Slack / Private Message Drop — page 525

[Kristian Andersen] BMI of 28,000 - only in Texas would that be possible... :bacon: Hilarious - good sport on Twitter too. [shared file(s): Screen Shot 2021-02-18 at 13.31.01.png] [2021-02-18 13:33:08] [Eddie Holmes] COVID's Stonehenge from Spinal Tap moment [2021-02-19 00:52:54] [Eddie Holmes] Got this from a colleague. Any thoughts about what might explain this? "You may have heard that folks are having real trouble culturing genetically homogenous VOCs. We always knew that culturing prototype viruses in "plain" Vero cells could lead to the selection of furin cleavage site deletion mutants, but this was rarely a problem in practice, and could be avoided altogether by using Vero-TMPRSS2. However, with B1.351 (and to an extent B1.1.7 - we don't yet know about P.1) the problem has become way worse. Alex Sigal and Tulio de Oliveira at Durban ran into problems immediately when growing up their variant, which they thought they'd sorted with a fresh primary isolation and passage in Vero-TMPRSS2. They sent us and a few other labs this virus, together with the earlier dFCS isolate just after Christmas. However, since then, they ran into further problems with the uncontrolled build-up of a range of substitutions and deletions on re-passage, and this seems to be happening to colleagues in London. (We are not yet sure whether we have this problem, owing to the slowness of WTCHG turn-round!). So, the question is, what's going on, and does it tell us interesting about the biology and phylodynamics of the virus?" [2021-02-19 01:50:21] [Andrew Rambaut] This is something we are trying to grapple with - I really think there is a shift in the fitness landscape globally and these VOCs (and many other lineage) seem to be converging on a new fitness peak. Once you have the core set then there are lots of compensatory or epistatically linked mutations that get selected for (such as the spike and nsp6 deletions, FCS tweaks). The question is what is the global shift in the fitness landscape? Is it population level (i.e., lots of NPI driving higher transmissibility or rising sero-prevalence?) or an individual level - treatment, prior exposure in sub-clinical infections? [2021-02-19 01:51:11] [Andrew Rambaut] I would love to get a collaboration together on this and put our heads together. [2021-02-19 06:39:24] [Robert Garry] Transmissibility is complicated as we have been. discussing:https://dash.harvard.edu/handle/1/37366884 [2021-02-19 10:08:56] [Kristian Andersen] That "California" variant is growing pretty quickly in CA to say the least... @Andrew Rambaut - do you see any growth of that lineage in the UK? (L452R). [shared file(s): image (1).png] [2021-02-19 10:49:42] [Andrew Rambaut] Will look but we are at about 95% B117 with rapidly falling case counts. [2021-02-19 10:50:11] [Andrew Rambaut] Don't like the look of this I just found in GISAID: [shared file(s): Image from iOS.jpg] [2021-02-19 11:00:21] [Kristian Andersen]