adsfew t1_jacuefn wrote on February 28, 2023 at 2:59 PM

Reply to comment by rayinreverse in Little-known scientific team behind new assessment on covid-19 origins by asdf3

96.2% actually seems massively different to me.

With a genome size of ~30 kb and proofreading ability, that's over 1000 SNPs acquired between a hypothetical leak and the sequencing of the wild-type virus. Omicron has > 30 amino acid mutations, so only ~100 SNPs—a whole order of magnitude lower than the link to a lab strain.

Obviously you can't directly compare a virus to a mammal and the generation times are wildly different, but humans and chimps share about 96% of the genome. 96% similarity means things were phylogenetically related at some point, but I'm skeptical that a direct leak would only be 96% similar.

Squirrel_Inner t1_jadl3dk wrote on February 28, 2023 at 5:52 PM

Actually, it was the entire sequence except for the RBD, according to virologist Bob Garry:

“I lined n-CoV” — so, the new coronavirus — “with the 96 percent bat Coronavirus, sequenced at the WIV. Except for the RBD” — and that means receptor-binding domain — “the S proteins are essentially identical at the amino-acid level, while all but the perfect insertion of 12 nucleotides, that adds the furin site, as to is over its whole length, essentially identical. I really can’t think of a plausible natural scenario where you get from the bat virus or one very similar to it to [SARS-CoV-2] where you insert exactly 4 amino acids 12 nucleotide[s] that all have to be added at the exact same time to gain this function…. I just can’t figure out how this gets accomplished in nature.”

Taken from this article: https://theintercept.com/2022/05/06/deconstructed-lab-leak-covid-katherine-eban/

rayinreverse t1_jacvbgs wrote on February 28, 2023 at 3:05 PM

That’s a really solid point, and I have no legitimate counter to it. But also the town that has a SARS lab is where a SARS virus originates and we are skeptical it came from the lab, and convinced it was from a wet market? If I show up with a piece of Swedish furniture that we need to build and the instructions have no words only pictures, you’re going to be pretty fucking convinced it’s from IKEA even if I continue to say it’s not.

adsfew t1_jad5q2k wrote on February 28, 2023 at 4:14 PM

I'm not an investigator and I don't have their facts or finding, so this is all just an extremely uninformed opinion.

I absolutely think a leak is plausible. But if 96% really is the similarity to the closest lab strain, then I just wanted to put in context how dissimilar that is genetically. I think it's one of those times where 96% sounds really high, but genetically it's pretty divergent imo.

It's still totally possible that it's a leaked strain and maybe the lab just destroyed the records of that strain or something. But taken on its own, 96% isn't that high in this context.

Electric-Frog t1_jad8b5c wrote on February 28, 2023 at 4:31 PM

And if all of the pieces were labelled "Ikeya", then it would be pretty obvious that it's not IKEA.

There is no way that 3 months of limited spread in a small area would cause 10 times as much variance as 2 years of borderline uncontrolled spread over a large portion of the world.