HK.8+Orf3a:S171L+S:D1153Y(108 seqs, 9 countries, 13% in Sichuan)

[xz-keg]

From sars-cov-2-variants/lineage-proposals#794

HK.8+C25904T(Orf3a:S171L)+C25019T(S:D1153Y)

GISAID query: G25019T,C25904T,G22927T
No. of seqs: 55(Belgium 1 Canada 2 Italy 1 Singapore 1 USA 4(1 from Singapore) China 46)

First: EPI_ISL_18241520, Yunnan, 2023-8-10
Latest: EPI_ISL_18445529, Belgium, 2023-10-24

usher

Already showing further Spike diversity such as S256L or P1162L.

[xz-keg]

85, Japan

[xz-keg]

17/135=13% in Sichuan's latest batch from multiple cities

[FedeGueli]

ping @corneliusroemer this is bringing up HK.8 that in itself is slower than HK.3, and it is quite well distributed in China

[xz-keg]

108, Austria, South Korea

[FedeGueli]

Thx @aviczhl2 for your tireless tracking of this.

[NkRMnZr]

there's a few or at least a sub-branch with S:N481del, G482S (del23004-23006)

[xz-keg]

there's a few or at least a sub-branch with S:N481del, G482S (del23004-23006)

13 seqs,GISAID shows this as del23003_23005 and G23006A.

[NkRMnZr]

Well so that's only a part of HK.8.1, not all of it, misguided by UShER label
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_18fdc_69fbc0.json?f_userOrOld=uploaded%20sample&label=id:node_3524325

[xz-keg]

Well so that's only a part of HK.8.1, not all of it, misguided by UShER label https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_18fdc_69fbc0.json?f_userOrOld=uploaded%20sample&label=id:node_3524325

This is certainly due to usher cannot handle deletions.

You shall make an issue to track this.

[FedeGueli]

please comment under the commit so @corneliusroemer could see if possible to designate it directly.

[AngieHinrichs]

I see the HK.8.1 path included C19032T which was not intended. I will fix it so it's one level up at G25019T (S:D1153Y). No need to make a separate issue for that.

[xz-keg]

I see the HK.8.1 path included C19032T which was not intended. I will fix it so it's one level up at G25019T (S:D1153Y). No need to make a separate issue for that.

Oh, it's not about this. The issue here is that there is an HK.8.1+S:481- ,S:G482S branch and usher cannot handle deletions.