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LB.1.8 (ORF1a:I785V)
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@corneliusroemer
corneliusroemer committed Jul 10, 2024
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9 comments on commit 05eee64

@FedeGueli
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Hi @corneliusroemer i was tracking this from some weeks. Just to be sure you know that it has no S:S31del that is listed as defining of LB.1 on Nextclade (while it wasn't defining at the time of Pango designation) I thought i wrote about this one to @AngieHinrichs but i cannot find the mail so maybe it never left my drafts.

@xz-keg
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@xz-keg xz-keg commented on 05eee64 Jul 10, 2024

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This branch doesn't have S:31del, I think it shall be designated LB.x instead of LB.1.x, as the designation of LB.1 actually includes 31del. This shall be a separate JN.1.9+FLiRT branch from LB.1 .

https://nextstrain.org/staging/nextclade/sars-cov-2?f_Nextclade_pango=LB.1&s=LB.1

@FedeGueli
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This branch doesn't have S:31del, I think it shall be designated LB.x instead of LB.1.x, as the designation of LB.1 actually includes 31del. This shall be a separate JN.1.9+FLiRT branch from LB.1 .

https://nextstrain.org/staging/nextclade/sars-cov-2?f_Nextclade_pango=LB.1&s=LB.1

exactly what i was saying, i m tracking this from som e weeks it was first sparse in the tree but agree 100% it is LB.X and not LB.1.X

@FedeGueli
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Big uplaod from Venezule where it is over 50% of samples in June (and over 10% in Guatemala)

@FedeGueli
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Big uplaod from Venezule where it is over 50% of samples in June (and over 10% in Guatemala)

a big chunk of it with S:T572I i m going to propose it

@FedeGueli
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@FedeGueli FedeGueli commented on 05eee64 Jul 29, 2024 •
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New query for LB.1.8: A2618G,G22111T,T3565C , catching old samples uploaded to Gisaid only recently, shows a reality that i missed: this sublineage it is circulating since December 2023 in Venezuela and central America predating the rise of LB.1, this could be another evidence that maybe it was better to designate it as LB.X !
First known sequence: EPI_ISL_19199611 Venezuela collected on December 29, 2023!

And infact the bunch of early sequences are misplaced by USher under a JN.1+183H branch that very likely doesn't exist and it was just JN.1.9 + Orf1a:I785V that then acquired FLiRT independently from LB.1
Screenshot 2024-07-30 alle 01 17 45
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_3aae5_81f570.json?f_userOrOld=uploaded%20sample&label=id:node_6963900
Screenshot 2024-07-30 alle 01 18 17

@xz-keg
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@xz-keg xz-keg commented on 05eee64 Jul 30, 2024

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New query for LB.1.8: A2618G,G22111T,T3565C , catching old samples uploaded to Gisaid only recently, shows a reality that i missed: this sublineage it is circulating since December 2023 in Venezuela and central America predating the rise of LB.1, this could be another evidence that maybe it was better to designate it as LB.X ! First known sequence: EPI_ISL_19199611 Venezuela collected on December 29, 2023!

And infact the bunch of early sequences are misplaced by USher under a JN.1+183H branch that very likely doesn't exist and it was just JN.1.9 + Orf1a:I785V that then acquired FLiRT independently from LB.1 Screenshot 2024-07-30 alle 01 17 45 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_3aae5_81f570.json?f_userOrOld=uploaded%20sample&label=id:node_6963900 Screenshot 2024-07-30 alle 01 18 17

Yeah maybe this shall be JN.1.9.x

@xz-keg
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@xz-keg xz-keg commented on 05eee64 Jul 30, 2024

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Better designate
JN.1.9.x for JN.1.9+Orf1a:I785V
JN.1.9.x.1 for this branch

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Better designate JN.1.9.x for JN.1.9+Orf1a:I785V JN.1.9.x.1 for this branch

Yeah i agree it is likely not descending from JN.1.9.2

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