Covid-19 Origin
A Bayesian probability approach to ascertaining Covid-19 origin.
I've been posting about covid a lot, but I think understanding this was intentional is the key to understanding the class character of it.
"They took advantage of the pandemic" falls short of the truth, and so it both lets the ruling class off the hook, and it makes other pieces of the story impossible to make sense of.
This is going to be sort of a layman's book report on Quay's Bayesian Analysis of SARS-CoV2 Origin. I don't know who my intended audience is for this, but writing it helps me at least.
A Bayesian analysis concludes beyond a reasonable doubt that SARS-CoV-2 is not a natural zoonosis but instead is laboratory derived https://zenodo.org/record/4477081
He's getting sucked up to be discredited the same way those nurses were, so I want to get out ahead of that.
As soon as his paper came out, people started putting Falun Gong imagery over his face, doing headline quote alchemy to try and make him sound like Steve Bannon. Reply-guys spamming "CCP Virus" under his posts. I read all 200 pages and they're lying to you about what he says. It's a bone-dry statistical analysis of what we know and how likely that makes lab vs nature origins.
Four big arguments make up the backbone of it, one of which I've already posted about (the furin site.)
I haven't talked about the others, and from a quick search I don't think they've made their way into lay discussions much at all.
The questions are what does a natural OUTBREAK look like, and what does a natural VIRUS look like itself.
Seroconversion:
In a real zoonosis an endemic animal disease spends time in a reservoir species picking up random mutations until by chance it's able to spread among humans
When that day comes as far as we're consciously concerned it appears out of nowhere. But previous versions of the virus have been trying and failing to live in humans all along, and once you know to look you can go back and check old medical samples for an immune response to the half-baked version.
SARS and MERS' failed attempts show up before the start of their outbreaks in about 1/200 samples from the region.
(More if you select for people likely to be exposed, obviously.) So far we've checked almost 10 times that many samples for evidence of a half-baked covid and found nothing. No one seems to have encountered covid at all until it was already a well-adapted human disease.
Lack of posterior diversity:
I didn't know what this one meant when I saw it on the table, but it's similar. If you imagine a virus living in some reservoir species gradually rolling dice until it ends up fit to spread among humans you have to bear in mind:
the host species is passing each version among itself. When it finally hits the right combination to become a human disease it doesn't suddenly disappear, that version ready to make the jump is still also an animal disease. So the jump doesn't only happen once; the cow who finally infects a human with the right version is also infecting other cows who themselves infect more humans.
What this means is the family tree for human cases does not look like a pyramid with a single human patient zero.
There are multiple "original" human infections. And six months later when you look at different human infections you don't always find the same chain of mutations in the human hosts. Sometimes you see one chain, sometimes you see a totally different one, because the human cases should only be cousins.
For the first 200-ish SARS cases only HALF of them were descended from a previous human infection. The other half were dead ends as far as the human family tree, they were acquired directly from civets.
For covid, we've sequenced 200 THOUSAND cases. Every single one of them shares the same human ancestral host.
Now, if that's what a natural epidemic looks like, what does a natural virus look like?
It's become some kind of meme truism that you can't tell whether a virus is natural or lab-made by looking, but it turns out that's true in the same way you can't PROVE a photo of a cat is really a cat, maybe it's just dust on the lens that happens to look exactly like a cat.
The furin site isn't just important because of its presence — the way covid's RNA spells it is important.
Each amino acid can be indicated by multiple different combinations of nucleotide bases. They mean the same thing, but different species of virus, bacteria, plants and animals have different spelling conventions.
Different nucleotide base combinations (codons) work better or worse under different circumstances, so species develop their own idiomatic patterns.
Arginine, for example, can be spelled CGC, CGA, CGG, CGU, AGA, or AGG.
Covid and its relatives almost always use one of the latter three spellings- CGU, AGA, or AGG. They all work, but that's sort of the idiomatic convention for coronaviruses. By far the least common spelling is CGG.
The furin cleavage site on covid's spike protein — which is already suspect for other reasons — includes two arginines next to each other, which it spells "CGG CGG." This is the only occurrence of that spelling across the entire genomes of all the coronaviruses that infect humans.
On its own this doesn't really transform into meaning though. Covid has a highly unlikely bit of spelling in its furin site, so what?
Like the insertion of furin cleavage sites, violating the spelling conventions of a virus is a common lab procedure.
To improve infectivity in a target host species you can change parts of the virus to use the host's spelling conventions.
CGG-CGG is unheard of for a coronavirus, but by a slim margin it's the most common human spelling for double arginine.
This is one of the SARS gain of function experiments people have been doing since 2003, Daszak and Shi published on it in 2017. Plenty of others have used it too.
Here are those posts re: the very existence of the furin site
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The Quay paper itself is definitely worth reading, I've only scratched the surface of few biggest arguments in it.
For example, the original RaTG13 sample doesn't look right to be a bat fecal swab. And when I said CGG-CGG doesn't happen in any "human infective" coronaviruses? There is a single other known example. In RaTG13 (but in an area where covid doesn't use it, so they didn't share.)
And as this thread demonstrates, logs of RaTG13 make it appear it was one of WIV's off-the-books viruses. Hence the need to doll it up as if it had been a fecal swab.
Unroll available on Thread Reader
"No see'em" technique for editing viruses is also relevant here, Quay mentions it.
It's true it leaves no mark on the final product, but if you have the final virus and the second-to-last version you can see the zipper. RaTG13 looks like it has a zipper where covid has furin site
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