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Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

biorxiv.org

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Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#171

Post by mikeyouse »

tripletao wrote: post #142
lamontcg wrote: post #131

Earlier quoted context omitted.

Oh dear... Yeah, the author affiliations on the title paper made me wonder if they knew what they were doing at all.

Their terminology would indeed seem wrong, but the WIV has apparently used a similar assembly strategy (leaving the sites in the final assembly) before: https://twitter.com/jbkinney/status/1583267221047869441 I'd worry about their false discovery rate, for the same reason I worry about the large number of parameters in Pekar's epi model. It's still an interesting result, though.

As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers. And even more worrying than the false discovery rate are all of the missing genomes they should be comparing. I fear they've left them off because they punch big ole holes in the theory... e.g.

https://twitter.com/zhihuachen/status/1583258714340892672

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#172

Post by natch »

AnonymousPlanet wrote: post #63
someuser54541 wrote: post #22

Genuinely surprises me that there are people out there who think or have been persuaded the virus is of natural origin. The lab right next to the market was literally studying and experimenting with the exact same type of virus. How can a someone think that that's just a coincidence? Add that to the fact that the funding for that research lab was approved by the same guy who become the de facto thought leader on the…

Studied and then escaped from a lab does not equal synthetic. Exactly nothing in your post supports a synthetic origin over a sample from nature that got studied in a lab. Jumping to these kinds of one sided conclusions should be a red flag.

It could also be studied and altered in a lab, and then escape.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#174

Post by bainsfather »

rossdavidh wrote: post #129

The opening line: "To prevent future pandemics, it is important that we understand whether SARS-CoV-2 spilled over directly from animals to people, or indirectly in a laboratory accident." Is that true? I mean I understand why people would be curious, but does it really matter, in terms of what we need to do? We know that viruses _can_ spillover from animals to people, and we know that viruses in a laboratory setting…

Yes, this is true.

If we knew that this pandemic came from a lab, that would have massive implications for how tightly we control this type of lab research - both in terms of whether we do the gof research, and also in how we run and regulate the labs. Surely you can imagine the reaction if, hypothetically, the world knew that this coronavirus was made in a lab and then escaped?

I'm amazed that you think otherwise - it's one of the nice things about hn that I occasionally encounter views that are so different from my own.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#175

Post by tripletao »

mikeyouse wrote: post #171
tripletao wrote: post #142

Earlier quoted context omitted.

Their terminology would indeed seem wrong, but the WIV has apparently used a similar assembly strategy (leaving the sites in the final assembly) before: https://twitter.com/jbkinney/status/1583267221047869441 I'd worry about their false discovery rate, for the same reason I worry about the large number of parameters in Pekar's epi model. It's still an interesting result, though.

As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers. And even more worrying than the false discovery rate are all of the missing genomes they should be comparing. I fear they've left them off because they punch big ole holes in the theory... e.g. https://twitter.com/zhihuachen/status/1583258714340892672

> As far as I've been able to read, those sites aren't in the final assembly in Shi's papers - just in the primers.

Where did you read that? Kinney explicitly asserts the opposite, but I can't figure out what he's referring to. Someone else linked to Figure S9 from their 2017 PLOS Pathogens paper, which indeed seems not to contain the site in the final assembly. I've edited my other comment here to reflect that.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#176

Post by whywhywhywhy »

rossdavidh wrote: post #129

The opening line: "To prevent future pandemics, it is important that we understand whether SARS-CoV-2 spilled over directly from animals to people, or indirectly in a laboratory accident." Is that true? I mean I understand why people would be curious, but does it really matter, in terms of what we need to do? We know that viruses _can_ spillover from animals to people, and we know that viruses in a laboratory setting…

> I don't know that I believe that the answer to which one happened in the case of covid-19, is all that important

It is when literally this week a version with an 80% kill rate but with the spread of the most transmissible was made in a lab for no good reason.

How many would die if that leaked out and the only reason it’s been made is just so some academic can get their name in a paper and earn some grant presumably.

The idea of we just have to trust that these labs are secure and competent enough when the fact they’re even making something so deadly raises questions about their competence. We need to start judging the people making these things with the potential to kill millions the same as we would anyone else building something that had the potential to kill millions.

I don’t see why playing with Weapons of Mass Destruction in a random lab is just considered fine when the weapon is invisible and can live inside your body or a mouse. At least Fat Man and Little Body couldn’t be carried off base by a single person.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#178

Post by jhanschoo »

callesgg wrote: post #15

I Honestly thought it was common belief that corona come from that lab in china. But now after reading this, I searched a bit and read up on it and I guess it is still a somewhat honest debate on the topic. Even if it was lab made, it would be sort of stupid to dig in to it, due to the political nature of the matter. What happened happened, most likely the release would have been accidental, so why play blame games.

I originally didn't think that it came from a lab. Primarily because flu epidemics have happened before and they were of natural origin and there hadn't been good evidence that it came from a lab. But my opinion changed as more good evidence started to turn up that suggested engineering.

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#179

Post by wnkrshm »

whywhywhywhy wrote: post #176
rossdavidh wrote: post #129

The opening line: "To prevent future pandemics, it is important that we understand whether SARS-CoV-2 spilled over directly from animals to people, or indirectly in a laboratory accident." Is that true? I mean I understand why people would be curious, but does it really matter, in terms of what we need to do? We know that viruses _can_ spillover from animals to people, and we know that viruses in a laboratory setting…

> I don't know that I believe that the answer to which one happened in the case of covid-19, is all that important It is when literally this week a version with an 80% kill rate but with the spread of the most transmissible was made in a lab for no good reason. How many would die if that leaked out and the only reason it’s been made is just so some academic can get their name in a paper and earn some grant presumably…

These kinds of experiments are going to be done either way - for example gain-of-function research on animal smallpox (which usually doesn't kill and can't infect humans) to make it lethal.

Experts on the matter (I read a book recounting smallpox research, not a domain expert myself [0]) were concerned more about the publishing of that research than about the research being done, since proliferation is deemed very easy in the field. You don't need resources as with nuclear weapons to reproduce research like that.

(Edit: typo)

[0] The Demon in the Freezer by Richard Preston

Re: Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2?

#180

Post by HelloNurse »

emsign wrote: post #155
rossdavidh wrote: post #129

The opening line: "To prevent future pandemics, it is important that we understand whether SARS-CoV-2 spilled over directly from animals to people, or indirectly in a laboratory accident." Is that true? I mean I understand why people would be curious, but does it really matter, in terms of what we need to do? We know that viruses _can_ spillover from animals to people, and we know that viruses in a laboratory setting…

I think the way in which we prevent lab made viruses to break free is fundamentally different from how prevention of a spill over would need to be done. Because it causes problems at the exact opposite ends of the chain of events. The first couldn't be more detached and isolated from nature, while the other happens if hygience and mixing of species is sloppily disregarded. This is a challenge if both sites are right…

> happens if hygience and mixing of species is sloppily disregarded

Evidence of lab negligence should not become a reason to neglect or defund research and prevention about animal spillover risks. Unfortunately, the two problem classes are synergic rather than mutually exclusive.

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