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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?

#111

Post by echelon »

tgsovlerkhgsel wrote: post #93
s1artibartfast wrote: post #61

Earlier quoted context omitted.

>Thirdly, this paper emphasizes the strong impact of the COVID pandemic and asserts that understanding the origins of the virus would necessarily aid in preventing future pandemics. I strongly disagree. If of natural origin, there are a plethora of simple controls that could be implemented. Control doesn't necessarily need to be perfect. Some simple controls could be restrictions or bans on Commercial trade or transp…

I believe the research on the bat viruses was being done under BSL-2 conditions, which basically means normal lab practices, an autoclave for waste, and some of the work needs to be done in a biosafety cabinet. Of course, that assumes the procedures are strictly followed.

BSL-2 biosafety cabinets only have laminar flow hoods. They're effectively open air and depend upon proper protocols being followed.

Typically you're more concerned about what's getting into your BSL-2 hood than out.

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

#112

Post by tiagod »

timr wrote: post #81
m0llusk wrote: post #18

There are at least a couple of suspicious points in this study: First and foremost the central claim is that 5 potential restriction binding sites versus 2 means that SARS-CoV2 is non natural. That does not necessarily follow. Just as SARS-CoV2 is unusually infectious and damaging to humans it could just happen to have an additional 3 restriction binding sites. So there is nothing inconsistent with natural selection…

> First and foremost the central claim is that 5 potential restriction binding sites versus 2 means that SARS-CoV2 is non natural. That does not necessarily follow. Just as SARS-CoV2 is unusually infectious and damaging to humans it could just happen to have an additional 3 restriction binding sites. So there is nothing inconsistent with natural selection of viral characteristics, only a comparison between wild and l…

We've seen horizontal gene transfer in fish, was it aliens or natural selection?

Extremely unlikely events happen when an extreme amount of attempts are made, and natural selection amplifies them if they increase fitness

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

#113

Post by alchemist1e9 »

byteduck wrote: post #101
alchemist1e9 wrote: post #95

Earlier quoted context omitted.

Does your razor include a previous pandemic originating from a Soviet lab leak? https://en.wikipedia.org/wiki/1977_Russian_flu

Virus that escaped from a lab != intentionally engineered synthetic virus.

Obviously. I’m just pointing out his razor isn’t well informed.

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

#115

Post by projektfu »

bee_rider wrote: post #36
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…

> 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? It seems plausible, at least, that it leaked from the lab, in the sense that labs aren't magically impenetrable and leaks could happe…

Absolutely incredible to think that the national institute of allergy and infectious disease might fund research into infectious disease.

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

#116

Post by yellowcake0 »

jpeloquin wrote: post #91

"To avoid losing power with multiple comparisons, we focus our analysis on the BsaI/BsmBI sites in SARS-CoV-2 and compare the BsaI/BsmBI map in SARS-CoV-2 to all other restriction maps of all other CoVs used in our analysis." It's important to know whether or not the authors picked BsaI & BmBI blind, before looking at the genome. If they picked BsaI & BmBI with knowledge of the SARS-CoV-2 genome, that doesn't dodge t…

> It's important to know whether or not the authors picked BsaI & BmBI blind, before looking at the genome.

You could never convince me that these restriction enzymes were picked blindly, no bioinformatician I have ever met does science this way. There is a preliminary period of exploratory data analysis which is done before any hypothesis is put forward, and data dredging and leakage are rampant in the literature.

That's not to say that the spacing of BsaI/BsmBI restriction sites isn't noteworthy, just something to keep in mind.

To your point however, could someone comment on the suitability of BsaI/BsmBI for the in vitro assembly of synthetic coronaviruses? Is it all just about finding sites in the genome at the right locations which can be turned into restriction sites without disrupting any existing functional genetic elements? or is there more to it than that. If a research team were to come along and decide they wanted to engineer their own coronavirus, how likely would it be that they would choose these restriction enzymes?

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

#117

Post by stonemetal »

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…

I thought it was common sense to not believe in a thing if there is no evidence of a thing. The only way I am going to believe it was a lab leak is if credible evidence shows up. Until then it is an unknown.

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

#118

Post by Proven »

beiller wrote: post #29
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…

I have the opposite Occam's razor thoughts. My opinion is we are not capable of developing in a lab a virus that is so transmissible and survivable in human species only. I think the complexity of the virus machinery and its interactions inside of our bodies and immune system is beyond astronomical in complexity. It's laughable to suggest that we are so intelligent as to invent a better version of the machinery that…

No post body was provided.

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

#119

Post by dang »

puffoflogic wrote: post #114

I see dang no longer bothers to comment when he editorializes a title with a "?" to indicate a non-narrative headline.

Sometimes I do and sometimes not. That's nothing new.

I don't think it's so unclear why we'd put that up there.

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

#120

Post by mikeyouse »

shikshake wrote: post #38
fdgsdfogijq wrote: post #17

True story, in early January of 2020, on an academic virology forum, which I wont link, it was known the virus was synthetic. Before the story hit the mainstream media, professors were sharing data about the virus fingerprint. There were concerns about the integrity of the data shared by the Chinese. One specific comment I will never forget by a Harvard professor when discussing the implications: "Should we turn on t…

> which I wont link Why not? HN promotes logical evidence-backed discussion. The least you can do is link the forum.

He's talking about virological and making up threads that never existed. There was a lot of discussion in the early days about how it seemed possible it was synthetic based on the binding site affinity but as scientists do, they researched the literature, conferred with their colleagues and almost all came around to the virus arising via natural origin.

The early threads are super interesting in an anthropological sense:

https://virological.org/t/tackling-rumors-of-a-suspicious-or...

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