[alevskaya]

As someone who was a genetic engineer for a long while, watching HN talk about dodgy papers like this is painful.

This paper posits a completely crazy cloning strategy that makes no sense (ie doing something far more convoluted than typical bsaI/bsmbi seamless cloning workflows that breaks the whole point of "seamless" workflows), and then tries to use that to make a case for a genomic signature that we could look for. They then look at a handpicked set of viral genomes, but leave a bunch out and duplicate others (I think WIV04 and WHu are the same), and largely seem to be observing without realizing it that yes, recombination occurs among these viral lineages.

This isn't even getting into the fact that a restriction-ligation based cloning strategy would leave glaringly obvious fingerprints behind in the form of the hundreds of nucleotide differences that are present outside the cutsites across the lineages... it would be blindingly obvious if someone just cut-and-pasted sars-cov-2 from other studied genomes.

[rcpt]

They "handpicked" those because they're some of the most common. This is discussed in their paper.

The "completely crazy" strategy was state-of-the-art and published by the WIV in 2016 https://twitter.com/R_H_Ebright/status/1583868000888795137

[alevskaya]

I'm pretty tired of debating people who don't know biology here. Using seamless cloning methods is super common - but they don't work like the paper authors suggest they do. I misspent my youth doing reactions and workflows like these for over two decades.

What they're observing is homologous recombination between strains - all the sites they're claiming are found in nature.

Again - there would be a genetic signal the strength of the noonday sun burning your eyes out if sars-cov-2 was made by cut-and-paste at these sites. You wouldn't need this ridiculous circular argumentation to prove that point.

If we're linking to tweets, these two go into great depth about how ridiculous this paper is: https://twitter.com/Friedemann1/status/1583519970902048768 https://twitter.com/acritschristoph/status/15834864034169692...

[drpixie]

Yeah - Covid seems to be one a few topics that bring out "special" opinions. It's a pity, and not confined to HN, but seems to be a sign of the times.