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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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LE.1 (JN.1.4.7.1) got FLiRT (19 , 5 countries) #2663

Open FedeGueli opened 1 week ago

FedeGueli commented 1 week ago

@aviczhl2 and me tracked abunch of sublineages stemming out from LE.1 with 456X:

LE.1.1 , LE.1.3.1 , https://github.com/cov-lineages/pango-designation/issues/2663 and Branch 107 of # 1253 (secondary repo) plus another singlet i found looking at a better query for 2663 Now two of them with S:F456L (T22928C) have been merged by usher in one only lineage (that absorbs both # 2663 and branch 107 of # 1253 in the other repo) hence here the new defining mutations: LE.1 >> S:f456L (T22928C) Query:G25445A,G22599C,C774T,T22928C,-C1471T Samples: 19 Countries: 5 ( with several GBW samples from Spain, France, Italy) Tree ( by @aviczhl2 ): https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice174_genome_test_5e445_fb01d0.json?label=id:node_5537613

Screenshot 2024-07-01 alle 10 37 13

IDs: EPI_ISL_19162370, EPI_ISL_19163658, EPI_ISL_19184862, EPI_ISL_19184966, EPI_ISL_19191540, EPI_ISL_19191560, EPI_ISL_19192761, EPI_ISL_19194079, EPI_ISL_19198272, EPI_ISL_19198420, EPI_ISL_19201070, EPI_ISL_19205799-19205800, EPI_ISL_19214361, EPI_ISL_19214463-19214464, EPI_ISL_19215296, EPI_ISL_19215375, EPI_ISL_19221231

Original proposal: LE.1> Orf1a:T1589I (C5031T), G5470A, S:F456L (T22928C) Query:C5031T, G5470A,T22928C Samples: 5 Countries: France ; Uk, US IDs:EPI_ISL_19163658, EPI_ISL_19198272, EPI_ISL_19198420, EPI_ISL_19205799-19205800 Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice24_genome_test_2f72b_43b540.json?c=userOrOld&label=id:node_12193340 Screenshot 2024-06-20 alle 17 09 33 **EDITED** **On Today 6-25** another branch of this appeared in GBW samples (from Italy) it lacks the defining proposed here but has some more interesting mutations , already seen with different AA in KP.2.3 and XBB.1: C176T, Orf1a:V84F (G515T),C12400T, C13761T, S:G252D (G22317A), Orf3a:K67E (A25591G) Query: C176T, G515T, G22317A Samples: 2 (GBW - Italy) Tree: Screenshot 2024-06-25 alle 20 58 30 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice19_genome_test_20ceb_b11030.json?c=userOrOld&label=id:node_11496828
FedeGueli commented 1 week ago

again for the third time in a row wrong repo.

FedeGueli commented 5 days ago

main branch now 6 from Spain (new country) plus a separate branch caught by GBW in a traveler from Italy.

FedeGueli commented 5 days ago

This is not Branch #107 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253

There are at least 4 lineages with 456X on LE.1 backbone: LE.1.1 , LE.1.3.1 , #2663 and Branch 107 of # 1253 (secondary repo) plus another singlet i found looking at a better query for 2663

aviczhl2 commented 10 hours ago

image

Those LE.1-FLiRT Branches are gathered now.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice174_genome_test_5e445_fb01d0.json?label=id:node_5537613

FedeGueli commented 7 hours ago

image

Those LE.1-FLiRT Branches are gathered now.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice174_genome_test_5e445_fb01d0.json?label=id:node_5537613

thx i have re-arranged the all proposals