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The origin of Covid: Did people or nature open Pandora’s box?

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Re: The origin of Covid: Did people or nature open Pandora’s box?

#121

Post by verbify »

seymore_12 wrote: post #87
dehrmann wrote: post #80

Earlier quoted context omitted.

I assume practically every city in China has wet markets. I wonder how many cities have facilities that do virus research. It might actually be more than you'd assume; I have no idea what sort of research might happen at universities, You also have to weigh this with SARS Classic originating in China.

"a leading world center for research on coronaviruses" presumes some form of uniqueness amongst potential other similar facilities

Presumably they specialised in coronaviruses because of the proximity to a bat population with coronaviruses, making sample gathering much easier? Are there other areas with significant coronavirus hosts? Are there other labs that specialise in coronaviruses to the same extent? The two seem linked to me, although I have no background in this area.

So we'd a priori expect coronavirus to originate in the area with coronavirus hosts, whether it was through the lab or the market...

Re: The origin of Covid: Did people or nature open Pandora’s box?

#122

Post by ximeng »

novaRom wrote: post #66

There is an interesting peer reviewed paper published last month with analysis of existing facts about the origin of covid-19. A part from their conclusion: More than a year after the initial documented cases in Wuhan, the source of SARS-CoV-2 has yet to be identified, and the search for a direct or intermediate host in nature has been so far unsuccessful. The low binding affinity of SARS-CoV-2 to bat ACE2 studied to…

https://www.sciencedirect.com/science/article/pii/S187350612... Here is a paper that states that the furin cleavage site appears naturally in a number of viruses.

I looked into these lab origin theories for the furin cleavage site last year. The problem with it being a laboratory insertion was that although performing an insertion is relatively easy once you know what to insert, generally it’s beyond current science to independently create mutations for a specific purpose.

It’s a bit beyond me as a non-biologist but my feeling based on the literature was that the lab origin was unlikely. However it is pushed in certain circles partly for ideological reasons, based on evidence that is plausible at first glance but with a lot more digging not entirely convincing evidence.

However, there didn’t really seem to be much neutral expert analysis of the evidence.

Re: The origin of Covid: Did people or nature open Pandora’s box?

#123

Post by nl »

roca wrote: post #101
nl wrote: post #77

Earlier quoted context omitted.

Yeah, it's pretty good with Pangolin. This is a good summary of the current consensus: It is clear from our analysis that viruses closely related to SARS-CoV-2 have been circulating in horseshoe bats for many decades. The unsampled diversity descended from the SARS-CoV-2/RaTG13 common ancestor forms a clade of bat sarbecoviruses with generalist properties—with respect to their ability to infect a range of mammalian c…

This paper doesn't seem to have anything to do with the experiment I suggested.

a) There's no need for there to be an intermediary species. The "What is the probability of this pattern occuring in the case of a natural spillover? It's 1:atoms-in-the universe level" statement in the comment I replied to is just wrong - it's unusual, but nothing like as mind bogglingly impossibly rare are they claim.

b) Genetic analysis indicates that it most likely came from bats directly to humans, but picked up the ACE2 receptors from a Pangolin virus that was passed back to bats, evolved there and then infected humans. To quote the same nature article I lined above:

However, on closer inspection, the relative divergences in the phylogenetic tree (Fig. 2, bottom) show that SARS-CoV-2 is unlikely to have acquired the variable loop from an ancestor of Pangolin-2019 because these two sequences are approximately 10–15% divergent throughout the entire S protein (excluding the N-terminal domain). It is RaTG13 that is more divergent in the variable-loop region (Extended Data Fig. 1) and thus likely to be the product of recombination, acquiring a divergent variable loop from a hitherto unsampled bat sarbecovirus28. This is notable because the variable-loop region contains the six key contact residues in the RBD that give SARS-CoV-2 its ACE2-binding specificity27,37. These residues are also in the Pangolin Guangdong 2019 sequence. The most parsimonious explanation for these shared ACE2-specific residues is that they were present in the common ancestors of SARS-CoV-2, RaTG13 and Pangolin Guangdong 2019, and were lost through recombination in the lineage leading to RaTG13. This provides compelling support for the SARS-CoV-2 lineage being the consequence of a direct or nearly-direct zoonotic jump from bats, because the key ACE2-binding residues were present in viruses circulating in bats.

and:

Although the human ACE2-compatible RBD was very likely to have been present in a bat sarbecovirus lineage that ultimately led to SARS-CoV-2, this RBD sequence has hitherto been found in only a few pangolin viruses.

https://www.nature.com/articles/s41564-020-0771-4

Re: The origin of Covid: Did people or nature open Pandora’s box?

#124

Post by DoreenMichele »

I don't really think it matters a whole lot whether it jumped species or was created in a lab. I think the issue is that there are nearly 8 billion people on the planet and that fact has somehow fundamentally changed how disease spreads and mutates.

We need to be figuring out how to deal with that. Wondering where it came from is mostly neither here nor there.

We aren't going to magically stop doing lab experiments if we can know for certain that it started in a lab. If we can determine for certain that this jumped species, welp, it isn't the first time and it won't be the last.

Re: The origin of Covid: Did people or nature open Pandora’s box?

#125

Post by dirtyid »

misja111 wrote: post #104
guesst wrote: post #31

Earlier quoted context omitted.

I really think it's just the other way around. The more people make this about China, the less likely we are to find out the truth. If it's used as a geopolitical chess piece, it will get bogged down forever in political mud, which is kind of where the question is right now anyways. People will decide what they think about it based on how they feel about China. That's crazy.

It's too late to keep politics out of this, politics were at the heart of this from the very start. Without politics the consequences of the outbreak would probably have been much less severe. In the beginning of January 2020, president Trump was already informed by an advisor who had close contacts in Wuhan that the outbreak was much more severe than China made it look like. But he chose not to act on that, because…

>So this is not about 'people making this about China', it has been China from the start

Military games / Fort Detrick vaping disease troll was in response to Tom Cotton and co. formally spewing lab leak theory. Note earlier date in Feb.

https://www.washingtonpost.com/politics/2020/02/16/tom-cotto...

US politicized first, when soft measures failed a month after warning Wuhan lockdown. There was ample warning, enough that many of PRC neighbors with high traffic contained well with at least some effort in coordination. PRC position up until then was let science figure it out, Wuhan was very covid19 was first discovered but doesn't mean originated there. The brief domestic deflection in early Feb was possible import from ASEAN. Even early PRC "dis"info campaigns emphasized harsh lockdown not lockdown skepticism. Countries that didn't take Wuhan lockdown seriously got burned. Queue west being prominent source of exporting covid world wide by taking lax measures. This is seen in import statistic of every country that rigorously tracked imported covid cases - PRC exported very little cases, and essentially none few weeks after lockdown. North America / Europe, magnitudes more.

Re: The origin of Covid: Did people or nature open Pandora’s box?

#126

Post by astrange »

seymore_12 wrote: post #61

If we apply Occam's razor [1] decision between "Wuhan, however, is home of the Wuhan Institute of Virology, a leading world center for research on coronaviruses" and "Wuhan, there is a wet market where under certain conditions virus can jump from bat to monkey to person" is relatively straightforward But then, we should probably also apply Hanlon's razor [2] "never attribute to malice that which is adequately explain…

> If we apply Occam's razor [1] decision between "Wuhan, however, is home of the Wuhan Institute of Virology, a leading world center for research on coronaviruses" and "Wuhan, there is a wet market where under certain conditions virus can jump from bat to monkey to person" is relatively straightforward

The conclusion that "the coronavirus originated in Wuhan therefore the Wuhan Institute caused the virus" could be backwards even if the correlation is real. It could be the virology institute is in Wuhan because there are bat coronaviruses near there.

Re: The origin of Covid: Did people or nature open Pandora’s box?

#127

Post by andreareina »

Clewza313 wrote: post #116
throwaway4good wrote: post #102

For an alternative perspective on this - the official WHO report covers the lab hypothesis: https://www.who.int/health-topics/coronavirus/origins-of-the... Origins of the SARS-CoV-2 virus And unlike the arrticle here, this report is based upon interviews with employees at the lab and various form of documentation provided by the lab. Including health records of the employees. For more from one of the WHO people: http…

So I've been pretty skeptical of the lab theory to date, but: > We visited the Wuhan Institute of Virology, which is an impressive research facility, and looks to be run well, with due regard to staff health. We spoke to the scientists there. We heard that scientists’ blood samples, which are routinely taken and stored, were tested for signs they had been infected. No evidence of antibodies to the coronavirus was fou…

I'm reading it as shorthand for, "The prior probability of a lab escape is low, and we didn't see much evidence for it in this particular case, therefore we conclude that this instance being a lab escape is low", which is a fine argument.

Re: The origin of Covid: Did people or nature open Pandora’s box?

#128

Post by astrange »

carlmr wrote: post #86
dehrmann wrote: post #80

Earlier quoted context omitted.

I assume practically every city in China has wet markets. I wonder how many cities have facilities that do virus research. It might actually be more than you'd assume; I have no idea what sort of research might happen at universities, You also have to weigh this with SARS Classic originating in China.

>SARS Classic The remakes are always worse.

This one's #3. MERS (#2) was the deadliest of all, though it didn't spread so well.

Re: The origin of Covid: Did people or nature open Pandora’s box?

#129

Post by strogonoff »

DoreenMichele wrote: post #124

I don't really think it matters a whole lot whether it jumped species or was created in a lab. I think the issue is that there are nearly 8 billion people on the planet and that fact has somehow fundamentally changed how disease spreads and mutates. We need to be figuring out how to deal with that. Wondering where it came from is mostly neither here nor there. We aren't going to magically stop doing lab experiments i…

The issue with COVID is the precedent of attempts of trying to identify the origin of this new disease being sabotaged for seemingly political reasons (and with no obvious repercussions).

It seems intuitive that knowing the origin of the virus (sample escaping a lab or pure nature) could help prevent similar cases in the future or deal with them more efficiently. Is my intuition wrong here?

Re: The origin of Covid: Did people or nature open Pandora’s box?

#130

Post by octoberfranklin »

thu2111 wrote: post #48
Mountain_Skies wrote: post #11

Earlier quoted context omitted.

It's important to know and it's important not to know. Both paths have mostly negative outcomes. The best path is for it to have been natural, second best is accidental. Intentional is unfathomable and has unlimited downside. We should all hope that's not the case here.

The article doesn't support the case for it being intentional. Negligence at best. One of the things Wade demonstrates is that China was most likely doing research on CoV viruses in ordinary labs with nothing more than gloves and a white lab coat. The standard photo of Dr Shi is of her in a pressurised bubble suit but that's bsl4 and virologists don't like working in those conditions because it slows them down. So th…

I don't believe the lab escape was even remotely deliberate; however:

> the virus has no characteristics that would make for a good weapon of any kind.

Quite the contrary. The virus clearly favors authoritarian societies whose citizens will let their government weld them into their apartments. Just look at the death rate in China compared to the US and Europe. The only free societies that have come out unscathed are isolated islands (NZ, Taiwan).

That said, there is zero chance that the CPC had foreknowledge of this. They got very, very lucky.

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