A single line often inverts meaning once you see what it
answers, so neighbouring messages are always shown.
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Really interesting but I haven't fully got my head around it - basically it means that the bat-like NTD is sub-optimal for humans, B.1.1.7 has converged on whatever the pangolin has as an adaptation to humans (given that B.1.1.7 is the most human adapted virus yet).
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So 69-70 deletion and the 144 deletion provide greater infectivity (and presumably when combined with 501Y RBD and 681H furin site) result in higher transmissibility.
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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.
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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
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2021-04-13 14:52
Andrew Rambaut
Had a lovely afternoon of geeky genomic virology.
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Intermediate host has a complex bat-pangolin recombinant?
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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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There could be other NTD point mutations that provide a similar effect.
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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.