Slack / Private Message Drop — page 297

Hu-1 should have 2 differences from WH04 (EPI_ISL_406801): T:8781:C, C:28143:T [2020-12-06 10:11:08] [Andrew Rambaut] Wuhan-Hu-1: T:8781:C|T:18059:C|C:28143:T WH04: T:18059:C WA1: 0: [2020-12-06 10:11:10] [Kristian Andersen] The version I have of Hu-1 (MN908947) is identical - weird... Lemme check again [2020-12-06 10:13:17] [Kristian Andersen] Yup, identical based on NCBI records (except the ends). Here's the Geneious alignment [shared file(s): 2020.12.06_alignment.geneious] [2020-12-06 10:13:57] [Kristian Andersen] WA1 has three differences to both WH04 and Hu-1 - all three ancestral. [2020-12-06 10:15:48] [Kristian Andersen] Lemme check these human sequences against the larger pango/bat alignment I have - since I have all the assemblies for those too. [2020-12-06 10:16:32] [Andrew Rambaut] Not sure that is the same WH04 - there are some confusing names [2020-12-06 10:16:55] [Kristian Andersen] [and I'll see if I can get the raw data for WA1 so I can check the assembly for that one too - although it's been sequenced multiple times, so I assume it's correct] [2020-12-06 10:17:11] [Kristian Andersen] Lemme get WH04 from GISAID (I have been using MT291829 from NCBI as WH04) [2020-12-06 10:32:34] [Kristian Andersen] Comparing to all the pango/bat sequences here is interesting - in two out of the three positions (8782 (C/T) and (18060 C/T) where WA1 is ancestral compared to RaTG13, all the other pango/bat genomes have the same as RaTG13 - so definitely ancestral. HOWEVER, RmYN01 has the same derived residues in those positions as WA1. (I can't check the third position - RmYN01 has bad sequencing around that position). Checking SARS... [2020-12-06 10:42:23] [Andrew Rambaut] hCoV-19/Fujian/8/2020 I EPI_ISL_411060 -> seems to be identical to WA1 and sampled around the same time. [2020-12-06 10:51:40] [Kristian Andersen] SARS splits the differences.