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Slack / Private Message Drop, p.310 [SLACK_000524] · slack_pm:msg:03257

Date: 2020-12-14 09:35
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut

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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.

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2020-12-14 09:32 Andrew Rambaut open

Oh my fuck
2020-12-14 09:33 Kristian G. Andersen open

Oh boy.
2020-12-14 09:33 Andrew Rambaut open

Here is a summary I have been sending round - is that this variant has spike N501Y (similar to an outbreak in South Africa but apparently independent and unrelated) but it also has 13 other non-synonymous mutations and 3deletions. There is some evidence that it is spreading quickly in SE England but it is not clear if this just means thatR is high in this region and this is just the variant that is involved. There is no evidence that the course of infection isdifferent but data is limited. Lab work is being started urgently.There is phylogenetic evidence that 3 cases in Denmark and one in New South Wales may have been the result ofimport from the UK cluster.
2020-12-14 09:34 Andrew Rambaut open

Some estimates that Erik Volz and I did independently suggests that this may be spreading at a higher rate than other variants but we can't rule out just the luck virus getting into high R areas.
2020-12-14 09:35 Andrew Rambaut

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 open

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

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