Slack / Private Message Drop — page 397

(clade 201/501Y.V1) strain. This is not on - you can't [Kristian Andersen] This is very cool - thanks Bob I need to take a closer look at this - the broader implication would suggest that these are very evolutionary active regions. Joel mentioned that SC2 has a lot of reversions back to "bat", which is quite peculiar. Totally unrelated, but can I just mention one gripe here - Apoorva Mandavilli at NYTimes is doing a friggin' terrible job with her reporting. Really frustrating she's now the main SC2 reporter at NYTimes - they used to do so well. The Atlantic it is (which is totally fine with me!). [2021-01-14 10:57:25] [Robert Garry] Yes indeed thank you -someone needs to look closely - I seem to have missed L18F and picked the wrong B1.1.351 without it, but corrected here. L18F still very much fits the pattern. Indeed, these are the evolutionarily active regions. [shared file(s): image.png] [2021-01-14 11:03:17] [Robert Garry] Yes, the deletions at 69/70 and 145 as well as the cell culture insertions as 214/5 and around the FCS and do bring the sequences back closer to bat. [2021-01-14 13:11:52] [Andrew Rambaut] Jeez: ```We report the presence of a viral isolate from late December 2020 in Columbus Ohio that has acquired the S N501Y variant. This amino acid change was first described in a clinical sample in the United Kingdom in association with other novel S variants and a clade 20B backbone (ECDC, 2020; Davies et al, 2020), with the combination named as the B.1.1.7 strain and a Next Strain designation as 20I/501Y.V1 (Bedford et al, 2021). The same N501Y mutation was subsequently found in a clade 20C strain in South Africa, where it was associated with a different set of additional S variants (Tegally et al, 2020), with Next Strain designation as 20H/501Y.V3. ``` What a fucking mess Trevor has created. "It has acquired the N501Y variant". [2021-01-14 13:19:55] [Andrew Rambaut] On that note, I am sure I read this hypothesis somewhere before: https://twitter.com/trvrb/status/1349774308202094594 [2021-01-14 13:23:06] [Eddie Holmes] Aye on both counts. Fucking Trevor! [2021-01-14 13:25:23] [Andrew Rambaut] That Ohio paper is well out of order. They say - UKnB.1.1.7 (clade 20I/501Y.V1) strain. This is not on - you can't label stuff geographically. [2021-01-14 13:26:57] [Andrew Rambaut] `containing several likely pathogenic but distinct mutations in the Spike (S) gene, particularly N501Y.` - what? 'likely pathogenic'? Garbage [2021-01-14 13:30:51] [Eddie Holmes] I think you can give this one a kicking on Twitter. Unfortunately, given the discussion about it yesterday I think I had to post it. The reviewers can resolve all that stuff. [2021-01-14 14:00:07] [Kristian Andersen]