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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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JN.1.1.5 (Original proposal) with a S:F456L /Orf9b:T72I sublineage (9 samples) #2492

Closed FedeGueli closed 4 months ago

FedeGueli commented 4 months ago
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: Screenshot 2024-02-20 alle 11 29 30 Screenshot 2024-02-20 alle 11 28 56 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
Orf9b:T72I (C28498T) > S:F456L (T22928C) / (Edited) Query for the 456L lineage :C28498T ,T22928C,G22599C,C1762A 3 seqs Us,UK, Jap
FedeGueli commented 4 months ago

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 commented 4 months ago

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 commented 4 months ago

66 total , 6 with 456L

FedeGueli commented 4 months ago

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

FedeGueli commented 4 months ago

Designated JN.1.1.5 via https://github.com/cov-lineages/pango-designation/commit/d262c30317b0d73763fc23b108b5732c2a9a7103 i keep this open to track the S:F456L lineage

FedeGueli commented 4 months ago

Designated KR.1 via https://github.com/cov-lineages/pango-designation/commit/1cce5001d341a63b5b5a056933ecd9908780f0aa

FedeGueli commented 2 months ago

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

Screenshot 2024-04-30 alle 11 45 49

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