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Slack / Private Message Drop, p.388 [SLACK_000602] · slack_pm:msg:04035

Date: 2021-01-12 14:38
Type: chat message · slack
recipient: Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker: Robert F. Garry

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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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2021-01-12 14:17 Edward C. Holmes open

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.
2021-01-12 14:33 Robert F. Garry open

Thank you Eddie - very important!
2021-01-12 14:35 Robert F. Garry open

I think this is an important clue: [shared file(s): image.png]
2021-01-12 14:37 Andrew Rambaut open

That is interesting, Bob!
2021-01-12 14:38 Robert F. Garry

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!
2021-01-12 14:38 Andrew Rambaut open

Are they in the civet versions of SC1?
2021-01-12 14:39 Andrew Rambaut open

Or the closest bats to SC1 (could check this myself of course).
2021-01-12 14:39 Robert F. Garry open

Good question - that would be interesting...
2021-01-12 14:42 Andrew Rambaut open

It is a bit tricky - my alignment is a bit different (I did a nucleotide alignment)

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