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Lab Leak 2.0?

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Re: Lab Leak 2.0?

#181

Post by cassepipe »

civilized wrote: post #129

This post takes many screens of text to get to the point: we don't know how omicron evolved from its last known ancestor in Spring 2020 to November 2021, when it burst into the world stage. Ergo, lab leak. It's a great deal of throat-clearing for a one-sentence argument from ignorance. Alina Chan has pointed to a more plausible alternative in this comment https://news.ycombinator.com/item?id=29789480

The main argument is the ratio of silent vs non-silent mutations. So you are actually making a false presentation of her argumentation and I believe this is called... slander ?

Although the claim that there's little chance for Omicron to have developped resistance to antibodies in an immunodepressed patient (that is without antibodies) needs to be adressed to.

I would love to see a reasonable fact-based response to the article that actually take into account the points being made.

Re: Lab Leak 2.0?

#182

Post by zarzavat »

TeeMassive wrote: post #159
epgui wrote: post #154

Earlier quoted context omitted.

Such gaps in phylogenetic trees actually happen all the time.

Other viruses are not scanned and studied for other variants like Covid-19 is and Omicron is the only outlier by a large margin.

Sure and if it had arisen in Europe then those questions would have to be asked. But it's a safe assumption that very little analysis is happening in southern central Africa. It doesn't seem that outrageous that a parallel line has been percolating there for quite some time and only recently gained a mutation or two that allowed it to shoot to stratospheric levels.

Re: Lab Leak 2.0?

#183

Post by scrumlord »

ayjchan wrote: post #37

This is Alina Chan, one of the co-authors of Viral: The Search for the Origin of Covid-19. In defense of a natural origin of Omicron, this study describes the remarkable evolution of SARS-CoV-2 during convalescent plasma treatment of an immunosuppressed patient for 3-4 months; the mutations also reduced sensitivity to neutralizing antibodies: https://www.nature.com/articles/s41586-021-03291-y We know that there is a…

[flagged]

Re: Lab Leak 2.0?

#184

Post by ufo »

dljones wrote: post #125
ufo wrote: post #46

Earlier quoted context omitted.

Another thing that the blog post appears to be unaware of is that the absence of samples showing the step-by-step evolution towards omicron doesn't mean that this didn't happen. A lot of places in the world don't have the resources to do covid testing and genomic surveillance.

Absence of evidence is not evidence of absence, yes. But take another look at the phylogenetic tree. Those are huge gaps. See also this article describing how good South Africa is at spotting and sequencing variants."The reality is that southern Africa is a top international powerhouse of COVID-19 surveillance." https://www.businessinsider.com/how-southern-africa-detected...

The hypothesis is that it could have originated in a different country and was only identified after it arrived in South Africa.

Re: Lab Leak 2.0?

#185

Post by TTPrograms »

The sample distribution of viruses is incredibly important for this sort of analysis, and much of the argument here only makes sense through the lens of uniform virus sequencing. If you have imbalanced sequencing and imbalanced transmission you can also explain these differences.

The important thing is that mutations occur at a certain rate per virus per unit time. If you have an isolated population that's sequenced infrequently then (1) that strain will appear to evolve more slowly as there's a smaller population capable of mutating, and (2) once that strain is sequenced it's going to look far from what you've seen already since you haven't been tracking the intermediate mutations in this population.

The S/N ratio can be analyzed in terms of a random walk in high dimension. Variance in these walks grows over time (in terms of distance from origin, i.e. number of mutations), so the discrepancy doesn't seem super far from what's plausible under the null hypothesis. Perhaps someone can do the math on that.

The hypothesis merits further investigation, but the strength of the evidence presented here really requires some complex statistical analysis to determine if innocuous explanations fit. The analysis is far more complex than I would expect an epidemiologist or virologist to apply in the course of their work.

Re: Lab Leak 2.0?

#186

Post by dawnerd »

ibejoeb wrote: post #35

There is no legitimate reason for this to be flagged. What happened to the vouch option?

There sure is. I flagged it because it’s speculation and conspiracy stuff shouldn’t be on HN. Sure it could be a leak but armchair detective work can be dangerous.

Re: Lab Leak 2.0?

#187

Post by molyss »

monocasa wrote: post #9

All of the GoF research procedures I've read stress natural evolution, but still rely on random mutations at the end of the day, which would still leave you with a natural looking count of silent mutations in the general case. As a GoF researcher you don't want to cull 'silent' mutations because those are a major source of building blocks for useful mutations.

Honest question : as a GoF researcher, wouldn’t I generate thousands (millions) of mutations from my 1st virus pool, which would each have a low number of mutation (s or n) compared to the original strain, then “select” the most resistant ones from that 1st pool of mutants, and use those to repeat the process ? I’d expect the result to be much richer in n mutation than in silent ones, just because I forced their selection. Am I missing something?

Re: Lab Leak 2.0?

#188

Post by zzt123 »

d23 wrote: post #167
Sevaris wrote: post #98

Earlier quoted context omitted.

I feel like you're unfairly biased. The author doesn't say what you think they do. All they're saying is that there was a lab leak of delta in 2021 as an example of lab leaks being possible. They do not argue that this was the source of delta, nor that this was the source of any other strain. Just that it happened. Sorry, the hysteria on HN is ridiculous. At least read the damn thing and try to be objective about it.

Where to even begin with this. I'm unfairly biased because I misread what he said? After re-reading, I can see that he may not have been making the point I thought he was making. I'd argue he should make a point like that more clear, but fine, it's on me that I misinterpreted. > the hysteria on HN is ridiculous. "Hysteria"? How do you get hysteria from my response? Because I asked for citations for what I thought was…

"For example, we know that the delta variant of SARS-CoV-2 leaked out of a lab in Taiwan in late 2021." - is exactly (mechanically) true in that Delta did leak out of a lab in Taiwan in late 2021.

This statement does not declare that Delta’s origins were a lab leak, since late 2021 is a year after Delta was first detected in late 2020. Can’t have your origins in the future until time travel is invented.

Seems therefore more proper to interpret the statement exactly as written rather than add additional conspiratorial inferences.

Re: Lab Leak 2.0?

#189

Post by zzt123 »

john_moscow wrote: post #115

What kinda raised suspicions about Omicron for me is that it propagates considerably faster in the bronchial tissue, while being much slower in the lungs [0]. Given the current state of biotech, it is not possible to just edit the viral RNA achieving the desired clinical result, but is entirely feasible to keep applying minor edits and measuring the propagation rate in different tissues in vitro, effectively optimizi…

I am reminded how even in as controlled an environment as China, He Jiankui broke the rules.

Re: Lab Leak 2.0?

#190

Post by boublepop »

> “If a $1000 PhD side project could kill millions of people, we must end viral [gain-of-function research], or it may end us.”

This sentimental reminds me of a talk given by a government bomb expert where a naive student asked “why do we allow the ingredients for bombs to be sold in store, shouldn’t we ban them all?”

The answer of cause is that if we do that, then we suddenly don’t have gasoline, orange juice, basic electronics, fertilizer or even just basic sanitation products available anymore, but of cause anyone who wanted to make a bomb would still be able to do so easily.

If it really is the case as pitched that 1000$ gets you a virus that will bring down nations, why on earth would we leave the field only to bad actors? Would that not just make it ever so more important that such researched happened openly and under well funded, strictly controlled conditions so we know what to expect and so we can start to develop plans for counter measures for when the next 9/11-like fanatic driven attack comes along?

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