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Slack / Private Message Drop, p.342 [SLACK_000556] · slack_pm:msg:03597

Date: 2020-12-23 05:41
Type: chat message · slack
recipient: Kristian G. Andersen, Edward C. Holmes, Andrew Rambaut
speaker: Robert F. Garry

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I'll map the deletion on the model, which is prob pretty accurate, when I get to the office after dropping off the dog. Ifit's in one of the loops would likely affect regulation and yes change virus behavior.

In context

A single line often inverts meaning once you see what it answers, so neighbouring messages are always shown.

2020-12-23 04:46 Andrew Rambaut open

One more intersting observation: Some of the South African variant viruses (possibly all of them - it seems their bioinformatics pipeline doesn't call deletions very well) have a deletion at sites 11288-11296 (amino acid 3675-3677 in ORF1ab - thus the in nsp6). Exactly the same deletion is seen in the UK B.1.1.7 lineage. I don't know the significance of this. Any thoughts?
2020-12-23 05:05 Robert F. Garry open

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7195303/ From this modeling NSP6 looks like a viroporin to me - would have to look at the exact deletion, but most viroporins are involved in virion entry and cytopathogenesis.Same wheelhouse as the RBD and FCS mutations.
2020-12-23 05:21 Robert F. Garry open

Covs have other viroporins (E protein) that are virion associated, but NSP6 is likely remodeling cell membranes insome way to benefit virus replication.
2020-12-23 05:22 Andrew Rambaut open

Mmm. So definitely could be associated with a change in virus behaviour. Cool
2020-12-23 05:41 Robert F. Garry

I'll map the deletion on the model, which is prob pretty accurate, when I get to the office after dropping off the dog. Ifit's in one of the loops would likely affect regulation and yes change virus behavior.
2020-12-23 05:45 Andrew Rambaut open

Seems to crop up with a small bunch in Australia with spike S477N, and a few others here and there.

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