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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.1.39 + S:R346T (29 sequences) with a FLiRT branch (2) #2563

Closed FedeGueli closed 4 months ago

FedeGueli commented 5 months ago

Former Branch 51 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089

Defining mutations: JN.1.39 (G2782T )> T111C > S:R346T (G22599C) Query: G2782T , T111C ,G22599C Samples: 23 Countries: US, Scotland, NZL, Nigeria, Sweden, France, Russia

FLiRT Branch: Br.51 > C5986T, ORF1a:F3677L (T11296G), C14220T, Orf1b:T760I (C15746T), S:F456L (T22928C),C24616T , S:V1104L (G24872T), C27389T Query: G2782T , T111C ,G22599C,T22928C Samples: 2 US , Malaysia

IDs: EPI_ISL_18902186, EPI_ISL_18913545, EPI_ISL_18916667, EPI_ISL_18923350, EPI_ISL_18927559, EPI_ISL_18935614, EPI_ISL_18937006, EPI_ISL_18956489, EPI_ISL_18973651, EPI_ISL_18983555, EPI_ISL_18988433, EPI_ISL_19006721, EPI_ISL_19019132, EPI_ISL_19022508, EPI_ISL_19022873, EPI_ISL_19038719, EPI_ISL_19041333, EPI_ISL_19055696, EPI_ISL_19060075, EPI_ISL_19060082, EPI_ISL_19060839

Tree:

Screenshot 2024-04-20 alle 23 40 44

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice27_genome_test_4ea4c_3683b0.json?label=id:node_7086977

FedeGueli commented 4 months ago

Designated JN.1.39.2 via https://github.com/cov-lineages/pango-designation/commit/dbfae3452ac61eee3ade4f9fa7025475b9a09c03