Another JN.1.11.1 sublineage got FLiRT after Orf1b:A2143V (NSP15_A92V) 63 sequences

[FedeGueli]

Formerly known as FLIRT Branch 63 (spotted by @aviczhl2) Defining: JN.1.11.1 > Orf1b:A2143V (C19895T) > S:R346T (G22599C) Query : C19895T,G22599C,T3565C

Samples: 5 On Gisaid from Australia , NJ , Scotland, Portugal and US but on USHER there are much more : 11 ( two with defining C19895T reverted) IDs:

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_51bc8_eece90.json?label=id:node_6968541

There is a sublineage of this with Orf8:Q18 Query: C3583T ,C27945T,T3565C Defining #2562>>C3583T, Orf8:Q18, C27945T Samples: 5

Now there is a FLiRT>TRIO JN.1.11.1 > Orf1b:A2143V (C19895T) > S:R346T (G22599C) > S:T572I (C23277T) Query: C19895T,C23277T,G24872T Samples : 1 (Illinois(

[FedeGueli]

There were in the mean while a big upload from Australia with 6 sequences placed by Usher in this tree but missing the defining Orf1a:A2143V:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a6ab_fa5210.json?c=userOrOld&label=id:node_6968619

cc @corneliusroemer @AngieHinrichs could you give a look at this please?

[AngieHinrichs]

Ah, Portugal/PT50701/2024|EPI_ISL_19033732|2024-03-24 has an N at 19895, and must have been pulled into that branch by the G22599C (S:R346T) after C19895T, with usher inferring C19895T -- incorrectly, in light of the Australia sequences. After the Australia sequences have been added to the tree, I should be able to fix it.

[FedeGueli]

Ah, Portugal/PT50701/2024|EPI_ISL_19033732|2024-03-24 has an N at 19895, and must have been pulled into that branch by the G22599C (S:R346T) after C19895T, with usher inferring C19895T -- incorrectly, in light of the Australia sequences. After the Australia sequences have been added to the tree, I should be able to fix it.

Thank you!

[FedeGueli]

10 on GIsaid 18 on Usher: [ i don't get why this discrepancy happens]

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_34212_113b40.json?label=id:node_6973994

[FedeGueli]

+1 Hawaii

[FedeGueli]

12 on Gisaid more on Usher also with TRIO: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1e741_ea7b60.json?c=userOrOld&label=id:node_6983815

Not sure if misplacement or real reversions tough

[FedeGueli]

Still around but designation not needed closing it

@corneliusroemer sublinegaes of this are stale

[FedeGueli]

34

[FedeGueli]

63 last sample from Malaysia but it is time to close this