Chat message

Slack / Private Message Drop, p.445 [SLACK_000659] · slack_pm:msg:04605

Date: 2021-01-23 17:49
Type: chat message · slack
mentioned: Andrew Rambaut
recipient: Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker: Robert F. Garry
Topics: Furin cleavage site and molecular features

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Andrew alluded to it and I agree it's true - some spots on the genome are "slippery" or prone to mutation. It's the variable and constant domain meme of HIV, fle etc. In one sense hopeful since it suggests that while the space for mutation/adaptation is large it's not infinite. As @Andrew Rambaut referenced a handful ofimmunosuppressed/cancer patients out there (two NEJM paper) with patients with overlapping or common mutation/deletions, a few of which actually flip back and forth in the "quasispecies.' The strongly immunosuppressed/persistent patients interesting - KGA aware of one of ours at Tulane that has stayed PCR positive for over 8 months. No provirus and a rudimentary proofing mechanism but still as Emma Hodcraft said aplayground for the virus.

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2021-01-23 17:32 Andrew Rambaut open

Which seems to be a web app with a 'premium' pay-for version. Tulio was involved in development which is probably why.
2021-01-23 17:33 Kristian G. Andersen open

I remember I came across that - I think maybe even reviewing a paper with it. Really need to use iVar if he's on theIllumina platform.
2021-01-23 17:34 Andrew Rambaut open

I have mentioned it to him.
2021-01-23 17:49 Andrew Rambaut open

Don't like this - L18F has cropped up quite a few times in B.1.1.7 but most of the 310 are in a single large cluster inone area of the country
2021-01-23 17:49 Robert F. Garry

Andrew alluded to it and I agree it's true - some spots on the genome are "slippery" or prone to mutation. It's the variable and constant domain meme of HIV, fle etc. In one sense hopeful since it suggests that while the space for mutation/adaptation is large it's not infinite. As @Andrew Rambaut referenced a handful ofimmunosuppressed/cancer patients out there (two NEJM paper) with patients with overlapping or common mutation/deletions, a few of which actually flip back and forth in the "quasispecies.' The strongly immunosuppressed/persistent patients interesting - KGA aware of one of ours at Tulane that has stayed PCR positive for over 8 months. No provirus and a rudimentary proofing mechanism but still as Emma Hodcraft said aplayground for the virus.
2021-01-23 17:49 Andrew Rambaut open

Got to go to bed and stop staring at mutations.
2021-01-23 17:54 Robert F. Garry open

Yes but I really don't want to think about the blissfully ignorant mess we'd be in if YOU hadn't been staring atmutations over the past several months.
2021-01-23 17:55 Edward C. Holmes open

Bob, you used the Q word.
2021-01-23 18:00 Kristian G. Andersen open

Oh oh.

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