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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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Undesignated JN.1.18 plus S:F59S went FLiRT (44) with a S:F65Y,Q183P branch (11) #2623

Closed FedeGueli closed 3 months ago

FedeGueli commented 4 months ago

EDITED VERSION (14/06/2024)

Initially it was tracked as Branch 118 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089 it is different from JN.1.18.2 because it lacks both T22321C and C4331T

JN.1.18 > S:F59S (T21738C)> S:F456L (T22928C) >> S:F65Y (T21756A), S:Q183P (A22110C), T28693C

Query for JN.1.18+S:F59S FLiRT T22928C : T22928C,T21738C,T3565C,G22599C,-C25680T,-C7113T,-G22111T,-G17334T,-C1762A,-C774T,-C25566T,-C26894T,-C7002T,-A3941G,-C26004T Samples:20 Countries: 7 Uk, US, Qatar, Spain, France, Germany IDs: EPI_ISL_19130874, EPI_ISL_19146801, EPI_ISL_19146863, EPI_ISL_19151361, EPI_ISL_19153096, EPI_ISL_19153109, EPI_ISL_19156827, EPI_ISL_19174104, EPI_ISL_19177941, EPI_ISL_19177998, EPI_ISL_19179355, EPI_ISL_19183059, , EPI_ISL_19185559-19185560, EPI_ISL_19186343, EPI_ISL_19189742,

Query for the S:F65Y,S:Q183P sublineage : T21756A, A22110C , T3565C,T22928C or new query : T21756A, A22110C, T28693C, T21738C by @aviczhl2 in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1634 Samples: 4 Countries: 3 IDs:EPI_ISL_19177691, EPI_ISL_19177998, EPI_ISL_19183070, EPI_ISL_19194774

Tree:

Screenshot 2024-06-14 alle 11 51 27

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_21aa9_c0b5d0.json?c=userOrOld&label=id:node_7143771

To be noticed that from JN.1.18> S:F59S stem out some more interesting lineages that i put below to the attention of @corneliusroemer : Lineage 2 Dead

Query for FLiRT T22930A : C18348T ,t3565C,T22930A
Samples:8 Countries:UK EPI_ISL_19088229, EPI_ISL_19088233, EPI_ISL_19088235, EPI_ISL_19130893, EPI_ISL_19151197, EPI_ISL_19151347

Lineage 3 This was designated JN.1.18.7 starting with D1260Y but not all the samples have S:T22N Query for S:D1260Y + S:T22N: A1900G, G25340T,C21627A Samples: 4 Countries: Uk, CHina, France IDs: EPI_ISL_19146983, EPI_ISL_19167472

Query: G25340T ,A1900G,T3565C

aviczhl2 commented 4 months ago

Is there a direct JN.1+S:F59S branch?

FedeGueli commented 4 months ago

Is there a direct JN.1+S:F59S branch?

Not that i am aware of

FedeGueli commented 3 months ago

@corneliusroemer please take a look at this branch.

FedeGueli commented 3 months ago

@corneliusroemer i have edited the proposal pls take a look.

FedeGueli commented 3 months ago

27 - 5 for the subbranch

FedeGueli commented 3 months ago

36/10

FedeGueli commented 3 months ago

44/11

aviczhl2 commented 3 months ago

Designated JN.1.18.6 and LY.1

FedeGueli commented 3 months ago

Lineage 3 designated JN.1.18.7 via https://github.com/cov-lineages/pango-designation/commit/8349a3841affe73bdae955739d9af75c7e2f46c3

FedeGueli commented 3 months ago

designated JN.1.18.6 via https://github.com/cov-lineages/pango-designation/commit/40ed9bf3ff1588edbd692b8fd33bdba066963c80 and LY.1 via https://github.com/cov-lineages/pango-designation/commit/3cdd87c309cd17351fa2f570fbe4cfb508516177