the virus lab is! It almost certainly would have come from somewhere else less suspicious.

 

[pinball1970]

Here's a spurious argument. Can you spot the mistake?

There are almost 40,000 wet markets in China. If it came from a wet market, there is only a remote chance that it would have come from Wuhan, where the virus lab is! It almost certainly would have come from somewhere else less suspicious.

I was more referring to zoonotic events, which species first then where, then where again then us.
Agree the lab is remote given all opportunities from the markets.

 

[artis]

Here's a spurious argument. Can you spot the mistake?

There are almost 40,000 wet markets in China. If it came from a wet market, there is only a remote chance that it would have come from Wuhan, where the virus lab is! It almost certainly would have come from somewhere else less suspicious.

Add to that - a lab that had a known history of coronavirus research, including gain of function...

How weird that as little as a year or more ago this would have been a banned topic on PF and many other places.Now I'm not a virologist nor a biologist and I do acknowledge that practically all past viral epidemics have been chance accidents of natural origins but what probably sways me most in the direction of thinking it was a lab is two things, firstly China is not exactly known for perfect safety culture within their industry, and they have had lab leaks before , like the SARS case
https://genomebiology.biomedcentral.com/articles/10.1186/gb-spotlight-20040427-03

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC416634/

and secondly that Covid was so well adapted to humans from the start and interestingly (thank god) it seems that it managed to make just few more perfections to it's ability to spread before running out of steam , as it seems to have now.

 

[PeroK]

Agree the lab is remote given all opportunities from the markets.

Okay, let's not confuse the issue with my spurious argument.

 

[TeethWhitener]

It should be a banned topic on PF because it’s not science. There’s nothing falsifiable here. It’s just going to end up being one of those terrible political arguments where cherry-picked scientific findings are misrepresented by people who don’t understand them in the first place to further a preconceived set of beliefs.