A single line often inverts meaning once you see what it
answers, so neighbouring messages are always shown.
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Also worth noting that the upstream residues QTQTN that Andrew et al and others have shown are often deleted in cell culture (SC2 doesn't need a FCS in culture apparently) are pretty much a PERFECT upstream context sequence for optimal FCS cleavage being small and hydrophilic amino acids. @Kristian Andersen maybe Karthik could look but I think this deletion or something like it showed up as a minor species showed up in the Vero passage that Brandon did. QTQTN is present in GD pangolin and RaTG13, but not SC1.
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We have also seen an odd import (possibly from Uganda - but quite possibly with an intermediate location) that hasP681R so making the FCS RRRK - any thoughts on that? Interestingly it also has V367F & Q613H (but not614G - it is in lineage A). A small cluster, possibly growing.
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Interesting - P681R would make the FCS RRRAR right? which is predicted to be a much better site than PRRAR but not as good as RRAR/KR. Q613H is pretty analogous to the lion mutation (from my virological christmas card) Q613R, both to a positive charge at pH >6.
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There are lions in Uganda.
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2021-01-09 07:42
Andrew Rambaut
(so I have heard - I was supposed to be going there last year, sigh)
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Ahhh yes - the Queen Victoria hotel is pretty special and you can take a side trip to the Ziika forest. Curious about Pooh, showing up in NIgeria (Christian Happi) and now Poor in Uganda. Not that many sequences from Africa, Something usual in Africans going on which I suspect relates to prior exposure to some yet uncharacterizedbetacornaviruses.
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Lot of immunosuppressed Africans, HIV and other causes, as well. So having the P681 changes may fit that meme.
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This is the new USA cluster with Eeek and Pooh: [shared file(s): image.png]
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All in Maryland? Worth keeping an eye on it for sure...