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Withdraw HK.3.11 as study of EG.5.1.1 shows that "HK.3.11" is actuall…
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…y part of EG.5.1.1 + 14988C sublineage not HK.3
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@corneliusroemer
corneliusroemer committed Nov 28, 2023
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3 changes: 2 additions & 1 deletion lineage_notes.txt
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3 comments on commit ce3f29b

@FedeGueli
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@FedeGueli FedeGueli commented on ce3f29b Nov 28, 2023 •
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@corneliusroemer @AngieHinrichs if you roll back the history of this lineage it has been discusse multiple times , originally (branch 18 of # 537) was stemming out from EG.5.1.1 held out from Hk.3 by a reversion flip flap at 22264. So when 22264 reversion was solved it went back to HK.3 and the 14988C went unobserved .

Schermata 2023-11-28 alle 17 27 40

One thing to notice is that 14988C in the EG.5.1.1 branch leading to HK.6 has also A23014T that is absent in all the HK.26/HK.3.11 sequences, although masked it is absent from all gisaid samples.
Schermata 2023-11-28 alle 17 27 55

It is easy to check looking for it (T14988C, A23014A) on covspectrum all the samples found are in the HK.3 tree leading to HK.26
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_12060_6143d0.json?c=userOrOld&f_userOrOld=uploaded%20sample&label=id:node_3541155

So i doubt it really belongs to the branch leading to HK.6 but at least it could be a "homologous recombinant" emerging from the variant magma we observed in China since mid summer 2023.

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Nothing inconsistent with 14998C happening once and then getting the two children HK.6 and HK.26 no? Yeah, recombination might well be involved, who knows, but impossible to detect

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Nothing inconsistent with 14998C happening once and then getting the two children HK.6 and HK.26 no? Yeah, recombination might well be involved, who knows, but impossible to detect

Yeah to me all the three choices are equally likely.

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