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Slack / Private Message Drop, p.380 [SLACK_000594] · slack_pm:msg:03958

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The Manaus/Japanese cluster has a very long branch (too long) - possibly another 'chronic infection' event?

In context

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2021-01-11 14:07 Robert F. Garry open

"It seems like all of these lineages are converging to the same set of mutations." Agree - Spike is covered with glycan - there are only a few places where antibodies can slip in - Eeek and the NTD mutations are in those spots. Once this virus got a furin cleavage site it opened up the possibility for Doug and its 613 twins to destabilzed thetrimers so you could get surface entry. The furin cleavage site is continuing to optimize itself possibly in epistasiswith Doug.
2021-01-11 14:41 Andrew Rambaut open

The Japanese/Manaus cluster has the same nsp6 deletion that the UK and South African lineages have
2021-01-11 14:43 Edward C. Holmes open

Wowser. That's not chance.
2021-01-11 14:51 Robert F. Garry open

Places where the polymerase has tendency to slip and skip?
2021-01-11 15:05 Andrew Rambaut

The Manaus/Japanese cluster has a very long branch (too long) - possibly another 'chronic infection' event?
2021-01-11 15:06 Kristian G. Andersen open

What does nsp6 do again? Is it possible it's directly interacting with the spike protein to determine e.g., binding?
2021-01-11 15:06 Andrew Rambaut open

```ORF1ab synT733C F681L I760T synC2749T S1188L K1795Q del11288-11296 (3675-3677 SGF) synC12778T synC13860T E5662D spike L18F T20N P26S D138Y R190S K417T E484K N501Y H655Y T1027I ORF3a: C174G ORF8: E92K N: P80R synA28881T synG28882C```
2021-01-11 15:06 Kristian G. Andersen open

Bloody hell
2021-01-11 15:07 Edward C. Holmes open

WTF.