Slack / Private Message Drop — page 471

[2021-01-31 16:26:06] [Kristian Andersen] Lol. Jens was right about one thing though - that was indeed a dumb question. "What do you mean, we can't fit these little things into neat little boxes?! Nein!!" [2021-01-31 16:37:16] [Eddie Holmes] The WHO nomenclature thing will be horrendous. Tulio and Jens is an interesting combination. [2021-01-31 16:43:38] [Robert Garry] Germans and their neat little boxes - yes I believe it's a thing... [2021-02-01 01:07:00] [Eddie Holmes] More stuff from Weifeng. The tree for 6-20k looks pretty clean. No surprise that HA379 is closely related to RmYN02 as they were both sampled in Yunnan. Interestingly, all the sampling locations for these bats are only ~50 km from the border and close to Burma and Laos. Species are as follows: HA379 Rhinolophus pusillus, HA321 Rhinolophus stheno, HA363 Rhinolophus malayanus, HA442 Rhinolophus malayanus. Bob, I don't have the sequences but I asked Weifeng to add the new ones your alignment which is attached. This figure won't be in Weifeng's paper but I think it's useful. [shared file(s): Batsnn20210201v1.pptx, ALL_Beta_REP_S_aa_clustalnum_AIv4.pdf] [2021-02-01 04:58:45] [Robert Garry] This is really awesome - the thing that popped for me is the remarkable similarity of HA379 and GDpango in the N terminus and NTD. Thereafter in the RBD totally different. It's a funhouse mirror of RaTG13, GX pangolin coronavirus and SARS-CoV-2 that share a similar indel structure and several common or similar sequences in the N-terminus and the NTD. Then there is the mind-blowing new indel with dicysteines in the HA363 group. I'm guessing a new short loop but need to look at the structure. [2021-02-01 04:59:59] [Robert Garry] @Kristian Andersen will notice new cysteine loop in the NTD, which is something that arose in one of his long patients. [2021-02-01 05:30:28] [Robert Garry] @Eddie Holmes The HA379 and RmYN02 similarity is after the NTD and into the RBD - INTERESTING! Before that HA379 is much closer to GD pango. [2021-02-01 06:47:36] [Robert Garry] The dicysteines in - one C in a new indel in Weifeng alignment in the HA321 Rhinolophus stheno, HA363 Rhinolophus malayanus, HA442 Rhinolophus malayanus viruses likely do form their own little loop in NTD. Basically on the other side of the NTD From where the other cysteines are (in pale green). [shared file(s): image.png] [2021-02-01 07:11:49] [Robert Garry] Also CRAZY that the HA321 Rhinolophus stheno, HA363 Rhinolophus malayanus, HA442 Rhinolophus malayanus viruses are as far as I can see Identical in spike. Three differnt species of bats - - how does that happen??? [2021-02-01 07:21:23] [Robert Garry] ALSO - it would not surprise me to see HA321 Rhinolophus stheno, HA363 Rhinolophus malayanus, HA442 Rhinolophus malayanus viruses binding to human ACE - pretty sure that they have the equivalent of E484 though it's a little off in the align.