Chat message

Slack / Private Message Drop, p.445 [SLACK_000659] · slack_pm:msg:04602

Date: 2021-01-23 17:33
Type: chat message · slack
recipient: Robert F. Garry, Edward C. Holmes, Andrew Rambaut
speaker: Kristian G. Andersen

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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.

In context

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2021-01-23 17:27 Kristian G. Andersen open

There was a reason we developed more robust tools...
2021-01-23 17:27 Kristian G. Andersen open

But as always - any one of these tools used in the wrong hands > disaster.
2021-01-23 17:31 Andrew Rambaut open

Yeah, he is using the ARTIC protocol on Illumina but then some crazy semi commercial software called Genome Detective
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

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 open

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.

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