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Slack / Private Message Drop, p.311 [SLACK_000525] · slack_pm:msg:03261

Page text: p.311 · original PDF

Date: 2020-12-14 09:44
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut

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This is the set of mutations that are unique to this cluster: [shared file(s): image.png]

In context

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2020-12-14 09:35 Andrew Rambaut open

However - and this is what really interests me is the 14 mutations and 3 deletions in one short (in time) branch. Ithink this must be the result of transmission from a chronic infection.
2020-12-14 09:39 Kristian G. Andersen open

Thanks Andrew for the background - that's very interesting (and I'll keep this to this channel for now). It's great tohear that the UK now have systems in place to even detect "mutations of potential interest" - what it means isobviously a much longer affair.I get annoyed with all the communication that's completely dug in - "it's no issue at all" and "OMG it's mutating". Canwe just agree that the truth is somewhere in-between and that it always takes time to figure out?
2020-12-14 09:40 Kristian G. Andersen open

As for chronic infection - I can totally believe that. Here's a case we recently picked up - seven month of SARS2 infection with negative PCRs in-between. Sky high titers when picked up in late October (6 months after infection -he remained positive into December). [shared file(s): fake-reinfection.pdf]
2020-12-14 09:42 Andrew Rambaut open

I am normally fairly relaxed about RBD mutations - sure they happen and they may have antigenic effects but we can be pretty sure that they are not being antigenically selected for because there isn't enough standing immunity (inmost places) or vaccination yet. BUT... this chronic infection scenario worries me because it may well have selected for escape from the immune response raised by the wild type virus (and thus the vaccine). And now it is circulating widely.
2020-12-14 09:44 Andrew Rambaut

This is the set of mutations that are unique to this cluster: [shared file(s): image.png]
2020-12-14 09:44 Kristian G. Andersen open

Yes, agreed. Although reinfections also a concern here - I'm worried about selection in e.g., healthcare settings.Mink transmission also a concern here.My default is always "probably not an issue", but SARS2 really does appear to be pretty 'adaptable' and there's ALOT of transmission going on.
2020-12-14 09:44 Andrew Rambaut open

Here is the tree... [shared file(s): Kent_N501Y_836.ml_annotated_collapsed_tree.pdf]
2020-12-14 09:44 Kristian G. Andersen open

That's A LOT of mutations - all in one 'jump'?
2020-12-14 09:45 Andrew Rambaut open

There is one intermediate with some of the mutations... hence thought of a chronic shedder

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