Slack / Private Message Drop — page 86

Yup - definitely well before the outbreak began (ohhhh, but what about all those parked cars, huh...?) [2020-06-18 17:51:49] [Eddie Holmes] I can easily imagine that the Liu et al. data has influenced the assembly in the later papers but (i) why would this only impact nonsynonymous sites and (ii) how could it possibly have produced the human sequence when no one knew what that was? Liu et al. is clearly a 'blind' study. I've just emailed Tommy if he can assemble the same RBD without the Liu et al. data and/or if it has been Sanger sequenced. The other group have a second paper on the clinical manifestations that I am helping them with. They've sequenced the virus again. I've also asked if they can assemble the same RBD without the Liu et al. data and/or if it has been Sanger sequenced. [2020-06-18 17:58:51] [Eddie Holmes] The similarity between the RBD and the Guangdong pangolins from the Liu et al. study alone was noted on Virological in late January. How can Liu et al. have possibly known what the human RBD would have looked like? ht tps://virological.org/t/ncov-2019-spike-protein-receptor-binding-domain-shares-high-amino-acid-identity-with-a-coron avirus-recovered-from-a-pangolin-viral-metagenomic-dataset/362 [2020-06-18 18:26:41] [Kristian Andersen] Here's the manuscript from her - please keep confidential. I haven't read it yet. [shared file(s): Matters Arising Chan Zhan 2020.pdf] [2020-06-18 18:28:37] [Kristian Andersen] I think the main problem here is not really how that pangolin sequence ended up having that RBD, but rather whether there's anything sketchy here from a scientific standpoint. These studies are presented each as independent evidence of the pangolin virus RBD, but if all those papers are relying on a third data set - and don't actually have _any_ data from this very critical CoV RBD, then that's an issue. [2020-06-18 18:30:48] [Kristian Andersen] I don't really see how this changes anything from the evolutionary perspective - because seeing it even once is very strong evidence. But there's no denying that if these studies have to be modified (or possibly even retracted), then that is going to send a nuke into the whole evolution conversation - whether justified or not. [2020-06-18 18:36:25] [Eddie Holmes] Can we do a quick Zoom now. [2020-06-18 18:39:58] [Eddie Holmes] Tommy's paper very clearly stated the provenance. Can't speak for the others. [2020-06-18 18:40:09] [Kristian Andersen] https://us02web.zoom.us/j/9673242666 [2020-06-18 19:14:39] [Eddie Holmes] [thread - ID: 2020-06-18 19:14:39] Hi Eddie, Although the pangolins used in Liu's study overlap with ous, we did not used Liu's data in this new paper,and assemble four new virus genomes. In addition, we amplied and sequenced (Sanger sequencing) the complete S genes from lung tissues and virus isolate independently, and comfirm the high-throughput sequencing. As showed in Figure S2, the new genomes almost the same as our previous genome and Lam's. Therefore, i am sure that the previous data is correct.