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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.1.18.1 + S:F456L (FLiRT) with S:P272H (14 sequences 8+ countries) #2596

Closed FedeGueli closed 5 months ago

FedeGueli commented 6 months ago

This lineage has been tracking both as Br.55 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253 by @aviczhl2 and Br.84 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089 by me. I am proposing even if it is still 13 sequences only because it covers a vast geographical area and it carries S:P272H that is a known T-Cell escape mutation ( even f we know that the impact from T Cell escape should be limited). it has 4 spike mutations in comparison to JN.1: S:250N, 272H, 346T, 456L

Defining mutations: JN.1.18.1 (S:T250N) > C14220T > S:F456L (T22928C) >S:P272H (C22377A) Query: T22928C,C14220T,C22311A Samples:13 Countries: Taiwan (travel) 2, South Korea 2, India, Ireland, Canada, England 2 , Australia, USA 3(California, Virginia,Colorado) IDs: EPI_ISL_19022944, EPI_ISL_19024740, EPI_ISL_19030222, EPI_ISL_19065225, EPI_ISL_19070982, EPI_ISL_19122458, EPI_ISL_19130958, EPI_ISL_19136201, EPI_ISL_19141968, EPI_ISL_19143326, EPI_ISL_19143579, EPI_ISL_19144247, EPI_ISL_19145819 Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice6_genome_test_1658a_affac0.json?label=id:node_7125107

Screenshot 2024-05-20 alle 10 34 13
FedeGueli commented 5 months ago

Designated LQ.1 and LQ.1.1 via https://github.com/cov-lineages/pango-designation/commit/cba648fc3935708f8c8c6eefa329dd9ee301375b