Chat message

Slack / Private Message Drop, p.700 [SLACK_000914] · slack_pm:msg:07343

Date: 2021-04-13 14:55
Type: chat message · slack
recipient: Kristian G. Andersen, Robert F. Garry, Edward C. Holmes
speaker: Andrew Rambaut
Topics: Natural origin / zoonotic spillover

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I think you could argue that the pangolin is actually less likely to be the intermediate for SC2. The original Wuhan was more bat like in its NTD and it took all the way to B.1.1.7 before it hit its stride (you also see the same mutationsin chronic infections - so again that might explain the fitness jump to get there).

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Statement	Grade	Attribution	Stance
I think you could argue that the pangolin is actually less likely to be the intermediate for SC2.	needs context	uncertain explicit hedge	asserts

Statement

Grade

Attribution

Stance

I think you could argue that the pangolin is actually less likely to be the intermediate for SC2.

needs context

uncertain explicit hedge

asserts

In context

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

2021-04-13 14:49 Andrew Rambaut open

Other thing I got today was that the 3 nucleotide mutation in the middle of N that arose in the early Italian lineage probably create a new sgRNA - the resulting nucleotide sequence is complementary to the sgRNA transcriptionleader at the 5' end. That 3 nucleotide mutation had been bugging me for ages.
2021-04-13 14:51 Andrew Rambaut open

The cool thing is that explains the N:D3L (also a 3 nucleotide mutation) in B.1.1.7 - Sheffield showed this probably enhances the recombination with the leader two - so it may be compensating to create more N
2021-04-13 14:52 Andrew Rambaut open

Had a lovely afternoon of geeky genomic virology.
2021-04-13 14:52 Edward C. Holmes open

Intermediate host has a complex bat-pangolin recombinant?
2021-04-13 14:55 Andrew Rambaut

I think you could argue that the pangolin is actually less likely to be the intermediate for SC2. The original Wuhan was more bat like in its NTD and it took all the way to B.1.1.7 before it hit its stride (you also see the same mutationsin chronic infections - so again that might explain the fitness jump to get there).
2021-04-13 14:56 Andrew Rambaut open

There could be other NTD point mutations that provide a similar effect.
2021-04-13 15:01 Edward C. Holmes open

I think that's what I was I trying to say - that the intermediate host is a different species....but has a virus with acomplex recombinant history, like SIVcpz.
2021-04-13 15:04 Edward C. Holmes open

Or that WIV weren't finished in their engineering job
2021-04-13 15:09 Robert F. Garry open

Probably good to keep in mind that GX pango is very similar to SC2 in much of the NTD except IR2 where some of the magic may be happening.

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