Slack / Private Message Drop — page 88

P.S. Tommy also told me that some other (EgoHealth Alliance I think) pangos were CoV positive. Not quite sure what CoV though. [2020-06-19 00:42:39] [Eddie Holmes] From Tommy: For the accuracy of the RBD, the GD sequences available now: 1. GD/P1L (ours), which is a 'reassembly' of the SRA dataset from Liu et al Viruses paper - this is clearly stated in the methods section of our paper. 2. GD/P2S (ours), which is the assembly from the NGS SRA data by Guangdong custom. 3. GD/1/2019 (Xiao), which is assembly from NGS SRA data of their pangolin samples, plus confirmation with PCR amplicon sequencing (Sanger/NGS unknown). 4. GD/MP789 (Liu), which is so called re-sequencing of the Viruses sample by NGS and re-assembly if I remember correctly. Their RDBs are all highly similar (almost identical), and so I think this somehow proves that this RBD sequence is real. Yes, as you said, some other papers are very nasty, they just down the pangolin sequences from GISAID and do some analysis and published, and without mentioning the source or citing the original papers. Readers are highly misled and confused where these sequences come from... [2020-06-23 11:38:43] [Kristian Andersen] Bill's good... https://virological.org/t/identification-of-a-common-deletion-in-the-spike-protein-of-sars-cov-2/451/15 [2020-06-23 12:26:20] [Robert Garry] Definitely he's on to something! The palindrome at some basal level drives the hypervariability in the region. Probably not restricted to SARS-Cov-2. I also encouraged him to post the "lima bean" post on Virological - a little more thinking behind it than just "fun with Blast[TM] and I though his cautious tone was good. [2020-06-23 15:17:49] [Eddie Holmes] Bill's a star. He has a paper going through Archives of Virology. Hope it get published soon. [2020-06-23 16:19:41] [Kristian Andersen] In other news - Joe invented a cool new tool called genomic epidemiology (caution, reading may induce gagging). https://www.bloomberg.com/graphics/2020-opinion-chan-zuckerberg-biohub-covid-tracing/ [2020-06-23 16:23:47] [Eddie Holmes] The only good thing about Joe is that he winds-up Lipkin so profoundly. Always a pleasure to watch. [2020-06-23 16:44:31] [Kristian Andersen] I used to respect both of those men a great deal. I must have been either dumb or naive. Or both. [2020-06-23 17:37:01] [Eddie Holmes] Ego >>> ability [2020-06-24 06:46:55]