Chat message

Slack / Private Message Drop, p.525 [SLACK_000739] · slack_pm:msg:05469

Date: 2021-02-19 00:52
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Andrew Rambaut
speaker: Edward C. Holmes
Topics: Furin cleavage site and molecular features

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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 tobe happening to colleagues in London. (We are not yet sure whether we have this problem, owing to the slowness ofWTCHG turn-round!). So, the question is, what's going on, and does it tell us interesting about the biology andphylodynamics of the virus?"

Extracted statements

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Statement	Grade	Attribution	Stance
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.	quoted / not their view	quoted_external inside quotation marks	asserts

Statement

Grade

Attribution

Stance

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.

quoted / not their view

quoted_external inside quotation marks

asserts

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2021-02-19 00:52 Edward C. 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 tobe happening to colleagues in London. (We are not yet sure whether we have this problem, owing to the slowness ofWTCHG turn-round!). So, the question is, what's going on, and does it tell us interesting about the biology andphylodynamics of the virus?"
2021-02-19 01:50 Andrew Rambaut open

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 Andrew Rambaut open

I would love to get a collaboration together on this and put our heads together.

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