Multiple JN.1 + S:R346X + FliRT + Trio : 155 branches as July 30

[HynnSpylor]

Intro

**i think the original proposal should be updated in this way** (_Edited and Updated_ BY MOD): I would like to recapitulate current situation looking at the downsampled tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_19c8e_3c4600.json?label=id:node_6806774 I can determine as separate branches:

Branch 1: Now designated JN.1.1.3

JN.1.1 >C11747T>G22599T (S:R346I), then further >C20629T> (ORF1b:H2388Y)>T22599C (S:I346T) query: C20629T, G22599C, T22926C Samples 40

Branch 2 : Now designated JN.1.1.5 from https://github.com/cov-lineages/pango-designation/issues/2492

JN.1.1 > C11747T > C9142T > S:R346T (G22599C)
Query: C11747T, C9142T ,G22599C,C1762A Samples: 76 fast with a further FLIRT branch with S:F456L: Branch2 > C28498T > S:F456L (T22928C) / 3 seqs Us,UK, Jap (query:C28498T ,T22928C,G22599C,C1762A) Designated KR.1

Branch 3: Broadened to JN.1.1.3 via https://github.com/cov-lineages/pango-designation/commit/0c19ec354cacce2f1703927bc9d863947e9afba3

now proposed in https://github.com/cov-lineages/pango-designation/issues/2591 (Unreliable query) JN.1.1 > C11747T >S:R346T (G22599C) Query: -G4720A,-C21952T,C11747T,G22599C, -C9142T,-C20629T,C1762A,-T3488C,-C21654T,-G22703A,-G23120T,-T22928C,-C21654T,-T25207C Samples: 175 (query catches many unrelated samples the Usher count is around 83)

Branch 4 : canceled it is not monophyletic

JN.1.1 > C11747T > T3488C > S:r346T (G22599C) Query : T3488C,C11747T,G22599C,C1762A Samples: 5 Senegal

Branch 5: now designated JN.1.6.1

JN.1 > S:R346T (G22599C), G22627A Query : G22599C, G22627A,C18894T ,T3565C Samples: 118

Branch 6: now designated JN.1.18

JN.1 > > S:R346T (G22599C) Query: C18894T ,-G27915T ,T3565C,G22599C,-C1762A,-G22627A,-C774T,-C2536T,-C27371T,-T21973C,-C2395T,-C5654T,-C18687T,-C19145A, -C6040T,-T20241C,-T21738C,-A9935G,-C1938T,-A28795G,-C19944T, -T14526C,-G10271T,-G17562T,-C27476T, -C11747T, -G25012T, -G22111T,-C5986T, -C20930T, -G17334T, -A3776G,
Samples : 230 (the query much more improved now according to nextclade on 31/01)

Branch 7: Designated JN.1.44.1

Jn.1.44 , Orf6:P57L (C27371T) >S:R346T (G22599C) Query: G22599C, C27371T,C18894T ,T3565C Samples : 29 France, Cameroon ( likely more than 4), Oman , Can, Finland

Branch 8: dead

JN.1 > C2536T, S:R346T (G22599C)
Query: C2536T, G22599C,T3565C Samples: 20 Sweden, Japan

Branch 9: Designated JN.1.8.2 from https://github.com/cov-lineages/pango-designation/issues/2495

JN.1.8 > A12928G,> S:R346T (G22599C), Query: > A12928G, G22599C,C27476T Samples : 61 fast Singapore, US, Uk, Nigeria

Branch 10: dead

now proposed in https://github.com/cov-lineages/pango-designation/issues/2600 JN.1 >G17562T > C2395T > S:R346T (G22599C) Query: C2395T, G22599C,C18894T,-C1762A,-C774T, Samples : 33 Uk , Qatar, US , Ireland

Branch 11: Dead

JN.1 > C5654T, C9763T , C7840T, S:R346T (G22599C) Query: C5654T, C9763T , C7840T Samples: 8 Uk Sweden NZL dead

Branch 12 : Dead

JN.1.31 (Orf3a:V13L = G25429T) > C19186T > C18687T > Orf1a:M1448T (T4608C), C24553T > C3912T, C4009T, C9169T,S:R346T (G22599C), C27161T Query: C3912T, C4009T, C9169T Samples 4 Spain dead

Branch 13 : Dead

JN.1.3 > Orf1a:F499L (C1762A) >S:R346T (G22599C), C22978T, C27012T Query: C1762A, C22978T, C27012T Samples: 5 Uk dead

Branch 14 : Designated JN.1.13.1

JN.1 with S:A1087S > S:R346T > S:F59S Query: C26894T,C25680T,G24821T Count: 227

Branch 15: Designated JN.1.7.3

JN.1.7 + 346T ( the branch w S:S680Y proposed by @fearuncle in #1343 ) Query (edited) : C25566T,C23277T,G22599C,-C29144T,-G18960A Samples : 23 UK, Pennsylvania

Branch 16: now proposed in https://github.com/cov-lineages/pango-designation/issues/2601

JN.1.4.5 (Orf8:S103L )>C28201T9 > C28948T > S:R346T (G22599C) that further gained S:T732I Query: C774T, C28948T, G22599C Samples : 47(Japan , Singapore, Fujian)

Branch 17: Slow

JN.1.1>C11747T>G22599T (S:R346I) Query: -C9142T,C1762A,G22599T,T3565C
Samples: 27 Japan, India

Branch 18: Dead

JN.1 > Orf1b:P1821S (C18928T) > A18991G, S:R346I (G22599T), S:S1241I (G25287T) Query: C18928T, A18991G Samples: 2 Uk slow

Branch 19: Dead

JN.1 > Orf3a:N119Y (A25747T) > T19866C > T27851A > S:R346I (G22599T),S:V622I ( G23426A) Query: G22599T,G23426A,T19866C Samples : 3 NZL slow

Branch 20: designated JN.1.7.1 from #1371

Jn.1.7 > S:R346K

Branch 21 : Designated KQ.1

JN.1.4 > S:t572I > S:R346T 6 seqs proposed in https://github.com/cov-lineages/pango-designation/issues/2487

Branch 22 : Dead

JN.1.4.5 [T18453C >Orf8:S103L (C28201T)] >T9799C, S:R346T (G22599C) Query: C28201T,T9799C, G22599C Samples : 4 (Israel) dead

Branch 23: Designated LE.1 and LE.1.1

Now proposed in https://github.com/cov-lineages/pango-designation/issues/2493 JN.1.4.7 [Orf3a:G18D (G25445A)]> S:R346T (G22599C) Query: G25445A,G22599C,C774T Samples: 100 ( Ghana, Kenya) With a FViRT branch designated with S:F456V Query : G25445A,G22599C,T22928G 12 samples

Branch 24: Now proposed in https://github.com/cov-lineages/pango-designation/issues/2602

Jn.1.4 > T18453C > C7732T, Orf1a:D4117N (G12614A),S:T22N (C21627A), G22111A, S:R346T (G22599C), C27944T Query: C27944T,G12614A,C774T, G22599C Samples : 37 ( US)
With a further branch with a dead S:G35C branch (5) spotted by @ryhisner

Branch 25: Dead

JN.1.4 > T18453C > Orf1a:A486V (C1722T), C9979T, Orf1a:K4348R (A13308G), S:R346T (G22599C) Query: T18453C,C1722T, C9979T Samples : 2 (Uk)

Branch 26 : Dead

JN.1.4 > T18453C > Orf1b:N168K, C13971A,S:R346T (G22599C), T25542A Query: C13971A,, T25542A Samples : 4 (NZL)

Branch 27: Dead

JN.1.4 > T3400C, Orf1b:Y597C (A15257G) ,S:R346T (G22599C) Query: T3400C, A15257G, G22599C Samples : 2 (NY) slow

FLiRT Branch 28:Designated JN.1.30.1 from https://github.com/cov-lineages/pango-designation/issues/2514

JN.1.30 ( G21255T) > T7789C > S:R346T (G22599C) Query: G21255T , T7789C, G22599C Samples : 25 (India) fast

With further FLIRT S:F456L branch Designated KU.2

JN.1.30 (G21255T )> T7789C > S:R346T (G22599C) > S:F456L (T22928C) Query: G22599C,T22928C,G21255T,T3565C Samples :5

Branch 29 :Dead

JN.1 > S:T22I (C21627T) > S:Q23H (A21631T) > S:R346T (G22599C) > S:Q183H (A22110G), T23671C, T25139C Query: G22599C,A22110G,T25139C,T3565C Samples : 6 UK dead

Branch 30 Dead

JN.1.1 > C11747T > C9166T >Orf1a:L3930F(C12053T)> A7024G , C14649T, C20115T,S:R346I (G22599T) Query: C14649T, C20115T,G22599T Samples : 10 (Japan) dead

Branch 31 Dead

JN.1.1 > C11747T > S:P174S (C22082T),S:R346I (G22599T) Query: C22082T,G22599T,C11747T Samples: 8 (India)

Branch 32 FLIRT now proposed in https://github.com/cov-lineages/pango-designation/issues/2557

JN.1.1.6 (C11747T > S:F456L=T22928C) [Branch6 of #1253 ] > C11704T, S:R346T (G22599C) NEW Query: C11704T, C11747T,G22599C,T22928C,-G16741T Samples : 17 UK, Singapore, India, South Korea , Canada, USA THX @aviczhl2 for spotting that the query fell short in finding more sequences. There is one more sample from Thailand without C11704T and with S:S680Y.

Branch 33 Dead

JN.1.1 > Orf1a:S2224F (C6936T), G21138A, S:R346K (G22599A) Query:C6936T, G21138A,G22599A Samples: 5 Scotland

Branch 34 :Now Designated JN.1.26

JN.1 > C26894T > S:R346T (G22599C) Query: C26894T ,G22599C,-C25680T,A6183G,
Samples: 29 US Fast

Branch 35 : Designated JN.1.42.2

now proposed in https://github.com/cov-lineages/pango-designation/issues/2494 JN.1.42 ( C5581A) > S:R346T ( G22599C ) Query: C5581A ,G22599C,T3565C,-A405G Samples: 63 (Peru', Guatemala, Costarica) There is now (May 1) a FLiRT sublinegae of this one apparently misplaced by USher to Jn.1.16 JN.1.42> S:R346T (G22599C) > Orf1a.P1640S (C5183T), C7594T, ORF1a:A4285V (C13119T) Query: C5183T, C7594T,C13119T Samples: 3 (PuertoRico , Brazil via GBW)

Branch 36: Designated JN.1.48.2

JN.1.48 [T18471C > G29134T] > Orf1a:A427V C1545T, A3829G,S:R346T (G22599C) Query: G29134T,A3829G,C1545T Samples: 29 (India) a DelRT branch tracked in #1502 as branch 7 20 with S:S31del (del21653-216355) Query:C1545T, A3829G, del21653

Branch 37 designated JN.1.24.1 from https://github.com/cov-lineages/pango-designation/issues/2520

JN.1.24 [ S:C1243F (G25290T)] > S:R346T (G22599C)
Query : G22599C, G25290T, A6183G
Samples: 23 (Texas - Sweden) JN.1.24.1 FLIRT sub branch with S:F456L (query for 456L :G22599C, G25290T, A6183G,T22928C
or G22599C, T22928C, G25290T,T3565C) now 10

Branch 38 Dead

JN.1.38[ [#2475](https://github.com/cov-lineages/pango-designation/issues/2475 = Orf1b:R1736K (G18674A) ]C11572T > Orf3a:G100S (G25690A) >S:G35S (G21665A) > S:R346T (G22599C) Query : G21665A,G22599C,C11572T Samples : 11

Branch 39: REMOVED

sublineage of branch 7 with C5842T, Orf1a:A3615V (C11109T) from Cameroon Query : C5842T, ,C11109T,C27371T,T3565C 16 seqs dead

Branch 40: designated LC.1

JN.1.1.7 (S:S31F ) > S:R346T (G22599C) spotted. by @aviczhl2 (Sublineage of #1157) Query:C21654T,G22599C,C1762A Samples: 14 (India, Australia) Branch with S:F456L FLiRT LC.1 [JN.1.1.7 (S:S31F ) > S:R346T (G22599C)] > Orf1a:R1464L (G4656T) > S:F456L (T22928C) Query: G4656T,T22928C,G22599C,T3565C ( edited thx @aviczhl2 that found the new two samples) Samples: 3

FLIRT Branch 41: Designated JN.1.16.1

https://github.com/cov-lineages/pango-designation/issues/2511 JN.1.16(S:F456L) > S:R346T (G22599C) Query: T22928C, T3565C, G22599C, T27810C,-A405G,-A18093G,-G25290T,-C26894T,-G24872T ,-C1762A,-C774T, Samples: 31 (Singapore,US)

Branch 42: Dead

Jn.1.1 > Orf1a:T1589I (C5031T) > T508C, S:R346T (G22599C) Query: C5031T , T508C, G22599C Samples: 2 India/US

Branch 43 : Dead

JN.1.1 > > C11747T > C9142T > C9286T > C29095T > S:R346T (G22599C), A27938G Query: G22599C, A27938G, C9286T Samples: 2 California

Branch 44 : Dead

JN.1.1 > C11747T > C9142T > C23557T > Orf1b:D2138N (G19879A) > S:R346T ( G22599C) Query: C23557T ,G19879A, G22599C Samples : 2 New Jersey

Branch 45 : REMOVED:

it is now placed under JN.1.8 so it is a sublineage of branch 9 JN.1> S:R346T (G22599C) > Orf1a:F536V (T1871G) Query:T1871G,G22599C,T3565C Samples: 33 Nigeria

FLIRT Branch 46 : Designated KP.1.1 spotted by @aviczhl2 from in https://github.com/cov-lineages/pango-designation/issues/2510

KP.1 > S:R346T Query: A24819G,C7113T,G22599C Samples : 9 India, Singapore,Argentina

Branch 47: dead

JN.1.4 > T18453C > T4342C, C5869T, T17154C, Orf1b:A1662V (C18452T) > S:R346K (G22599A ) Query: T4342C, C5869T, T17154C, G22599A Samples: 4 (US)

Branch 48: Dead

JN.1.4.2 > C29311T > S:R346T (G22599C) Query: C29311T ,G22599C,A22115G,T3565C Samples: 4 US , Brazil

Branch 49 : Excluded

cause very likely a sublineage of JN.1.18 and very likely an artifact JN.1.18 (346T) + S:K356M (A>C22629T) then acquired S:A771V or and S:L368P) Query: C23874T,A22629T, G22599C for 771V. >> 7 Samples Query for 368P: T22665C,A22629T, G22599C >> 9 Samples Query for 356M: A22629T, G22599C, T3565C >> 17 Samples Country : Nigeria ( very likely or an artifact or a relatively big lineage splitted by reversions)

Branch 50: Dead

JN.1.4 > T18453C > orf1a:N1442H (A4589C), Orf1a:T1754I (C5526T), A13722G,S:R346T (G22599C), T28019C, A29782G Query:C5526T, A13722G, A29782G Samples: 5 Brazil (via GBW) SLOW

Branch 51: Designated JN.1.39.1

Now Proposed in #2563 JN.1.39 (G2782T )> T111C > S:R346T (G22599C) (thx to the analysis by @aviczhl2 here )) Query: G2782T , T111C ,G22599C Samples: 28 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

FLIRT Branch 52: designated KP.4.2 from https://github.com/cov-lineages/pango-designation/issues/2523

JN.1.11.1 > C6070T > S:K187R (A22122G), S:R346T (G22599C) Query: C6070T,G22599C,C7113T,G24872T,-C19884T Samples: 9 Australia, New Jersey, Lebanon, China , India

FLIRT Branch 53: desingated KP.4.1 from https://github.com/cov-lineages/pango-designation/issues/2521

JN.1.11.1 > C6070T > C19884T > S:R346T (G22599C) Query: C6070T,G22599C,C7113T,G24872T, C19884T Samples: 7 Australia , Canada, Texas, India (GBW)

FLIRT Branch 54: Designated KP.2

JN.1.11.1 > S:R346T (G22599C) Query: C7113T,T22928C,T3565C,G22599C,-C6070T,-A24819G,-G943A,-C19895T,-A2745G (edited post designation) Samples: 8 Qatar,UAE, Nepal, South Korea Singapore

Branch 55 found by @corneliusroemer designated JN.1.25.1

JN.1 > C706T > A7708T > S:R346T (G22599C) Query: C706T,A7708T , G22599C

Branch 56 spotted by @krosa1910 FLIRT designated KZ.1.1 from #2548

JN.1.1.6 (C11747T > S:F456L=T22928C) [Branch 6 of #1253 ] > Orf1b:V1092F (G16741T) > S:R346T (G22599C) Query : G16741T,G22599C, C11747T ,T22928C Samples: 10 UK US AUs

Designated KZ.1.1.1

with further TRIO branch with S:T572I Branch 56 >> >Orf1a:L1546I (C4901A),S:T572I (C23277T) Samples: 5 (South Australia)

Branch 57 thx to @DailyCovidCases i noticed that this is not monophyletic at all, among the lineages caught by query the most interesting is this one JN.1.4 >> T18453C > C7732T>> Orf1a:D4117N (G12614A) > G22111A > C27944T >S:T22N (C21627A ) > S:R346T (G22599C) > A17256G, S:F58L (T21734C ) Query: A17256G, T21734C Samples: 12 (US) Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_601bd_fe5200.json?label=id:node_7136106 Original:

spotted by @aviczhl2 JN.1.4 > T18453C > S:R346T (G22599C) Query: C774T,T3565C ,-A29799G,G22599C,T18453C ,-A4589C,-C7732T,-A13308G,-C28201T,-T18471C,-A22115G,-C16308T,-C25710T ,-C13971A,-C5090A,-G6536T,-T1623C,-T4342C,-C5724T,-T4120C,-C501T,-C4551T,-C15277T,-A1819G,-C3884T,-T28098C,-C4832T,-G6362A,-C1625T,-G12940T,-C25721T,-A405G,-G22317T,-C29580T,-C27982T Samples: 168 Guatemala, Russia , South Africa (Query updated 8 still there are a bunch of samples unsure if belonging to this)

Branch 58 now designated JN.1.4.4 thx to @aviczhl2 that highlighted me the new JN.1.4 tree.

JN.1.4 > S:R346T (G22599C) Query: C774T,T3565C ,-T18453C,G22599C,-G25445A,-C23277T,-T3400C,-C27982T,-C2395T,-G533T,-C6870T,-G22627A,-T25542A,-C10078T, Samples:46 Canada

Branch 59 Dead

JN.1.4 > T18453C > A29799G > S:R346T (G22599C) Query: T18453C, A29799G,G22599C,-C27630T Samples : 3 on Usher 1 on Gisaid

Branch 60: Dead

JN.1.4.5 > T18453C > T18471C > S:S680F (C23601T)> S:R346T (G22599C) Query: T18471C ,C23601T,G22599C Samples: 2 US

Branch 61 Designated JN.1.11.2

now proposed in https://github.com/cov-lineages/pango-designation/issues/2542 JN.1.11 > S:R346T Query: G22599C,T3565C,-C7113T,G24872T,G17334T,-T22928C Samples : 28 SRI LANKA, India (WB,Odysha) , Wales 3 samples with S:F59S

FLIRT Branch 62 Designated JN.1.9.2 & LB.1 from https://github.com/cov-lineages/pango-designation/issues/2546

JN.1.9 > S:R346T(G22599C) > C835T , S:F456L (T22928C) Query for 346T: -A21282G,-C10626T,G22111T , G22599C ,T3565C,-C25688T,-T3913A Samples: 15 (Rep.Dominicana , Us, India) Query for Flirt : G22111T , G22599C , T22928C,T3565C Samples : 11 US GBW India

Branch 63 FLiRT first spotted by @aviczhl2 now proposed in https://github.com/cov-lineages/pango-designation/issues/2562

JN.1.11.1 > Orf1b:A2143V (C19895T) > S:R346T (G22599C) Query : C19895T,G22599C,T3565C Samples: 10 Australia , NJ , Scotland, Portugal with a TRIO branch: JN.1.11.1 > Orf1b:A2143V (C19895T) > S:R346T (G22599C) > S:T572I (C23277T) Query: C19895T,C23277T,G24872T Samples: 1

Branch 64: Duplicate it was KZ.1.1.1

It is JN.1.1 (Branch 17 of #1097) plus S:R346T tracked there. JN.1.1 > C11747T > S:T572I (C23277T)> S:R346T (G22599C) Query : C11747T ,C23277T ,G22599C ,T3565C Samples : 19

Branch 65: FLiRT spotted and proposed by @aviczhl2 in #1445 (https://github.com/cov-lineages/pango-designation/issues/2530)

JN.1> C24023T > S:S31F (C21654T) S:R346T Query:C24023T,C21654T,C18894T,G22599C
Samples: 31 With FLiRT branch: JN.1> C24023T > S:S31F (C21654T) S:R346T >T21015C > S:F456L (T22928C) Query: T22928C,T21015C,T3565C or C24023T,C21654T,C18894T,G22599C ,T22928C Samples:18

Branch 66 Dead

JN.1 > T18471C>G29134T > Orf3a:A99V (C25688T) > T3913A > S:Q183H (G22111T) > S:R346T (G22599C) Query:T18471C,G29134T ,G22111T ,G22599C Samples : 2 (3) India

FLiRT branch 67 Dead

KP.1 > C11704T> S:R346T (G22599C) Query: C11704T,A24819G,T3565C,G22599C Samples 7 on Uhser (2 by the query)

FLiRT Branch 68 dead

now proposed in https://github.com/cov-lineages/pango-designation/issues/2603 KP.1 > Orf1a:G519S (G1820A)> S:R346T (G22599C) Query:G1820A,A24819G,G22599C,T3565C Samples : 5 Oman India

Branch 69 Dead

JN.1 > T18471C > S:P85Q (C21816A) > C2773T, C20646T > S:R346T (G22599C) Query:C2773T, C20646T,G22599C Samples: 3 Australia

Branch 70 : Dead

Jn.1 > S:A684S G23612T > S:R346G (A22598G ) Query: G23612T,A22598G Samples : 2 ( Spain , Usher places them not exatcly in the same branch but very close)

Branch 71 : Tracked now in #1462

S:S60A + S:R346S JN.1 >S:S60A (T21740G )> C11020T > S:R346S (A22600T) Query: T21740G ,A22600T Samples : 23 NY with a dead FLiRS sample : JN.1 >S:S60A (T21740G )> C11020T > S:R346S (A22600T) > Orf1a:I1159T(T3741C)>C5654T > Orf1a:P885S (C2918T),S:F456L (T22928C) Query: T3741C, C5654T , C2918T

Branch 72 dead

JN.1 > C25782T > C5884T > S:R346T (G22599C) Query: C25782T , C5884T , G22599C, T3565C Samples: 8 (US,India)

Branch 73 FLiRI> dead

Then FLiRT highlighted first by @AngieHinrichs It seems this one went from 346I to 346T: KP.1> S:R346I (G22599T), C24034T> Orf1a:H81Y (C506T)> S:I346T (G>T22599C) Query for FLiRI (Dead):G22599T, C24034T,G24872T Samples: 2 (Canada) Query for FLiRT:G22599C, C24034T,G24872T,C506T Samples: 3 (Query not reliable)

Branch 74 : Undersampled area needed to check if dead

FLIRT spotted by @krosa1910 and @aviczhl2 sublineage of Branch 13 of #1253 JN.1.29.1 [A9935G=Orf1a:T3224A > S:F456L (T22928C)] > C8917T > S:R346T (G22599C) Query: A9935G,C8917T ,G22599C,T3565C Samples : 23 (Brazil)

Branch 75 : Dead

FLiRT JN.1.11.1 > Orf1a:P885S (C2918T) > A742G > S:R346T (G22599C), C27923T Query: A742G,C27923T ,G22599C Samples: 2 (GBW India)

Branch 76 FLiRI Designated LA.2 from https://github.com/cov-lineages/pango-designation/issues/2555

JN.1.16.1 > C4777T > S:R346I ( G22599C>T) Re placement see comment by @aviczhl2 below, the likely path is: JN.1 > C4777T > S:F456L > S:R346I Query : C4777T , G22599T,T3565C Samples: 7 (England, Malaysia,California) Proposed by @aviczhl2 all together with sibling 346T branch hidden by JN.1.16.1 misplacement Query: C4777T, T22926C, T22928C, G22599C

Branch 77 dead

identified using Dave McNally's tool DEAD JN.1.5 > > Orf1a:K714R (A2406G), Orf1b:S1779G (A18802G), S:R346T (G22599C), T29524C Query: A2406G,A18802G Samples : 25 UK

Branch 78 FLiRT: dead

KP.1 > Orf1b:P2256S (C20233T) > [Artifact G13427A], S:R346T (G22599C) Query: C20233T ,G22599C,T3565C, A24819G Samples 4 : UK, Qatar via GBW

Branch 79 Dead

sibling of non flirt Singlet 1 JN.1.4 > T18453C > T4342C, C5869T, T17154C, Orf1b:A1662V (C18452T) > S:R346K (G22599A) Query: T4342C, C5869T, T17154C,G22599A Samples: 5 NY,IL

Branch 80 Dead

(G17562T is a big undesignated branch with multiple R346X lineages most dead except Branch 10,80,81) Jn.1 > G17562T > Orf1b:L2560F (C21145T) > Orf1b:G128S (G13849A) > T961C, A7429T, S:R346I (G22599T),N:A50V / ORF9b:R47C (C28422T) Query:T961C, A7429T Samples : 8 (Canada likely a cluster)

Branch 81 Dead

JN.1 >> G17562T > Orf1a:G519S(G1820A) > S:R346T (G22599C) Query: G17562T, G1820A , G22599C,T3565C Samples: 12 (UK)

Branch 82 Dead

mini saltation three spike mutations JN.1> S:V>G213E (G22200A)> C20436T, S:R346T (G22599C), S:G482S (G23006A), Orf7b:I7N (T27775A), N:T379N (C29409A) Query: C20436T, G23006A, T27775A Samples: 2 UK

Branch 83 Dead

JN.1 > C24034T > S:R346T (G22599C) Query:-A2345G,-A29700G,-C541T,-A80G,-G2782T,-T4793G ,C24034T ,G22599C,T3565C,-T20802C,-C5184T Samples : 3 ( 2 by the query) Hubei, GBW

Branch 84 Designated LQ.1 and LQ.1.1

now proposed in https://github.com/cov-lineages/pango-designation/issues/2596 FLiRT former singlet 11, tracked as branch 55 of #1253 JN.1.18.1 (S:T250N) > C14220T > S:F456L (T22928C) > >S:P272H (C22377A) Query: T22928C,C14220T,C22311A Samples 12 Uk,CA,Aus

Branch 85 FLiRT now proposed in https://github.com/cov-lineages/pango-designation/issues/2606

JN.1.11.1 >> C5467T > C9857T > S:R346T (G22599C ) Query: C9857T ,C5467T, G22599C,T3565C Samples: 10 India UK

Branch 86 DEAD

JN.1 > Orf1b:A2480S (G20905T) > T8323C > Orf1a:D2492N (G7739A), C10369T, S:R346T (G22599C) Query:G7739A, C10369T, G22599C Samples: 14 Mexico Canada Further branch with S:N603S,S:N641K (Query:A23370G, T23485A, A25590G)

Branch 87 JN.1.18.4

Now proposed in #2567 JN.1> C27143T > S:R346T (G22599C) Query: C27143T ,G22599C,T3565C Samples: 133 Further FLiRT branch Br.87> S:F456L (T22930G), T23036C, Orf6:I60T (T27380C) Query: T27380C,T22930G Samples: 135

Branch 88 dead

found by @HynnSpylor proposed in #1499 LC.1 [JN.1.1.7->S:R346T(G22599C)]->C5407A, C9442T, S:L455S->A (T22925G), ORF7a:T28I (C27476T) Query:T22925G,C5407A Samples 3

Branch 89 Designated JN.1.56.1

FViRT now proposed in https://github.com/cov-lineages/pango-designation/issues/2582 JN.1 > Orf3a:Q213K (C26029A) > Orf1a:T1638I (C5178T) >T8278C, S:G181R (G22103A), S:R346T (G22599C), S:F456V(T22928G) Query: C26029A,C5178T,T8278C Samples: 8 Singapore

Branch 90 spotted and proposed by @aviczhl2 in #1503 #2679

JN.1 >T20285C,A20284T(Orf1b:I2273S)> S:R346T (G22599C)> S:F456L (T22928C), C29218T Query for 346T: T20285C, A20284T, C18894T, G22599C Samples: 47 Query for FLirt :T20285C, A20284T, C18894T, G22599C,T22928C Samples: 38

Branch 91 : Designated KW.1.1.1 and LG.1

TRIO proposed in #1504 by @Sinickle [ ex Singlet 21 here ] KW.1.1 > S:T95S (C21846G), S:R346T (G22599C), C27600T Query: C21846G, G22599C, C27600T,T3565C Samples : 10 Australia

Branch 92 : Dead

FLiRT Former Singlet 9 JN.1.11.1 > rev G17334G > G7936A, Orf1b:P1821S (C18928T), S:R346T (G22599C), C23191T Query: C18928T,G22599C, C23191T,T3565C Samples: 4 California

Branch 93 DEAD

FViRT former Singlet 14 JN.1> G17562T S:F456V S:R346T Query: T22928G, C18657T Samples: 5 US

Branch 94 FLiRT Now proposed in https://github.com/cov-lineages/pango-designation/issues/2565

former Singlet 15 & SInglet 5 JN.1 > S:H1101Y > S:F456L > S:R346T > S:S71F Query: C24863T, G22599C, T3565C,C21774T Samples: 19 Uk,US, Canada

Branch 95 Dead

FLiRT former Singlet 20 KP.1 > Orf8:F3S (T27901C) > S:R346T (G22599C) Query: T27901C,A24819G,G22599C Samples: 3 USA

Branch 114 Now designated KP.2.9 TRIO former Singlet 22 = Branch 96

KP.2 > C15579T > [artifact Orf1a:E4388K (G13427A)],C19512T, S:T572I (C23277T), S:R683L (G23610T) Query: C19512T, C23277T,G23610T Samples: 2 California

Branch 97 proposed in #1682

FLiRI (merging Singlet 26 and 12): JN.1.11.1 > S:R346I (G22599T) Query: G22599T,C7113T,T22928C,T3565C,-T416A,-A24819G Samples: 10 Bangladesh with a DeFLIRI branch spotted by @aviczhl2 Query: G22599T,C7113T,T22928C,T3565C,del21653 Samples: 9

Branch 98

FLiRT Former singlet 23 now tracked also as Branch 84 in #1253 JN.1> C1612T> Orf3a:A103T (G25699A) > G13045A > G25770A > C583A, T16263C, S:R346T(G22599C), S:F456L (T22928C), Query: C583A, T16263C, , T3565C Samples: 36 Scotland Usa Russia

Branch 99 FLiRT now proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1648

JN.1 >S:S71F (C21774T) > S:r346T ( G22599C )> S:F456L (T22928C) Query: C21774T ,G22599C ,T22928C,T3565C,-C7113T,-C24863T,-G4067A,-C28674T Samples: 46 (France, England)

Branch 100 FliRT now proposed in https://github.com/cov-lineages/pango-designation/issues/2583

Former singlet 8 sibling of Branch 85 JN.1.11.1 > C5467T > S:R346T (G22599C) Query: C5467T, G22599C,C7113T,-C9857T,T3565C Samples: 86 Uk, Taiwan , Singapore Branch with S:F59S : T21738C,C5467T,C7113T Samples:2

Branch 101 JN.1.18.5

now proposed in https://github.com/cov-lineages/pango-designation/issues/2588 FLiRT [sublineage of Branch 20 of #1253 by @aviczhl2 ] Jn.1> F:456L (T22930A) > S:R346T (G22599C) Query: G22599C,T22930A, T3565C, T22926C,-A2543G,-C4455T,-T8862C,-C25658T,-G260A,-A6705G,-A2251G,-C1762A,-C774T,-G25552T,-A6705G,-T23031C,-T24364C,-C2061T,-G18756T,-C26684T,-A4005G,-A720G,-G16377T,-C14724T,-C2574T,-A23598G,-C18657T,-G6183A Samples: 14 (Uk France US Singapore three of them with S:D936H (G24368C) Query: G22599C,T22930A, T3565C,G24368C,-C1762A)

Branch 102 Dead

FLiRT Former Singlet 4 JN.1 > Orf1a:K4483R (A13712G) > Orf1a:K1407N (G4486T) > A3058G > S:F456L (T22928C) > S:R346T(G22599C) Query: G4486T,A3058G, G22599C Samples: 2 (Eng,Can)

Branch 103 Dead

JN.1> C3397T > G16269A> C8140T, T8248C > A16947G, S:R346I (G22599T) Query: C8140T, T8248C ,A16947G Samples : 4 (California)

Branch 104 Dead

JN.1.22 > C13019T >T20241C > S:R346T (G22599C) Query: C13019T ,T20241C ,G22599C Samples: 9 Canada

Branch 105 Dead

JN.1> Orf1a:A3523V (C10833T) > G2782T >S:S31F ( C21654T) > S:R346S (A22600C) Query: G2782T , C21654, T3565C,A22600C Samples: 11 (US, France)

Branch 106 Dead

JN.1 > S:T883I(C24210T) > S:I883M (T24211G) >S:R346T (G22599C) Query: C21297T, G22599C,T3565C fInds 2 Australian samples while: T24211G,G22599C,T3565C finds a French sample all put together by USher)

Branch 107 MP.1 and MP.1.1

one recent upload from SA
BA.2.86 > T10819C,C28720T > Orf1b:Y1344H (T17497C) > C21646T, S:N487D (A23021G) ,A23089G, C28115T > S:A348P (G22604C), S:R346T (G22599C) Query for 487D : T17497C,T10819C,C28115T
Samples: 13 : SA Mozambique Query for 346T 348P A23089G, C28115T ,G22604C,G22599C Samples : 3 South Africa

Branch 108 now proposed in https://github.com/cov-lineages/pango-designation/issues/2605

FLiRT (Branch 30 of #1253 spotted by @aviczhl2 ) JN.1.26 > S:F456L (T22928C) Query: C26894T, C7732T,G22599C, T22928C Samples: 71 Canada,Us

Branch 109 Spotted and proposed by @aviczhl2 As branch 62 of #1253

JN.1+G17562T+S:F456L,
Query: G17562T,T3565C, T22928C,-8716 Samples: 184 partially misplaced in LB.1

Branch 110 Dead

Former singlet 3 JN.1.1.6 > S:H625R (A23436G) > S:R346T (G22599C)
Query: A23436G,G22599C,T3565C Samples: 2 (UK)

Branch 111 now designated Kp.2.27

https://github.com/cov-lineages/pango-designation/issues/2568 FLiRT TRIO former branch 63 of #1097 JN.1.11.1 >S:T572I (C23277T) > C3811T > C2197T, C9857T, S:R346T (G22599C) ,A23080G Query:C3811T , C2197T, C9857T,T3565C Samples: 39 (US)

Branch 112: Proposed in https://github.com/cov-lineages/pango-designation/issues/2645

FLiRT ( originally spotted in Branch 73 of #1253 by @aviczhl2 ) JN.1>C27110T>S:F456L(T22928C) >C3244T, A18432T> G29383A > S:R346T (G22599C), Query:C3244T, A18432T,G22599C Samples: 19 (Ireland, Scotland, California) ( 5 with S:M153I Query: C9169T, T12987C) with S:S31F Query: C21654T, C9169T, G22021C Samples: 7

Branch 113 KR.3 see branch 87 of # 1253

FLiRT [recombinant JN.1.11.1/Singlet 31 ??] JN.1.1 > > C11747T> C9142T > ,S:R346T (G22599C),S:F456L (T22930A) ,Orf1a:T2283I (C7113T) Query: T22930A, C9142T, G22599C,T3565C ( new query from Br.87 of #1253 by @aviczhl2 ) Samples: 26

Branch 114 Duplicate now KP.2.9

TRIO KP.2 >C15579T >C19512T ,S:T572I (C23277T) Query:C19512T ,C23277T,C15579T,T3565C Samples:6

Branch 115 Dead

FLiRT former Singlet 30 JN.1.1 >> > C11747T > Orf3a:T24I (C25463T) > C25710T > , S:R346T (G22599C), S:F456L (T22928C) , C28603T Query:C25463T, C28603T,T3565C Samples: 15 (US,England Australia)

Branch 116 Dead

FLiRT ex Singlet 39 JN.1.13.1 > C28789T > G12718A,Orf1b:V1760A (T18746C), S:F456L (T22928C) Query:G12718A,T18746C,T3565C Samples : 3

Branch 117 Dead

FLiRS Jn.1.39 > S:F456L or Jn.1.16 > G2782T > S:R346S A22600C, T25054C Query: G2782T,T3565C,A22600C, T25054C Samples: 5 NY

Branch 118 Dead

FLiRT JN.1.18> S:F59S (T21738C) > C18348T > [ G260A ?? ]> S:F456L (T22930A) Query: C18348T ,t3565C,T22930A Samples : 9 (Uk)

Branch 119 Dead

FLiRT Jn.1.13.1>C7945T> S:F456L (T22928C) Query: C7945T, T22928C, T21738C,T3565C Samples: 4 ( GBW from Austria and UAE likely two patients only)

Branch 120 Designated KR.2

FViRT now proposed in https://github.com/cov-lineages/pango-designation/issues/2586 JN.1.1.5 > T6095C,C6541T, C21911T, S:L176F (C22088T), S:F456V (T22928G ) Query: T6095C,C6541T,C21911T,T3565C Samples: 24(Canada, US)

Branch 121 Dead

FLiRT JN.1.11.1 > Orf1a:K2148R (A6708G),C18060T, C20457T, S:R346T (G22599C) Query: A6708G,C18060T,T3565C Samples: 3 India

Branch 122 : Dead

FViRT JN.1.18> C28603T > T15993C, S:F456V (T22928G) Query:T15993C , T22928G Samples: 2 Singapore

Branch 123 dead

KR.5 [JN.1.1.5 > Orf1a:L642F (C2189T), Orf1a: T2087I (C6525T)]> A23746G > S:F456L (T22928C) Query: C2189T, C6525T, A23746G ,22928C Samples: 4 Brazil

Branch 124 Designated LF.3

now proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1558 The tree has changed and it is now under Jn.1.16.1 again so not to be tracked here JN.1.16 > C5581A > C7594T, Orf1a:A4285V (C13119T), S:R346T (G22599C) Query: C13119T, C7594T, G22599C, C5581A Samples: 5 [ 3 WITH S:V455P Query: T22896C,C5581A,C7594T ] California

Branch 125: Designated LV.2 it is a MOV lineage- intercontinental

Ba.2.86+ Mov got FLiRT found&tracked by @JosetteSchoenma (Ex SInglet 43) BA.2.86>G1738T, Orf1a:G1069R (G3470A) > C27059T > Orf1a:E148G (A708G), Orf1a:W630C (G2155T), G10902A, Orf1b:A520V(C15026T), C22594T, S:R346T (G22599C), S:L455S (T22926C), S:F456L (T22928C), N:A211S (G28904T), N:A398V (C29466T) Queries:A708G, G2155T, C15026T or G28904T, C29466T, T22928C finds 2 (Australia)

Branch 126: It has now split in two: one proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1623 with A22108C, C23277T, T23599C and the other tracked as Branch 149

TRIO found by @ryhisner KP.1.1.1 > S:T572I (C23277T) Query:C23277T,A22108C,C20104T Samples: 11 USA

Branch 127: Dead

FLiRT ex singlet 56 JN.1.13.1 > C28603T > ,S:F456L (T22928C) Query: C28603T ,22928C,T3565C,T21738C Samples: 20 Japan/UK/HK/China/Canada

Branch 128 Dead

FliRT Mini saltation NY Jn.1.11.1 > G7393T > C337T , C22570T, S:R346T(G22599C), S:T574K (C23202A), S:H1159R (A25038G), ORF3a:S253Y (C26150A) Query: C23202A,A25038G,T3565C Samples: 3 NY

Branch 129 TRIO duplicate of Branch 126

KP.1.1.1 > T9769C, S:T572I (C23277T), C27143T, ORF7a:R78L (G27626T) Query: T9769C ,C23277T, C27143T,T3565C Samples: 2 (USA)

Branch 130 Dead R346T

JN.1 > > C15960T > C3253T, A12772G, S:R346T (G22599C), A26019G, N:N29T/Orf9b:A29L (A28359C) Query: A28359C, T3565C Samples: 10 (South Africa, France)

Branch 131 Dead

FLiRT JN.1.4 > > C774T > T18453C > A29799G > C27630T > C17172T >Orf1b:A1662V (C18452T) > C12781T > Orf1a:G3704S (G11375A) > Orf1a:P959A (C3140G), S:R346T (G22599C), S:F456L (T22928C), N:T391A (A29444G) Query: C17172T ,C3140G Samples: 3 (South Korea one with further S:Q271H, S:N955D > Query for it : G4409A, A4783G, A8143G )

Branch 132 dead

FLiRT JN.1.11.1 > Or1b:P2633L (C21365T) > S:R346T (G22599C) Query: C21365T,G22599C,G24872T,-C25162A Samples: 3 India ( + 2 Thailand not caught by query)

Branch 133 designated LF.6

now proposed in https://github.com/cov-lineages/pango-designation/issues/2589 FLiRT ex singlet 35 JN.1 >T17859C > T3172G >>S:R346T (G22599C), S:F456L (T22928C) Query: G22599C, T22928C, T17859C, T3172G, T3565C Samples: 6 (Portugal, Spain)

Branch 134 Proposed in https://github.com/cov-lineages/pango-designation/issues/2659

FLiRT ex Singlet 81 JN.1.11.1 > G29711T > 3277G, Orf1b:K469N (G14874T), S:R346T (G22599C), ORF9b:T72I (C28498T) Query: G14874T,G22599C,C28498T
Samples: 32 (Canada + 2 French not found by the query)

Branch 135 FLIRT NOW DESIGNATED JQ.2.1.1 VIA https://github.com/cov-lineages/pango-designation/commit/1ff69c9ea3d7baf3bdb7db3563e1f425aa109b61

BA.2.86 FLiRT ex Singlet 79 JQ.2.1> ORF1a:T265I (C1059T), C7639T, S:F456L (T22928C),ORF3a:I123T(T25760C) Query: C7639T,T25760C T22928C,C1059T Samples: 3 ( Australia, South Africa)

Branch 136 designated MH.1

now proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1583 DelTRIO (First ever) former Singlet 71 LB.1+S:S31Del > S:T572I (C23277T)
Query: C23277T,G22111T , G22599C , T22928C, del21653 (Israel then a branch with S:V642G and S:P809S found by @HynnSpylor ) Samples: 3 Israel, Us, Uk

Branch 137 designated MF.1 proposed in https://github.com/cov-lineages/pango-designation/issues/2461

Ex Singlet 61 TRIO JN.1 >> Orf3a:L85F (G25647T) > A5053G, T23629C > ORF1a:T2152I (C6720T)> S:T572I (C23277T)>C5884T, A10420G, S:F456L (T22928C), C29149T > , A13776G, T14586A, T21673C, S.R346T (G22599C), T22981C (S:Y473Y) Query: A13776G, T14586A, T21673C , T22981C Samples: 2 US,Spain

Branch 138 now designated LU.1

proposed in https://github.com/cov-lineages/pango-designation/issues/2604 sublineage of Branch 12 of #1253 FLiRT ex singlet 72 JN.1.15 (S:A688V) > C19269 ,Orf3a:R122S (A25758T)> S:F456L (T22928C) > S:R346T (G22599C) Query: C23625T,G22599C,C19269T,T3565C Samples: 4 Spain, US

Branch 139 Designated LM.1

Now proposed in https://github.com/cov-lineages/pango-designation/issues/2608 FliRT JN.1.25.1 >> C7318T > G26648A > C28948T > S:F456L (T22928C) Query: C7318T , G26648A ,T22928C Samples: 8 Canada , UAE (GBW), Uk
the sample from Canada has also S:S31del DeFLiRT (Query: G26648A,del21653_21655, T22928C)

Branch 140 dead

JN.1.13.1 > C4276T > S:F456L (T22928C) Query: C4276T , T22928C,T21738C,T3565C Samples: 7 ( 2 on Gisaid, Scotland, Uzbekistan)

Branch 141 ex singlet 50 dead

JN.1.49.2 [Orf3a:T89I (C25658T) > S:F456L (T22930A)] > S:R346T (G22599C) Query: T22930A,C25658T,G22599C,T3565C ,-T13279C Samples : 13 (Sweden uk)

Branch 142: dead

JN.1 > > A8080G, Orf1b:Q2203R (A20075G), S:R346T (G22599C), N:G238D (G28986A) > Orf1a:E913G (A3003G) > A19077T > S:F456L (T22928C) [FLip FLop at orf6:61] Query: A8080G, A20075G,G22599C new query Samples: 6 Sweden

Branch 143 Dead

ex singlet 38 JN.1.11.1 > Orf1:D147N (G704A) >T9499G, C11020T,, G14118T, S:R346T (G22599C),Orf3a:A110S (C24358A), G25720T, Orf8:G77S(G28122A) Query: G704A,T9499G Samples: 9 UK

Branch 144 dead

ex Singlet 46 JN.1.11.1 > G22927T > A13132G,S:R346T (G22599C), Orf7a:A66V (C27590T) Query : G22927T, A13132G,T3565C Samples: 4 NZL

Branch 145 dead

JN.1.13.1 > C6781T > Orf1a:T2846I (C8802T), S:F456L (T22928C) Query: C6781T ,C8802T,T22928C Samples: 2 (GBW)

Branch 146 proposed in https://github.com/cov-lineages/pango-designation/issues/2677

JN.1 > C823T > S:R346T (G22599C) > A12772G, N:N29T / Orf9b:A29L(A28359C) Query:A12772G, A28359C Samples: 11 (South Africa)

Branch 147 Designated LZ.2 via https://github.com/cov-lineages/pango-designation/commit/2c6deafbe1cc1a52cd7c282d9bd5719189962d0c

now proposed in https://github.com/cov-lineages/pango-designation/issues/2653 JN.1.18.2 ( S:F59S) > Orf1a:K1226E (A3941G) > S:F456L (T22928C) > Orf10:Q29* (C29642T) Query: A3941G ,T22928C, T21738C Samples: 23 NZL

Branch 148: dead

JN.1.18> Orf1a:P892S (C2939T) >C4276T, G18315A, S:F456L (T22930G), Orf3a:V77A (T25622C), N:R41L/ORF9b:G38C (G28395T), C28849T Query:T25622C, G28395T ,C4276T Samples: 2 (Philippines GBW)

Branch 149 (ex branch 126) now proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1755

KP.1.1.1 > C27143T > T9769C,S:T572I (C23277T), G27626T> Spike_I100L (A21860T) Query:T9769C, G27626T ,C27143T Samples: 15 (Colorado)

Branch 150 ex singlet 25 Fvirt designated MB.1

JN.1.49.1 [Orf3a:T89I (C25658T), S:R346T (G22599C)] > C8917T, S:S31F (C21654T), S:F456V (T22928G) Orf10:I27K (T29637A)> G7393T> S:T22N (C21627A),S:K182N (A22108C) Query for Fvirt+ S:S31F: C8917T, C21654T,T22928G >Samples: 5 Query for Fvirt +S:S31F S:T22N S:K182N : G7393T ,C21627A, A22108C >Samples: 3

Branch 151 Dead

Undesignated JN.1 branch got FLirt + S:G35C then S:L10I and S:V1104L JN.1 > Orf3a:L41F (C25513T) > S:F456L (T22928C) >Orf1a:L1110F (C3593T), S:G35C (G21665C), S:R346T (G22599C),M:D>H3Q (T26531A) > C9661T, T14064C, T20892A, S:L10I (C21590A), S:V1104L(G24872T) Query for flirt: C3593T,G21665C Samples:2 Query for S:L10I:C21590A ,G24872T,T3565C Samples: 1

Branch 152 dead

FLIRT subbranch of #https://github.com/cov-lineages/pango-designation/issues/2613 with FLiRT 182N and 445P Query: A10027T, A10317G, A22108T Samples: 1

Branch 153 Now proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1773

JN.1.43.1 > C19488T> C29218T> S:R346T (G22599C) > S:D287E (T22423A) Query: C19488T, C29218T,T22423A Samples: 19

Branch 154 Designated MJ.1 JN.1.29.1 > S:R346T > Orf1a:E2070K (G6473A), T17364C, S:S31P ( T21653C) Query: G6473A, T21653C,A9935G Samples: 19 (Likely from Latin America)

BRANCH 155 now designated MQ.1

Trio now proposed in https://github.com/cov-lineages/pango-designation/issues/2710 JN.1.7.8 (456L+S:185-89DEL) > C16954T,S:T95I (C21846T), S:R346T (G22599C), T24499C QUERY: C16954T,del22115,T3565C SAMPLES:5 COUNTRY: SPAIN

FLIRT Singlets (also FVIRT or FLIRI or FLIRS):

1) transferred to Branch 63

JN.1.11.1 > Orf1b:A2143V (C19895T) > S:R346T (G22599C) Query : C19895T,G22599C,T3565C

2) Dead

JN.1.1 346T 456L Query: , C10138T, G4656T,T22928C

3) Now Branch 110

JN.1.1.6 > S:H625R (A23436G) > S:R346T (G22599C) Query: A23436G,G22599C,T3565C

4) Now it became Branch 102

JN.1 > Orf1a:K4483R (A13712G) > Orf1a:K1407N (G4486T) > A3058G > S:F456L (T22928C) > S:R346T(G22599C) G4486T,A3058G, G22599C ( see Branch 47 #1253 )

5) Now Branch 94

JN.1 > S:H1101Y ( C24863T )>S:F456L (T22928C) > S:R346T (G22599C ) see comment in #1253 Query: C24863T, G22599C, T3565C [remainder always check the tree it could be just JN.1.16.1 misplaced)

6) Dead

JN.1.49 [Orf3a:T89I (C25658T)] > Orf1b:A167V (C13967T )> C27297T >S:R346T G22599C, S:F456V (T22928G) Query: C13967T , C27297T ,G22599C, T22928G

7) Dead

JN.1.1.5 > Orf1a:P971S (C3176T), S:F456L(T22930A), S:D936H (G24368C) Query: C3176T,T22930A,G24368C

8) Now Branch 100

JN.1.11.1 > C5467T >Orf1a:A967V (3165T), Orf1a:T2859I (C8841T), Orf1b:Q813E (C15904G), T21934C, S:R346T (G22599C) Query: C3165T, C15904G, T21934C

9) Now Branch 92

JN.1.11.1 > rev G17334G > G7936A, Orf1b:P1821S (C18928T), S:R346T (G22599C), C23191T Query: C18928T,G22599C, C23191T,T3565C

10) Dead

JN.1.30.1 > Orf1a:V2130A (T6654C), T11593C S:F456V (T22928G), C25603T Query : T6654C, T11593C spotted by @aviczhl2

11) Proposed in https://github.com/cov-lineages/pango-designation/issues/2596

Now branch 84 of this and branch 55 of #1253 by @aviczhl2 JN.1.18.1 (S:T250N) > C14220T >S:P272H (C22377A), S:R346T (G22599C) Query: C14220T,C22377A,G22599C

12) now Branch 97

JN.1.11.1 > Orf1a:L590F (G2035T), Orf1a:P971L (C3177T), C18261T,S:R346I (G22599T) Query: G2035T, C18261T,C3177T,

13) As expected it conflated then in Branch 63

JN.1.11.1>ORF1a:A1049V (3411T), Orf1a:S1517F (C4815T), ORF1a:A2614V (C8106T), ORF1b:L1698I (C18559A), ORF1b:A2143V (C19895T), S:R346T (G22599C), ORF8:S54L (C28054T) Query: C3411T, C8106T, C18559A (Having C19895T it could be part of Branch 63)

14) Now Branch 93

JN.1> G17562T S:F456V S:R346T Query: T22928G, C18657T

15) Now Branch 94

JN.1 > S:H1101Y > S:R346T S:F456L Query: C24863T, G22599C, T3565C

16)Dead

JN.1.4 + 346T +456L Query: C27791T,C20178T, G22599C, T22928C

17) Dead

JN.1.6.1 > S:F456L Query G1156T, C10416T, T22928C,

18) Now Branch 51

JN.1.39 / Branch 51 > C5986T, ORF1a:F3677L (T11296G), C14220T, Orf1b:T760I (C15746T), S:F456L (T22928C),C24616T , S:V1104L (G24872T), C27389T Query: G2782T , T111C ,G22599C,T22928C

19) Dead

TRIO KQ.1 (346T+572I) > ORF1b:M624V (A15337G), C20719T, ORF3a:V55F(G25555T), ORF3a:T64A (A25582G), S:F456L (T22928C) query: G25555T,A25582G

20) Now Branch 95

KP.1 > Orf8:F3S (T27901C) > S:R346T (G22599C) Query: T27901C,A24819G,G22599C

21) Now proposed by @Sinickle in #1504

TRIO KW.1.1 > T16692C, S:T95S (C21846G), S:R346T (G22599C) ,C27600T, Orf7a:V74A (T27614C) Query: T16692C, C21846G

22) Now Branch 96 Now designated KP.2.9

TRIO KP.2 > C15579T > [artifact Orf1a:E4388K (G13427A)],C19512T, S:T572I (C23277T), S:R683L (G23610T) Query: C19512T, C23277T,G23610T

23) Now Branch 98

JN.1> C1612T> Orf3a:A103T (G25699A) > G13045A > G25770A > C583A, T16263C, ORF1b:E1871K (G19078A) , S:R346T(G22599C), S:F456L (T22928C),T26861C
Query: C583A, T16263C, T26861C, T3565C

24) Dead

sublineage of Br.87> C12415T, Orf1b:G1756R (G18733A), S:F456L (T22930G), T23036C, S:F1103S (T24870C), T27380C Query: C12415T, G18733A,

25) now Branch 150

JN.1.49.1 [Orf3a:T89I (C25658T), S:R346T (G22599C)] > C8917T, S:S31F (C21654T), S:F456V (T22928G) Orf10:I27K (T29637A) Query: C8917T, C21654T,T22928G

26) Now Branch 97 with Singlet 12

JN.1.11.1 > S:R346I (G22599T) > Orf1a:S531I, (G1857T), Orf1a:T1760I (C5544T), Orf1a:K3351R (A10317G), A12787G,S:D1153V (A25020T), M:E12D (G26558T),C28603T Query: C5544T, A10317G,G1857T

27) Dead

JN.1.30.1 > Orf1a:Y182H (T809C) > C21590T >C228T,S:F456L (T22928C), ORF9b:T72I (C28498T) query: T809C, C21590T ,C228T

28) TRIO now JN.1.48.1+ 572I spotted and proposed by @aviczhl2 in https://github.com/cov-lineages/pango-designation/issues/2547 Query: C23277T,C25378T, T3913

JN.1>T18471C>C25688T(Orf3a:A99V)>T3913A> C8092T, S:S60P (T21740C), R346T(G22599C), C25378T> S:F456L (T22928C) > S:T572I (C23277T) Query: C23277T,C25378T, T3913 samples: 5

29) Dead

JN.1.11.1> G17334G rev >C2509T A4822G,A7842A REV, S:R346T (G22599C), G23222G REV, T26561C, Orf10:R24C (C29627T) Query: A4822G, T26561C

30) Now Branch 115

JN.1.1 >> > C11747T > Orf3a:T24I (C25463T) > C25710T > ORF1b:H716Y (C15613T), S:R346T (G22599C), S:F456L (T22928C), M:G6V (G26539T), C28603T Query:C25463T, C28603T,T3565C

31) Dead

JN.1.1 > > C11747T> C9142T > C28957T > C2371A , S:R346T (G22599C),S:F456L (T22930A), C24748T Query:T22930A, C24748T,T3565C

32)Dead

JN.1 > M:L46F (G26660T) > G4162A > S:F456L (T22928C) >ORF1a:S558F (C1938T),S:R346T (G22599C) in #2531 Query: C1938T, G22599C,G1126A

33) Now Branch 112 ( = Branch 73 of #1253 found by @aviczhl2 )

JN.1+C27110T+S:F456L> >C3244T, A18432T> G29383A > C17373T, S:R346T (G22599C), G29383A Query : C3244T, A18432T,G22599C

34) Dead

TRIO XDK.1 > G11596A > C18664T > S:F456V (T22928G), T22930A , Orf6:P57L (C27371T), C29762T, Orf10:L37F (C29666T) Query:T22928G, C18664T Spotted by @aviczhl2

35) Now Branch 133

JN.1 >T17859C > T3172G >>S:R346T (G22599C), S:F456L (T22928C), C25413T Query: G22599C, T22928C, C25413T ,T3565C (Spain)

36) Dead

JN.1.13> C4777T, C7765T, S:F456L (T22928C), T28088C,T29685A QUERY: C7765T, T28088C,T3565C QATAR

37) Proposed in #2493

JN.1.4.7 [Orf3a:G18D (G25445A)]> S:R346T (G22599C) > C1471T, A8882T, C15222T,, A15864G, Orf1b:L2218V = Nsp15_L167V (T20119G) , C20719T, S:A435T (G22865A), S:F456L (T22928C), S:V1264L (G25352C), C26625T Query: A8882T, A15864G

38) Now Branch 143

JN.1.11.1 > Orf1:D147N (G704A) >T9499G, C11020T,, G14118T, S:R346T (G22599C),Orf3a:A110S (C24358A), G25720T, Orf8:G77S(G28122A) Query: G704A,T9499G UK

39) Now Branch 116

JN.1.13.1 > C28789T > G12718A,Orf1b:V1760A T18746C, S:F456L (T22928C) Query:G12718A,T18746C,T3565C

40) Dead

JN.1 > C643T > S:R346T (G22599C) > A5524G, Orf1a:D2026E (T6343A), A14457T, N:N27Y (A28352T) > T643C (rev), Orf1a:A4357V (C13335T), S:F456L (T22928C) Query : C13335T,T22928C,A14457T

41) Dead

FLiRS JN.1 > ORF9b:S50L(C28432T) > Orf1b:D275N (G14290A), A22600T > C1684T, Orf1a: (D2136G),A6672G, S:F456L (T22928C), T25464C, C27982T Query: G14290A, A22600T, C1684T Scotland

42) Dead

FLiRT Australia under a suspicious A23054C (R498R) + Jn.1.4.5like branch JN.1> A23054C> Orf1a:T170I (C774T) > S:R346T (G22599C) >G17334T (Art.?) , S:F456L T22928C, 25806G,Orf8:S103L (C28201T), C29632T Query:A25806G, C29632T,C28201T

43) Now Branch 125

BA.2.86 found by @JosetteSchoenma
BA.2.86>G1738T, Orf1a:G1069R (G3470A) > C27059T > Orf1a:E148G (A708G), Orf1a:W630C (G2155T), G10902A, Orf1b:A520V(C15026T), C22594T, S:R346T (G22599C), S:L455S (T22926C), S:F456L (T22928C), N:A211S (G28904T), N:A398V (C29466T) Query:A708G, G2155T, C15026T or G28904T, C29466T, T22928C

44) Dead

JN.1.22 > C13019T > T23485C > S:F456L (T22928C) > G2764T, G2944A, T13033C,Orf1b:M1397I (G17658T), S:R346T (G22599C), C25006T Query: G2764T, G2944A,T3565C

45) XDK/JN.1.11.1 recombinant spotted by @JosetteSchoenma Query: T2950A, C18115T, G24872T

46) Now Branch 144

JN.1.11.1 > G22927T > A13132G,S:R346T (G22599C), Orf7a:A66V (C27590T) Query : G22927T, A13132G,T3565C NZL

47) Dead

Different from Branch74 JN.1.29 (A9935G=Orf1a:T3224A) > S:F456L (T22928C) > Orf1a:T2124I (C6636T),Orf1a:T2408I (C7488T), A13165G, S:R346T (G22599C), S:D936Y (G24368T), C27881T Query:C7488T, A13165G, G24368T

48) Dead

FLiRS JN.1.11 > Orf1a:R287K (G1125A), A20763G, S:R346S (A22600C), T23455C > ORF1a:T4164N(C12756A),Orf1b:A2143V (C19895T), S:F456L (T22928C), N:P383L (C29421T) Query:C12756A,C19895T,T3565C

49) Dead

Sibling apparently unrelated of Singlet 42 in a JN.1.4 branch with A23054C JN.1.4> S:R346T (G22599C) > T5179C, S:F59S (T21738C), S:F456L (T22928C), T24499C, Orf7a:K2Q (A27397C), C28115T, A29725G Query: T24499C, A27397C

50) Dead

sublineage of Branch 54 of #1253 JN.1.49 [Orf3a:T89I (C25658T )]> C17172A, S:F456L (T22930A) > T10084C, T13279C, S:V70I (G21770A), S:R346T (G22599C), T25827C Query: T22930A,T10084C, T13279C India

51) Dead

Sublineage of Branch 58 of #1253 JN.1 > > G16269A > C12781T > S:f456L (T22928C) > S:R346T (G22599C), G29734T Query: G16269A , C12781T ,T22928C,G22599C Canada

52) Dead

Jn.1.13.1 > C751T > S:f456L (T22928C, T26573C) Query:T22928C, T26573C,C751T (S.Kor)

53) Dead JN.1.11.1 > Orf1a:T4087I (C12525T) > ORF1a:S2030L (C6354T), A13237T, Orf1b:K2557R (A21137G), A21694G, S:R346T(G22599C), S:Q675H (G23587C), S:D1146E (T25000G) Query: C6354T, A13237T,T3565C (Scotland)

54) Dead

JN.1.16> Orf6:M19K (T27257A, G27258A double nuc)>Orf1b:D1848Y (G19009T), S:R346T (G22599C) Query: T27257A,G19009T,T3565C England

55) Dead

sub of Branch 70 #1253 , JN.1 > C14676T > S:Q677L (A23592T) > S:F456L (T22928C)> Orf1a:T4300I (C13164T), Orf1b:D53G (A13625G), S:R346T (G22599C) S:P1162L (C25047T) Query: C14676T, A23592T,A13625G (England)

56) now Branch 127

JN.1.13.1 > C28603T > Orf1a:K247N (G1006T), Orf1a:S1517F (C4815T), G20397A,S:F456L (T22928C) Query: G1006T, C4815T, G20397A (England)

57) Dead

JN.1.13.1 >C7420T> C10834T, S:f456L (T22928C), Orf7a:L5F (C27406T) Query: T3565C,C7420T, C10834T Taiwan

58) Dead

JN.1.4 > S:P1263L (C25350T) > Orf1a:N1540D (A4883G), C9391T, C9430T, orf1a:K4348R (A13308G), T18453C, S:S31Del (del21653-21655) ,S:F456L (T22928C) Query: C25350T,A4883G,del21653 England

59) Dead

Jn.1 > > C2902T > Orf1b:D275N (G14290A), C19164T > S:R346T (G22599C) > T2827C, Orf1a:Q1021H (G3328T), C4990T, Orf1a:N2405S (A7479G), S:S31F (C21654T), S:F456L (T22928C), C24023T, S:Q1208H (G25186T), T25689A Query: T2827C, ,G3328T, C4990T (US but branches with a SA sample)

60) Dead FViRT JN.1 > Orf1a:G519S (G1820A) > S:A288S (G22424T) > S:R346T (G22599C) > A13992G, G17562T, C19524T S:F456V (T22928G) Query: A13992G, G17562T, C19524T (UAE)

61) Proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1678

sub of Branch 24 of #1253 JN.1 > Orf1a:K399R ( A1461G) >Orf1b:P2321H (C20429A) > S:F456L ( T22928C)> > T22928C > Orf1a:I368T (T1368C), Orf1a:S2132R (T6661A), C9803T, Orf1a:K3821R REV (A11727G rev) , C19269T, S:R346T (G22599C), S:Q677H (G23593T), Orf3a:L52F (C25546T), C27741T Query: T1368C, C9803T, C19269T (Uk via GBW)

62) Now Branch 136

TRIO SubBranch of #2461 JN.1 >> Orf3a:L85F (G25647T) > A5053G, T23629C > ORF1a:T2152I (C6720T)> S:T572I (C23277T)>C5884T, A10420G, S:F456L (T22928C), C29149T > Orf1a:D996Y (G3251T), Orf1a: S1189R (A3830C), A13776G, T14586A, T21673C, S.R346T (G22599C), T22981C (S:Y473Y) Query: G3251T, A3830C, T14586A (US)

63) Dead

Recombinant Xbb/Jn.1 #991 query: A19326G, T22930A,T21738C,G24872T

64) Now Branch 131

JN.1.4 >> > T18453C > A29799G > C27630T > C17172T > Orf1b:A1662V (C18452T) > C12781T > Orf1a:G3704S (G11375A )> Orf1a:P959A (C3140G) , Orf1b:P1936S (C19273T), S:R346T (G22599C), S:F456L (T22928C), N:T391A (A29444G ) Query: C17172T ,C3140G (South Korea)

65) Dead

JN.1.16 > T78G, S:R346T (G22599C), Orf3a:Q245R (A26126G) Query:T78G, A26126G (Singapore)

66) Dead

JN.1.18 > C8251T >C17703T, C19011T > Orf1a:T2648I (C8208T), S:F456L(T22928C), S:S1170F(C25071T) Query:C8208T, C25071T,T3565C Singapore

67) Dead

KR.5 [JN.1.1.5 > Orf1a:L642F (C2189T), Orf1a: T2087I (C6525T), ] ,A23746G > ORF1a:R207H (G885A), C22224T, S:F456V (T22928G) Query: G885A, C22224T, ,T22928G (Brazil)

68) Dead

JN.1.18 > Orf1a:T4090I (C12534T) > C10228T, Orf1a:L3829F (C11750T), S:F456L (T22928C ) Query:C10228T, C11750T, T22928C,T3565C (US)

69) Now Branch 141

JN.1.49.2 [Orf3a:T89I (C25658T) > S:F456L (T22930A)] > Orf1a:K292N (G1141T),Orf1a:A3889T (G11930A), C12295T, C14805T, T16723C, S:R346T (G22599C) Query: T22930A,G1141T,G11930A (England)

70) Dead

JN.1.4.7 > S:R346T (G22599C) >S:P1263L (C25350T)> T5680C, S:F456V (T22928G) Query: C25350T, T5680C, T22928G

71) Now Branch 136 DelTRIO (First ever) LB.1+S:S31Del > S:T572I (C23277T)
Query:C23277T,G22111T , G22599C , T22928C,del21653 (Israel)

72) Now Branch 138

Branch 12 of #1253 JN.1.15 >C19269 ,Orf3a:R122S (A25758T)> S:F456L (T22928C) > S:R346T (G22599C) Query: C23625T,G22599C,C19269T,T3565C Spain

73)Dead

FLIRI JN.1.16 > N:T135I (C28677T) > T1918A, Orf1a:P804S (C2675T), S:R346T (G22599T) Query:T1918A, C2675T, G22599T (Uk)

74) Dead

KP.1 > Orf1a:T1881I (C5907T) > Orf1a:F1594L (T5047A) , Orf1a:A4357V (C13335T), S:r346T (G22599C), Orf7b:L18S (T27808C) Query: T5047A, T27808C , C13335T Wales

75) Dead

XDV.1 > C3535T, ORF1a:L3116F (C9611T), T17688C, S:R346T /G22599C), C27657T, N:I292T (T29148C) and three reversions: G6183A, T9142C, C13339T Query: C3535T, C9611T, T17688C,C27657T (Shanxi)

76) Dead

Jn.1 > T27810C > Orf1a:T2846I (C8802T) > S:R346T (G22599C) > S:F456L (T22930G), Orf9b:Q18R (A28336G) Query: T22930G, A28336G Australia >> 2

77) Dead

Jn.1 > T27810C > C8802T > G22599C > C66A, C13551T, ORF1b:N189S (A14033G),A18009G, S:F456L (T22928C), N:A311S (G29204T) Query: (Russia)

78) Designated JN.1.50

Proposed in https://github.com/cov-lineages/pango-designation/issues/2587 Sub of Branch 83 of #1253 JN.1 >> C9298T > S:L249F /G22309C) > S:A67V (C21762T), S:F456L (T22930G) > C4456T, S:H445P (A22896C)> T8749G, C11704T, S:R346T (G22599C) Query:G22309C, C4456T,C9298T,G22599C (Texas)

79) Now Branch 135

JQ.2.1> ORF1a:T265I (C1059T), C7639T, S:F456L (T22928C),ORF3a:I123T(T25760C) Query: C7639T,T25760C T22928C,C1059T (South Africa)

80) Dead

JN.1.16 > Orf1a:G1155C (G3728T) > T5749A, C15951T, G16959T, S:R346T (G22599C), G23149A, A23368G, C25324T, G27047A, C27297T, Query: C15951T, G16959T,T3565C (Delaware) 4

81) Branch 134 now

JN.1.11.1 > G29711T > 3277G, Orf1b:K469N (G14874T), S:R346T (G22599C), ORF9b:T72I (C28498T) Query: G14874T,G22599C,C28498T (Canada)

82) Dead

sub of Br. 36 /#1253 by @aviczhl2 Jn.1 > C10741T > Orf10:P10S (C29585T) > T19092C, C26753T > S:F456L (T22928C) > T21802C > [Artifact: ORF1a:S1027R (T3346A), ORF1a:F1028N (T3347A, T3348A)], ORF1a:K1855N (G5830T), ORF1a:L2655I (C8228A), T14835C, T17811C, ORF1b:D2039N (G19582A), C21910T, T22558C ,S:R346T G22599C Query: T14835C, T17811C,T3565C

83) Now Branch 145

JN.1.13.1 > C6781T > Orf1a:T2846I (C8802T), S:F456L (T22928C) Query: C6781T ,C8802T,T22928C ( GBW )

84) JN.1.11.1 > C29095T > G18816T, S:R346T (G22599C), S:N641S (A23484G), T24073C Query: G18816T, A23484G, T24073C (Spain)

85) JN.1 > A871G, T3172G,C1170T, T17859C, S:R346T (G22599C), S:F456L (T22928C) Query:A871G, T3172G,C1170T (Spain)

86) now proposed in #1571

KP.3.1 (G15372T, A19722G) > ORF1a:Q998H (G3259T), T5773C, C4586T, G19962A, S:R346I (G22599T) Query: T5773C, C4586T, G19962A,T3565C (France)

87) FLiRI JN.1.29 > S:F456L(T22928C) > T8053C > Orf1b:1588C (A18230G), S:R346I (G22599T), Orf3a:D155H (G25855C) Query: A18230G, G25855C (Finland)

88) JN.1.4> C5284T >S:F456L (T22928C) > S:R346T(G22599C), Query: C6433A, T22928C, T18453C,G22599C S.Korea likelyy misplaced under br.89 of #1253

89) Now Branch 147

JN.1.18.1 ( S:F59S) > Orf1a:K1226E (A3941G) > T18471C, S:F456L (T22928C), C25075T, Orf7a:Q62 (C27577T), Orf10:Q29 (C29642T) Query: T18471C, C25075T,A3941G (Taiwan)

Singlets will be no more tracked since May 21.

Interesting Singlets:

1) Dead >sibling of branch 79 JN.1.4 > T18453C > T4342C, C5869T, T17154C, Orf1b:A1662V (C18452T) > S:R346T (G22599C) Query: T4342C, C5869T, T17154C,G22599C NY Now **2** 2)Dead >JN.1 > C23896G > C186T > A19782G > C829T, Orf1a:T2093I (C6543T), S:L293I (C22439A), S:R346K (G22599A), S:S884F (C24213T) Query: C829T, C6543T, G22599A NY 3)Dead >JN.1.4 > C25710T > C28312T +346T +456L UK Query: C27791T ,C20178T, G22599C, T22928C 4)Dead >JN.1.33 > Orf1a:Y1846C (A5802G)> C3092T, S:R346K (G22599A) Query: C3092T ,G22599A,T3565C 5) Proposed in # 2560 PANGO >JN.1> Orf1a:N2147S (A6705G) > T24892C > Orf1a:S135R>K (G669A), Orf1a:I368T (T1368C), C4189T, Orf1a:Y1619H (T5120C), S:R346T (G22599C), A24241G, N:N192D(A28847G) Query:G669A, T1368C, C4189T

:::::::::::::::::::::::::::::::

Original proposal

Branch 1 Defining mutations: JN.1>T3565C>T27810C(ORF7b:F19L)>C1762A (ORF1a:F499L)>C11747T>G22599T (S:R346I), then further >C20629T> (ORF1b:H2388Y)>T22599C (S:I346T) for R346I GISAID query: A6183G, G22599T for R346T GISAID query: C20629T, G22599C, T22926C _Alternative query by Cornelius for 346T_: G22599C,C20629T,C11747T,C1762A (**edited**) Earliest seq: 2023-10-02 (France- EPI_ISL_18412591) Most recent seq: 2023-11-06 (Italy- EPI_ISL_18510429) Countries detected: R346I seqs: France (1), Sweden (1) R346T seqs: Italy (1), Australia (1) Usher Tree:  https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_293e4_7364f0.json?c=gt-S_346 S:R346 is a key site and S:R346T was successful in BF.7*, BQ.1.1*, CH.1* and recently XBB* lineages. Nowadays JN.1* is the fastest growing lineage, while this JN.1* branch has a two-step evolution as S:R346I>T. We can see how the R346I/R346T work on the JN.1 seqs. Genomes: R346I: EPI_ISL_18412591, EPI_ISL_18489980 R346T: EPI_ISL_18510429, EPI_ISL_18513742 ****************************+ Branch 2 Defining : JN.1.1 > C11747T > C9142T > S:R346T (G22599C) then A18600G , S:Q173H (G22081T) Query: C11747T, C9142T ,G22599C,C1762A Samples: 5 IDs: EPI_ISL_18552979, EPI_ISL_18553493, EPI_ISL_18577478, EPI_ISL_18577484, EPI_ISL_18577493 [Tree](https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_65447_db1820.json?c=gt-S_346&gmax=25384&gmin=21563&label=id:node_4493811)

[FedeGueli]

44 branches now. query for branch 3 updated

[xz-keg]

There is a new JN.1+T58C,C59A+S:R346T branch though

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice48_genome_test_2b752_5a2c60.json?label=id:node_6968232

[FedeGueli]

There is a new JN.1+T58C,C59A+S:R346T branch though

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice48_genome_test_2b752_5a2c60.json?label=id:node_6968232

Thank you, i think i saw that too but i was unsure if the 58/59 comboi nuc mutation is real, @AngieHinrichs @ryhisner @corneliusroemer what do you think

Anyway thank you very much for the help in tracking this and any new branch u will find

[xz-keg]

Thank you, i think i saw that too but i was unsure if the 58/59 comboi nuc mutation is real, @AngieHinrichs @ryhisner

Yeah you're right. I checked and these seqs seem to have no coverage on the 5' part instead of real 58/59.

[FedeGueli]

Thank you, i think i saw that too but i was unsure if the 58/59 comboi nuc mutation is real, @AngieHinrichs @ryhisner

Yeah you're right. I checked and these seqs seem to have no coverage on the 5' part instead of real 58/59.

Thank you vm ! i highlighted to @AngieHinrichs so she could fix it!

[FedeGueli]

There is also this branch with C9142T as branch 2 but branching off from a reversion of a defining nucleotide mutation defining of all BA.2.86 T13339C reverted to T13339T . i am not sure if real or not cause that C9142T mutation in the tree, https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_31b94_5cb940.json?label=id:node_6955284 Also it is possible to gain a query for this just starting it from the next node that , notably , is Orf6:L61P . Query for it: A27383C,G22599C,C9142T,C897A, Samples 2.

[FedeGueli]

Branch 9 flied to 27 with 5 samples from Nigeria one from Australia and one from Scotland

[AngieHinrichs]

Thank you, i think i saw that too but i was unsure if the 58/59 comboi nuc mutation is real, @AngieHinrichs @ryhisner

Yeah you're right. I checked and these seqs seem to have no coverage on the 5' part instead of real 58/59.

Thanks! Will mask, should take effect in today's build (2024-02-21).

[AngieHinrichs]

There is also this branch with C9142T as branch 2 but branching off from a reversion of a defining nucleotide mutation defining of all BA.2.86 T13339C reverted to T13339T . i am not sure if real or not cause that C9142T mutation in the tree

There is a regain of T13339C on that branch so the reversion looks like an artefact to me.

[FedeGueli]

There is also this branch with C9142T as branch 2 but branching off from a reversion of a defining nucleotide mutation defining of all BA.2.86 T13339C reverted to T13339T . i am not sure if real or not cause that C9142T mutation in the tree

There is a regain of T13339C on that branch so the reversion looks like an artefact to me.

Thank you!

[xz-keg]

Thanks! Will mask, should take effect in today's build (2024-02-21).

That's not a masking problem but more of an algorithmic problem that mutated branches attracting seqs without coverage on that site.

I suggest a way to solve this,

Backup the original seqs and count the percentage of seqs with mutation/without coverage under every branch, if that percentage is below like 20% this means the branch is mainly made up of seqs without coverage, Under such scenario the branch mutations for seqs without coverage shall be removed and they shall be place elsewhere.

[AngieHinrichs]

That's a good idea @aviczhl2. However, without masking, the branch could continue to attract sequences with Ns.

[xz-keg]

That's a good idea @aviczhl2. However, without masking, the branch could continue to attract sequences with Ns.

Yeah. This bug was also the bug in https://github.com/sars-cov-2-variants/lineage-proposals/issues/861

This is a general bug that can happen on any positions and not caused by wrongly sequenced samples. All those samples truthfully report "no coverage" on the mutation site, so there's no artefact in sequencing. Masking will solve a certain branch but without an algorithmic fix such branches will continue to pump up on other different mutations.

[FedeGueli]

That's a good idea @aviczhl2. However, without masking, the branch could continue to attract sequences with Ns.

Yeah. This bug was also the bug in #861

This is a general bug that can happen on any positions and not caused by wrongly sequenced samples. All those samples truthfully report "no coverage" on the mutation site, so there's no artefact in sequencing. Masking will solve a certain branch but without an algorithmic fix such branches will continue to pump up on other different mutations.

the bug in 861 was linked to a further nuc mutation in comparison to the defining , still not clear what happened there but i tend to think that is not a general bug and in stead a specific one for that part of the tree.

[xz-keg]

the bug in 861 was linked to a further nuc mutation in comparison to the defining , still not clear what happened there but i tend to think that is not a general bug and in stead a specific one for that part of the tree.

For every single seq it is not a bug. As all samples under the "bugged" branch have no coverage of the branch-specfic mutations, so possible to be actually belonging to the branch.

The problem here is that when looking at all seqs under that branch, we can see that instead of most having mutation while a few having "no coverage", most of the seqs have "no coverage" instead of really having the mutation. This is unrealistic for all those no coverage seqs to belong to the mutated branch.

[FedeGueli]

the bug in 861 was linked to a further nuc mutation in comparison to the defining , still not clear what happened there but i tend to think that is not a general bug and in stead a specific one for that part of the tree.

For every single seq it is not a bug. As all samples under the "bugged" branch have no coverage of the branch-specfic mutations, so possible to be actually belonging to the branch.

The problem here is that when looking at all seqs under that branch, we can see that instead of most having mutation while a few having "no coverage", most of the seqs have "no coverage" instead of really having the mutation. This is unrealistic for all those no coverage seqs to belong to the mutated branch.

Thank you i didnt get it until now.

[xz-keg]

There is a new KP.1+S:R346T branch emerging.

[FedeGueli]

There is a new KP.1+S:R346T branch emerging.

Will you propose it ? I will track here! Later adding new branches and updating the multiple lin issues and tracking the new branches you added (456)

[FedeGueli]

There is a new KP.1+S:R346T branch emerging.

Now added as Branch 46

[HynnSpylor]

Branch 14 reaches 206 and seems fast in US. It deserves a further tracking.

[FedeGueli]

Branch 14 reaches 206 and seems fast in US. It deserves a further tracking.

It is JN.1.13 isnt it?

[HynnSpylor]

@FedeGueli Yeah it is a branch of JN.1.13 but the pango lineages.txt shows JN.1.13 is only defined as S:A1087S. The S:R346T+S:F59S branch has not been designated.

[xz-keg]

@FedeGueli Yeah it is a branch of JN.1.13 but the pango lineages.txt shows JN.1.13 is only defined as S:A1087S. The S:R346T+S:F59S branch has not been desingated.

@corneliusroemer @AngieHinrichs is it also in usher?

[FedeGueli]

@FedeGueli Yeah it is a branch of JN.1.13 but the pango lineages.txt shows JN.1.13 is only defined as S:A1087S. The S:R346T+S:F59S branch has not been designated.

Yeah but the vast mayority of it has 346T for sure let me check only 27 out of 218 have not S:R346T

[AngieHinrichs]

@FedeGueli Yeah it is a branch of JN.1.13 but the pango lineages.txt shows JN.1.13 is only defined as S:A1087S. The S:R346T+S:F59S branch has not been desingated.

@corneliusroemer @AngieHinrichs is it also in usher?

JN.1.13 has been annotated in the UCSC usher tree since 2024-02-01. lineage_notes.txt mentions only S:A1087S, but the designated sequences in lineages.csv are on a branch with a couple mutations before S:A1087S: JN.1 > C26894T > C25680T > S:A1087S (G24821T) and yes, most of JN.1.13 has S:R346T (G22599C) and the majority of that subset also have S:F59S (T21738C).

[FedeGueli]

Branch 50 2 samples 1 patient from Brazil (GBW)

[FedeGueli]

Added branch 51 JN.1.4 from 4 continents 7 samples

[FedeGueli]

Added two branches of JN.1.11.1 with S.R346T one of them has also S:K187R.

[FedeGueli]

Added another JN.1.11.1 branch (54) with 346T consisting of 4 sequences from 4 countries , 2 of them are GBW samples from Middle East ( 2 countries)

[FedeGueli]

Branch 15 query edited now it is 7 (JN.1.7+346T)

[FedeGueli]

Branch 32 query modified thx to @aviczhl2 noticing the tree have changed since, notably it has also 456L.

[FedeGueli]

Thanks to @AngieHinrichs hardwork Branch 49 could be confidently assigned to JN.1.18 when the tree will further be fixed i will propose separately :

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5fcff_316f0.json?label=id:node_6971345

[FedeGueli]

Branch 2 designated JN.1.1.5 via https://github.com/cov-lineages/pango-designation/commit/d262c30317b0d73763fc23b108b5732c2a9a7103

[FedeGueli]

branch 54 JN.1.11.1 (456L+346T) doubled to 8 with new samples coming from Nepal, Middleast, Singapore and South Korea, def one to watch

[FedeGueli]

Branch 46 too jumped to 9 it is KP.1 plus 346T . @corneliusroemer i would evaluate an early designation for these combos

it got also S:K182N (XBB.2.3.3 defining) in most of samples. i ve proposed it in https://github.com/cov-lineages/pango-designation/issues/2510

[xz-keg]

Branch 46 designated KP.1.1 via https://github.com/cov-lineages/pango-designation/commit/a29effeda0cc9cfe0d1f858975988972387d54d7 and Branch 54 designated KP.2 via https://github.com/cov-lineages/pango-designation/commit/5e932aa5e13a88d48efc6c1efb8904c7f5c5013f

[FedeGueli]

branch 52 (combo 346 456) went to 4 a traveller to NY from Lebanon

[xz-keg]

Which one is this JN.1.4->S:R346T direct branch ? 54 seqs now.

usher

[FedeGueli]

Which one is this JN.1.4->S:R346T direct branch ? 54 seqs now.

usher

No idea , i see the tree has changed i will recheck everything

[FedeGueli]

Which one is this JN.1.4->S:R346T direct branch ? 54 seqs now.

usher

anyway this one is with 18453C but there. is another unproosed without it and directly bumping out of JN.4

[FedeGueli]

@aviczhl2 added as branch 57 thank you very much for re checking the tree. the query is not perfect i will imporve then. Added also JN.1.4 > S:R346T as Branch 58. queries are not perfect i m trying to tune them

[Over-There-Is]

Branch 52 China

[FedeGueli]

Branch 40 singlet with 456L query: , C10138T, G4656T,T22928C

[FedeGueli]

combo Branch 56 doubled to 4, traveller from India

[FedeGueli]

combo Branch 53 went to 5

[FedeGueli]

Branch 62 and 63 both combo branches with 346T 456L. @aviczhl2 note that the sample you highlighted this morning with S:S221L now has company in thetree but without S:S221L, and it has now become branch 63.

[xz-keg]

Branch 34 designated JN.1.26 via https://github.com/cov-lineages/pango-designation/commit/2fba814a213d781acab8f0d2913af127077f292e

Branch 58 designated JN.1.4.4 via https://github.com/cov-lineages/pango-designation/commit/46718c54fa201f64cee8c19daaa0aea593968a79

Branch 9 designated JN.1.8.2 via https://github.com/cov-lineages/pango-designation/commit/ce0782ace48769d2d5c5d502482ccd306cc5907f

[FedeGueli]

BRANCH 28 got S:F456L 4 seqs uploaded today from UK, i noticed a wierd thing about the defining of this subbranch that is T7789C that is hsown by Usher but it is absent from Gisaid ( @AngieHinrichs any idea why? ) from many samples of this branch : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_b36d_f0f8b0.json?branchLabel=nuc%20mutations&c=gt-nuc_7789&gmax=8789&gmin=6789&label=id:node_6907700

Edited : I ve already solved that nuc is shown as missing on nextclade sequences:

I m going proposing it

[AngieHinrichs]

BRANCH 28 got S:F456L 4 seqs uploaded today from UK, i noticed a wierd thing about the defining of this subbranch that is T7789C that is hsown by Usher but it is absent from Gisaid ( @AngieHinrichs any idea why? ) from many samples of this branch : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_b36d_f0f8b0.json?branchLabel=nuc%20mutations&c=gt-nuc_7789&gmax=8789&gmin=6789&label=id:node_6907700

Maybe because (as you said in cov-lineages/pango-designation#2514) many of those sequences have N at 7789, so GISAID would not report a mutation there, but UShER is imputing when it places them on that branch? It's not a good sign that two sequences (USA/CA-GBW-H20-360-1496/2024 and USA/CA-GBW-H10-020-5775/2024) seem to have a reversion on 7789 though, that implies that some of the imputations are not correct.

[xz-keg]

Branch 51: JN.1.4 > G2782T > T111C > S:R346T (G22599C) Query: G2782T , T111C ,G22599C Samples: 8 Countries: US, Scotland, NZL, Nigeria, Sweden, France

None of seqs in this branch have C774T or T18453C, why is it JN.1.4? Likely sibling branch of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1395, or recombinant of it and JN.1.18.