Slack / Private Message Drop — page 326

[Kristian Andersen] (as in - probably not N501Y alone, but N501Y with some other 'contextual' mutations) [2020-12-19 11:06:15] [Kristian Andersen] @Andrew Rambaut - is this true? In Emma's build, yes, but if you include basal lineages, does this still hold? I was trying to look at this on Nextstrain, but it's a mess trying to identify individual events on their tree and I can't move stuff around. Also trying to look at the alignment, but I don't have all the relevant sequence. Lord, do I hate GISAID. [shared file(s): Screen Shot 2020-12-19 at 11.04.37 AM.png] [2020-12-19 14:21:24] [Eddie Holmes] [thread - ID: 2020-12-19 01:52:11] @Andrew Rambaut They're in quarantine for 2 weeks so the is just about plausible although it seems a bit long to me. I'll ask. [2020-12-19 14:27:49] [Andrew Rambaut] I don't see it. I think it is just unsampled [2020-12-19 14:29:26] [Andrew Rambaut] It is really hard to do anything at the moment with this data. Our big tree is OK for local stuff but I am not sure how much I trust some of the deeper nodes anymore. We are working hard to improve the tree building. [2020-12-19 14:34:05] [Eddie Holmes] > Through the grape vine I've heard that the South Africans are claiming their lineage is "associated with disease in younger persons". Do you know anything about this? [2020-12-19 14:37:39] [Andrew Rambaut] No - not heard that. I can't imagine that can be anything other than anecdote surely? [2020-12-19 14:38:17] [Andrew Rambaut] They only have a few hundred genomes so they can't have enough power to discern that [2020-12-19 14:39:13] [Andrew Rambaut] I guess they could be seeing an increase in hospitalisation of young and then sequencing those ones. [2020-12-19 14:42:43] [Andrew Rambaut] I thought you should know that we call the N501Y mutation 'Nelly' (under the Doug naming scheme) and thus the new UK lineage is now being referred to internally as 'the elephant'. [2020-12-19 14:44:50] [Andrew Rambaut] [thread - ID: 2020-12-19 01:52:11] @Andrew Rambaut Given Australia sequences everything and Denmark has gone from bottom to 4th place in the sequencing league it seems that the new variant must be in many other countries now. [2020-12-19 14:58:43]