Private channel session 794
27 messages over 1h 46m, 2021-01-12 – 2021-01-12.
A “conversation” here is an activity session — a run of messages with under 60 minutes of silence inside it. The channel had no native conversation boundaries.
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Yes, I saw that. Waste of time. About 3-4 weeks I emailed GG to see if could meet up with Dominic Dwyer - my mate from Sydney who is on the WHOO commission. TODAY he replies saying that he will try and find a time-slot. She also implied that they would be looking at the early European data which is ridiculous.
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Ok, some CONFIDENTIAL pango news: UHK have animals confiscated in 2013 and 2018 in Hong Kong. Direct from Malaysia we think. Of those 9 are seropositive (using the Wantai ELISA SARS-CoV-2 assay) and 5 are PCR positive using Hybribio SARS-CoV-2 RT-PCR kit, although 4 of these have high CT values. Enrichment, meta-transcriptomics and luciferase immunosorbent assays (to rule out cross-reaction) ongoing. At face value suggests that SARS-like CoVs have been in Malayan pangos for a while but this needs to be confirmed. I'll update when I have more news. Obviously keep to yourself.
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Thank you Eddie - very important!
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I think this is an important clue: [shared file(s): image.png]
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That is interesting, Bob!
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Yeah Align SC1 with SC2 (and RatG13) just for completeness. The deletions that you see in the UK and ZA variants are EXACT deletions comparing SC1 to the others. Also note the deletion near 484 - these are hotspots!
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Are they in the civet versions of SC1?
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Or the closest bats to SC1 (could check this myself of course).
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Good question - that would be interesting...
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It is a bit tricky - my alignment is a bit different (I did a nucleotide alignment)
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THey are the same in the civet..
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Yes.
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And in some of the bats it looks
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Yes - lots of possibilities, but it looks like SC2 and RaTG13 spikes mostly diverging from SC1 by insertions - including the obvious PRRA.
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The insertions not needed so put SC2 under the right situation and it starts to delete. Just like im cell culture the FCS and the QTQTN can be deleted.
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@Andrew Rambaut yes indeed - may get a somewhat different alignment with the nucleotides but the point remains that these are hotspots for deletions. Mechanism TBD but could be swapping out a shorter sequence with end homologiesy via copy-choice.
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Wow Bob, that's amazing.
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Important for the origins argument as well - if these indels between SC1 and SC2 are natural and in play for variation, then the PRRA insert is natural as well.
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Of course the nefarious supervillain making this virus spent all that time putting those insertions in (from HIV or fish presumably) and all it does is delete them.
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PERFECT comment @Andrew Rambaut @Kristian Andersen will know that I appreciate it very much!
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@Robert Garry My thoughts exactly Bob...quick Virological post?
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@Robert Garry Certainly - it's important - whose with me?
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I'm in!
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I think Al has perfectly summed up my COVID feelings: https://www.youtube.com/watch?v=UPw-3e_pzqU
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All this science while I took a nap??!! Seriously - I need to take another nap.
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And btw - one day I want to write using prose like this: https://virological.org/t/mutations-arising-in-sars-cov-2-spikeon-sustained-human-to-human-transmission-and-human-to-animal-passage/578/2
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Yes, very nicely done.