"I’m talking about omicron, and no, it’s not a joke."
I'm lost, who is the author? Without names and credentials this just looks like some kind of covid fan fiction or something.
Lab Leak 2.0?
271–280 of 319 posts
Re: Lab Leak 2.0?
#272I'm open minded, but my bullshit detectors started going off around the point where it was casually implied that we all know and it is widely accepted that delta was leaked from a lab. I tried googling it but could find nothing. Then I looked at the two sources the author links: > https://www.taiwannews.com.tw/en/news/4371212 > https://www.taiwannews.com.tw/en/news/4382708 Neither of these have nearly enough evidence…
You’re missing something. The author is saying that there was a lab leak involving delta , not that delta originated via a lab leak . The latter claim would indeed be a red flag, but the former is just describing a very well-documented event.
"... very well documented event"
Re: Lab Leak 2.0?
#273Earlier quoted context omitted.
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 therefo…
Can you explain the Delta variant lab leak theory for those of us who aren't caught up on conspiracy theories?
Re: Lab Leak 2.0?
#274Earlier quoted context omitted.
Without looking more at the variants themselves and just going by the numbers in the post, it’s entirely plausible. It’s not likely, but plausible. Mainly because we are talking rare events. If the level of success is 33/3.5 (9.42), we’d expect that 4 (or less) silent variants would happen with a probability of ~ 0.042 (Poisson X Anytime you look at numbers like these, remember with a big denominator, even rare event…
If it was the case that the absolute number mattered, we would be able to sample different "Omicron-like" variants and observe various ratios such as 33N/10S, 33N/15S, etc. mutations. But according to the data presented, we don't: We only see a single (kind of) Omicron, the one with (about) 33N/4S mutations, presumably spilling over by a single event, so I don't see how your conclusion follows.
The sequence of mutations leading to Omicron is a one-off. Presumably, if there were a thousand variants with the same N mutations as Omicron, you'd see ratios like the ones you describe, but there's only one Omicron. The previous poster is pointing out it's plausible (~5% chance) that the path Omicron took has only 4 S mutations.
Re: Lab Leak 2.0?
#275I'm open minded, but my bullshit detectors started going off around the point where it was casually implied that we all know and it is widely accepted that delta was leaked from a lab. I tried googling it but could find nothing. Then I looked at the two sources the author links: > https://www.taiwannews.com.tw/en/news/4371212 > https://www.taiwannews.com.tw/en/news/4382708 Neither of these have nearly enough evidence…
The author did not claim that Delta's origin was a lab leak. Just that there was one isolated case of it. And so it stands to reason, other lab leaks may also be occurring.
"it stands to reason"
We should note you're talking about covered up lab leaks where all of the participants are conspiring to keep it secret because of convoluted motivations. It doesn't "stand to reason" that this happens at all, let alone is the normal case that we should all assume.
Re: Lab Leak 2.0?
#276Earlier quoted context omitted.
Without looking more at the variants themselves and just going by the numbers in the post, it’s entirely plausible. It’s not likely, but plausible. Mainly because we are talking rare events. If the level of success is 33/3.5 (9.42), we’d expect that 4 (or less) silent variants would happen with a probability of ~ 0.042 (Poisson X Anytime you look at numbers like these, remember with a big denominator, even rare event…
If it was the case that the absolute number mattered, we would be able to sample different "Omicron-like" variants and observe various ratios such as 33N/10S, 33N/15S, etc. mutations. But according to the data presented, we don't: We only see a single (kind of) Omicron, the one with (about) 33N/4S mutations, presumably spilling over by a single event, so I don't see how your conclusion follows.
There are two different (and independent) forces at play here: mutation and natural selection.
The question is, given a known ratio of 3.5 NS/S, what is the likelihood that there would be only 4 non-silent mutations in any random strain (like omicron)? What the mutations are is irrelevant to this question. (I will use mutations and variants interchangeably below, but both mean a single change in the genetic code for the virus).
Because we are dealing with integer counts, you can’t really have 3.5 mutations. You can only have 1, 2, 3, etc. So, 3.5 is just the average of all ratios. When dealing with count data like this, the Poisson distribution is what you use. When you have 33 non-silent mutations, you could have 1, 2, 3, etc silent mutations. We’d expect to see 9.4 (33/3.5), but you can’t have 0.4 of a mutation, only integers. There is a specific probability associated with each possible value (1,2,3…), and that can be calculated using the Poisson distribution.
You are most likely to see 9 or 10, but all other values are also possible. To calculate how likely you are to see exactly 4 silent variants, you use the Poisson distribution. Again, we will expect that the rate should be 33/3.5 silent variants.
In R, you’d do:
dpois(4, 33/3.5)
[1] 0.02647255
We normally think in terms of “how likely is it that we’d see 4 or fewer mutations”, so we re-run the test for 0:4 and add them up:
sum(dpois(0:4, 33/3.5))
[1] 0.04211515
Given these numbers, I’d say it is plausible that you’d see this ratio of NS/S mutations occur naturally. It would be rare, but still somewhat expected to occur.
Now this says nothing about what the mutations are, or why the omicron strain is so prevalent. This is where natural selection takes over and this combination of mutations is out competing all others.
Re: Lab Leak 2.0?
#277Earlier quoted context omitted.
If it was the case that the absolute number mattered, we would be able to sample different "Omicron-like" variants and observe various ratios such as 33N/10S, 33N/15S, etc. mutations. But according to the data presented, we don't: We only see a single (kind of) Omicron, the one with (about) 33N/4S mutations, presumably spilling over by a single event, so I don't see how your conclusion follows.
There are two different (and independent) forces at play here: mutation and natural selection. The question is, given a known ratio of 3.5 NS/S, what is the likelihood that there would be only 4 non-silent mutations in any random strain (like omicron)? What the mutations are is irrelevant to this question. (I will use mutations and variants interchangeably below, but both mean a single change in the genetic code for…
I was not taking an issue with the calculation of the 4% chance, but rather with this phrase: "But with millions of people infected, this ratio of S/NS variations would still happen at a pretty high absolute number."
I thought you were implying that since this was a 4% chance happening over millions of infection events, it was a virtual certainty, and thus the 4% factor made this highly probable. To which I counter argued, the 4% chance matters and should be accounted as a factor in a "natural vs lab leak" model, because everything seems to point that "a variant as infectious as Omnicron appears" was a single event.
Re: Lab Leak 2.0?
#278Earlier quoted context omitted.
The author did not claim that Delta's origin was a lab leak. Just that there was one isolated case of it. And so it stands to reason, other lab leaks may also be occurring.
"it stands to reason" We should note you're talking about covered up lab leaks where all of the participants are conspiring to keep it secret because of convoluted motivations. It doesn't "stand to reason" that this happens at all, let alone is the normal case that we should all assume.
No, we're not talking about cover ups. We're talking about studying the virus and it escaping by accident. Also, there is a history of lab leaks so it stands to reason...
Re: Lab Leak 2.0?
#279Earlier quoted context omitted.
You are confusing our lack of knowldege of the intermediate steps with the lack of interim steps. They might simply have been lost in the crowd or not even noticed, depending on where they were posted. How carefully have we studied the variants in animals?
No, I'm not doing that. We might not yet have sampled the intermediate steps, if they exist, but it's inevitable that we will do so if it has a natural origin. Given the phylogenetic distance between the omicron cluster and its root in the phylogenetic tree, there should be several hundred to thousand intermediates if it's naturally occurring, of which we should be sampling many dozens (modulo selective pressure and…
Why should it be inevitable?
How long do non dominant variants survive inside and outside a host?
We don't even know in which country omicron originated even less who was patient zero.
We could easily miss whole strains of the virus but because non of them lead to a new dominant variant we never know the even existed.
Re: Lab Leak 2.0?
#280Earlier quoted context omitted.
There are two different (and independent) forces at play here: mutation and natural selection. The question is, given a known ratio of 3.5 NS/S, what is the likelihood that there would be only 4 non-silent mutations in any random strain (like omicron)? What the mutations are is irrelevant to this question. (I will use mutations and variants interchangeably below, but both mean a single change in the genetic code for…
I was not taking an issue with the calculation of the 4% chance, but rather with this phrase: "But with millions of people infected, this ratio of S/NS variations would still happen at a pretty high absolute number." I thought you were implying that since this was a 4% chance happening over millions of infection events, it was a virtual certainty, and thus the 4% factor made this highly probable. To which I counter a…
It is a virtual certainty that a 4% likely event would occur given the millions of people that have been infected (and the subsequent mutations occurring within each of them). But that doesn't have anything to do with omicron specifically... and I certainly don't intend to suggest a correlation between NS/S and infectiousness. Mutations have a certain rate, but the events themselves are random.
I guess a different way to say this is -- It makes no sense to use the NS/S ratio as a rationale to claim that omicron was a lab-leak. The 33/4 ratio should be rare, but not unexpected. If you were going to claim that, the absolute increase in mutations would be a more compelling argument, but again, there are plausible reasons for how that could occur in the wild too.
We have very incomplete sampling data, so looking at a single strain and determining risk, or likelihood, is very difficult.