JN.1.1.5 (Original proposal) with a S:F456L /Orf9b:T72I sublineage (9 samples)

[FedeGueli]

Original JN.1.1.5 proposal

This is really a global lineage sampled multiple times in 6 continents including Kenya (GBW) , Chile, China, Brazil, Japan and New Zealand Defining mutations: JN.1.1 > C11747T > C9142T > S:R346T (G22599C) Query: -C593T,-C4012T,-C6730T,-C27804T,-G3308A,-A361G,-C2544T,-A20284T ,-A25165T,-C5784T,C11747T, C9142T ,G22599C,C1762A,-A405G,-C21057T,-C5031T,-A27938G, -C23557T,-G1855C, Samples :66 Countries: 21 Continents: 6 Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_47a0a_478a60.json?f_userOrOld=uploaded%20sample&label=id:node_6971315

Samples IDs:
<
EPI_ISL_18552979, EPI_ISL_18553493, EPI_ISL_18577478,
EPI_ISL_18577484, EPI_ISL_18577493, EPI_ISL_18602572,
EPI_ISL_18625028, EPI_ISL_18626559, EPI_ISL_18653083,
EPI_ISL_18653103, EPI_ISL_18653232, EPI_ISL_18671824,
EPI_ISL_18671835, EPI_ISL_18711304, EPI_ISL_18729840,
EPI_ISL_18756130, EPI_ISL_18766305, EPI_ISL_18766457,
EPI_ISL_18775638, EPI_ISL_18781064, EPI_ISL_18788484,
EPI_ISL_18799238, EPI_ISL_18799335, EPI_ISL_18805047,
EPI_ISL_18812146, EPI_ISL_18813647, EPI_ISL_18815566,
EPI_ISL_18818747, EPI_ISL_18829316, EPI_ISL_18833767,
EPI_ISL_18838796, EPI_ISL_18841908, EPI_ISL_18850380,
EPI_ISL_18853040, EPI_ISL_18853625, EPI_ISL_18861758,
EPI_ISL_18862164, EPI_ISL_18866350, EPI_ISL_18869939,
EPI_ISL_18870113, EPI_ISL_18876427, EPI_ISL_18877707,
EPI_ISL_18884609, EPI_ISL_18884617, EPI_ISL_18892917,
EPI_ISL_18893009, EPI_ISL_18895805, EPI_ISL_18902090,
EPI_ISL_18903018, EPI_ISL_18903686, EPI_ISL_18911317,
EPI_ISL_18911666, EPI_ISL_18912921, EPI_ISL_18915535,
EPI_ISL_18916267

This lineage now designated JN.1.1.5 has a small sub branch with S:F456L
JN.1.1.5 > Orf9b:T72I (C28498T) > S:F456L (T22928C) / (Edited)
Query for the 456L lineage :C28498T ,T22928C,G22599C,C1762A
3 seqs Us,UK, Jap

[FedeGueli]

71 + 2 samples both with 456L so it is now 5. it has to be noticed that 5 samples are coming from 5 different continents cc @corneliusroemer

[FedeGueli]

71 + 2 samples both with 456L so it is now 5. it has to be noticed that 5 samples are coming from 5 different continents cc @corneliusroemer

After the update of Nextstrain i was able to correct the query it is now 55 ( with 5 monophyletic with 456L) i changed also genomes ids to be consistent with the query. Being there a lot of exclusion it could be i excluded some related sequences while still maybe some sequences that could be or not part of this lineage.

[FedeGueli]

66 total , 6 with 456L

[FedeGueli]

74 with 9 in the 456L branch it seems growing fast. (edited and query adjusted again)

[FedeGueli]

Designated JN.1.1.5 via d262c30 i keep this open to track the S:F456L lineage

[FedeGueli]

Designated KR.1 via 1cce500

[FedeGueli]

There is a branch in South Korea with S:F59L : KR.1 > G3052A,C18807T, S:F59L (T21737C) Query: G3052A, T21737C ,C18807T,T3565C Samples: 6

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_1056e_fc4970.json?label=id:node_7015289