The latest version with major updates is here. [This version is substantially changed based on: (1) my realizing I’d forgotten to use coincidence in timing, analogous to coincidence in location; (2) A wonderful twitter exchange with pseudonymous users making me aware that codon usage in long insertions is substantially different from that in the overall genome. It’s awkward to make such big adjustments after posting an initial version, but this is an unusual area where the normal lively open pre-publication scientific conversations are almost impossible to find. The one sentence that has been in italic boldface from the start is unchanged.
https://twitter.com/daoyu15/status/1679455533743607810 there were actually human DNA from southeast Asia and not Wuhan residents inside, and it also happens to be sequenced within 2 weeks of December 2019–before the first WA1 genome and before even they removed the criterion for “wet markets in Wuhan” and “3 days antibiotics fail” requirement. Chinese firms are not allowed to preserve samples of unknown provenance for more than 14 days, and This makes these samples particularly significant. They were the first WA1 discovery anywhere in the world.
"The case data Worobey et al. used omitted about 35% of the known cases for unspecified reasons, a crucial problem". This has been clearly addressed, and is based on how "cases" are defined (well known challenge in epidemiology). Just one of many cases where you cherry pick from Lab Leak proponents and ignore more recent data that is in conflict with your belief (and it's really nothing more than that) in the Lab Leak origin. Much of the back and forth between experts is on Twitter.https://twitter.com/flodebarre/status/1632811845458227206
This is incredible work, Michael. Thank you. I'll share it in my weekly news review tomorrow.
Thank you Nik, but I prefer to think of it as credible work.
You have me there, sir, for my poor use of language :) I find it entirely credible.
Also, the issue with Sangon is that https://twitter.com/daoyu15/status/1705468874051948900
There is https://web.archive.org/web/20230705200145/http://adeno-news.com/2022/08/09/unique-sars-cov-2-genomes-found-in-antarctic-samples-raises-questions-about-sars-cov-2-origin-lineages/
https://twitter.com/daoyu15/status/1679455533743607810 there were actually human DNA from southeast Asia and not Wuhan residents inside, and it also happens to be sequenced within 2 weeks of December 2019–before the first WA1 genome and before even they removed the criterion for “wet markets in Wuhan” and “3 days antibiotics fail” requirement. Chinese firms are not allowed to preserve samples of unknown provenance for more than 14 days, and This makes these samples particularly significant. They were the first WA1 discovery anywhere in the world.
About that “two strains” claim— http://archive.md/JVFuc http://archive.md/GME5L https://www.biorxiv.org/content/10.1101/2022.10.10.511625v1 https://www.mdpi.com/2036-7481/14/1/33
In fact the very strains that Pekar say doesn’t exist is inside Pekar’s own alignments.
The very same A/B lineage intermediates.
"The case data Worobey et al. used omitted about 35% of the known cases for unspecified reasons, a crucial problem". This has been clearly addressed, and is based on how "cases" are defined (well known challenge in epidemiology). Just one of many cases where you cherry pick from Lab Leak proponents and ignore more recent data that is in conflict with your belief (and it's really nothing more than that) in the Lab Leak origin. Much of the back and forth between experts is on Twitter.https://twitter.com/flodebarre/status/1632811845458227206
It's not really a back-and-forth (just Flo) ,but I will modify to acknowledge that the omitted cases may well have been not lab-confirmed.