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 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 proposed in 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)

[Sinickle]

I'm not convinced that the French sequence in that tree is from the same parent. since I believe all of the mutations prior to its S:346i are actually pretty common in JN.1.

However, the Sweden, Australia, and Italy sequences appear to be related, despite that they contain a different mutation on S:346. A query of just "C11747T, C20629T" will return those 3 as the only JN.1 sequences. They also have regular expected BA.2.86 mutations in the area surrounding 346 (332, 356) so I don't think it's contamination.

At least the Australia and Italy sequences must represent onwards transmission of an S:346 mutation.

Also notable - the Italy sequence has a reversion on S:408, which is allegedly covered.

[Sinickle]

4th sequence for the query C11747T, C20629T -- France, R346T. As it stands, the 3 of them with R346T are...

Australia - Nov 4 Italy, France - Nov 6

[Sinickle]

Up to 6 seqs now with C11747T, C20629T.

All but one are with S:R346T. Australia - Nov 4 Italy, France x2 - Nov 6 Sweden - Nov 13

This should be moved to the main page, imo.

EDIT: I'm mistaken. One of the French sequences doesn't have S:R346T or S:R346i, so the query I'm using here isn't perfect now.

Correct list with R346T is

Australia - Nov 4 Italy, France - Nov 6 Sweden - Nov 13

[FedeGueli]

@HynnSpylor please propose it

[FedeGueli]

SCcratch this one:

The query for S:R346T is C11747T, C20629T,G22599C finds 5 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_13bf8_214840.json?label=id:node_4467378

[FedeGueli]

Other S:R346T popping up: 1 G10540T, C22088T 1 seq from Belgium with S:176F

2 C21952T,G22599C,C11747T,C1762A 1 seq from France

3 this one without a specific query

all the trees from :https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_13bf8_214840.json?c=userOrOld&label=id:node_4467536

[HynnSpylor]

It seems that several branches get S:R346T. I decide to arrange it and change the title as "Multiple JN.1+R346X Branches"

[FedeGueli]

It seems that several branches get S:R346T. I decide to arrange it and change the title as "JN.1+R346X Branches"

Ok thank you. in the comments you cna find some query i found for the other branches/singlets.

[corneliusroemer]

Transferred from #1118

There are around 40 JN.1 that have S:R346T, but most of them are poor quality sequences with lots of XBB mixed in.

When filtering out those pretty clear artefacts, we're left with 11-12 BA.2.86 that may actually have 346T. These are shown in the screenshot, where mutations are shown with respect to BA.2.86 parent, that's why there are so few mutation markers:

Interestingly, most of the 346T are within JN.1 (9 out of 11), much more concentrated than we'd expect by chance (around 1/4 of total BA.2.86 are JN.1 in GISAID).

Within JN.1, 8 out of 9 are on the JN.1 branch with C1762A (ORF1a:F499L) and C11747T. Again more concentrated than one would expect by chance (around 40% of JN.1 are on that branch).

4 out of those 8 share another mutation that's seen only once elsewhere within JN.1: C20629T (ORF1b:H2388Y).

Thus, it looks like at least these 4 sequences form a proper monophyletic lineage that could get designated. Though the numbers are still a bit small and there's a contamination issue as evidenced by the 3/4 of BA.2.86 + 346T being likely artefacts:

hCoV-19/Australia/NSW-ICPMR-50850/2023|EPI_ISL_18513742|2023-11-04
hCoV-19/Sweden/D-6556154176/2023|EPI_ISL_18538246|2023-11-13
France/GES-IPP26802/2023|EPI_ISL_18540862|2023-11-06
Italy/LOM_Unimi-3855-23/2023|EPI_ISL_18510429|2023-11-06

GISAID query: G22599C,C20629T,C11747T,C1762A

It's also possible that the 8 sequences are a single event - better wait for sequence numbers to double before making a decision. Due to the way the other 4 are scattered around, they look like independent events for now, though.

On Usher, things are a bit messy:

Here's how Nextclade arranges things with just the 346T sequences on the JN.1 branch:

[corneliusroemer]

Let's just track this one here for now, these collection issues can get overwhelming. This one is the biggest and clearest and most likely to be conclusive soon.

I think this is a fifth one for the 20629T cluster: hCoV-19/France/PAC-HCL723001520801/2023|EPI_ISL_18545255|2023-11-06

Further ones compatible with a single 346T even preceding C20629T rather than following:

hCoV-19/France/IDF-IPP26423/2023|EPI_ISL_18522061|2023-11-05
hCoV-19/France/ARA-CHUGA-3118929452/2023|EPI_ISL_18536531|2023-11-16

So we are at 5 (7) sequences for this cluster. The biggest question now is whether to designate broadly (not requiring 20629T) or narrowly (requiring it). We should know within a week.

[FedeGueli]

Thank you @corneliusroemer !

[FedeGueli]

Further ones compatible with a single 346T even preceding C20629T rather than following:

hCoV-19/France/IDF-IPP26423/2023|EPI_ISL_18522061|2023-11-05 hCoV-19/France/ARA-CHUGA-3118929452/2023|EPI_ISL_18536531|2023-11-16

Yes they are the ones i couldnt find a query for, i think they could be really one same lineage.

[HynnSpylor]

Thx @corneliusroemer @FedeGueli !

[FedeGueli]

@corneliusroemer maybe also Switzerland/ZH-UZH-IMV-47c6ebf0/2023|EPI_ISL_18541794|2023-11-13 belongs to the ones that could belong to this together with the two additional french sequences: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5ee2b_5c3250.json?c=userOrOld&label=id:node_4470384

[corneliusroemer]

New 20629T: hCoV-19/France/PAC-HCL723001570001/2023|EPI_ISL_18568815|2023-11-13, so 6 now

Extra ones compatible with event directly on polytomy:

hCoV-19/France/IDF-IPP26423/2023|EPI_ISL_18522061|2023-11-05
hCoV-19/France/ARA-CHUGA-3118929452/2023|EPI_ISL_18536531|2023-11-16
hCoV-19/Belgium/Jessa_11-2346-001845/2023|EPI_ISL_18566124|2023-11-14
hCoV-19/France/OCC-HCL723001552101/2023|EPI_ISL_18568662|2023-11-13

Making it 10 for that case. If it keeps going like this, we'll designate directly on the polytomy. Let's wait a few more days.

[FedeGueli]

R346I at 4

[FedeGueli]

Branch 2 at 6 (+1 Illinois)

[FedeGueli]

Branch 1 at 7 Branch 2 at 8 R346I at 5 while the branch stemming out from the politomy is 7 : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1c90d_99edf0.json?c=gt-S_346&gmax=25384&gmin=21563&label=id:node_4444768

cc @corneliusroemer still low numbers

[FedeGueli]

Branch 1 > 8 branch 2 > 10 S:R346I > 8

[FedeGueli]

Branch 1 > 12 Branch2 > 16 S:R346I > 15 S:R346S > 5

[FedeGueli]

Branch 1 > 12 Branch 2 > 16 S:R346I > 13 S:R346S > 5

[FedeGueli]

Branch 1 > 18 branch 2 > 17 R346I > 13 R346S > 5

they seem quite slow.

[FedeGueli]

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: JN.1.1 Branch 1:JN.1.1 >C11747T>G22599T (S:R346I), then further >C20629T> (ORF1b:H2388Y)>T22599C (S:I346T) query: C20629T, G22599C, T22926C Samples 18

Branch 2 : JN.1.1 > C11747T > C9142T > S:R346T (G22599C) then A18600G , S:Q173H (G22081T) Query: C11747T, C9142T ,G22599C,C1762A Samples: 17

Branch 3: JN.1.1 > C11747T >S:R346T (G22599C) Query: -G4720A,-C21952T,C11747T,G22599C, -C9142T,-C20629T,C1762A,-T3488C Samples: 18

Branch 4 : JN.1.1 > C11747T > T3488C > S:r346T (G22599C) Query : T3488C,C11747T,G22599C,C1762A

JN.1 Branch 5: JN.1 > S:R346T (G22599C), G22627A Query : G22599C, G22627A,C18894T ,T3565C Samples: 25

Branch 6: JN.1 > > S:R346T (G22599C) Query: Query: C18894T ,T3565C,G22599C,-C1762A,-G22627A,-C774T,-C2536T,-C27371T,-T21973C,-C2395T,-C5654T,-C18687T,-C19145A, -C6040T,-T20241C,-T21738C,-A9935G,-C1938T,-A28795G,-C19944T Samples : 27 (? - The query still catches unrelated samples)

Branch 7: Jn.1 > S:R346T G22599C, Orf6:P57L :C27371T Query: G22599C, C27371T,C18894T ,T3565C Samples : 9

Branch 8: JN.1 > C2536T, S:R346T (G22599C) Query: C2536T, G22599C,T3565C Samples: 4

Branch 9: JN.1 > A12928G, 17301C, T21973C, S:R346T (G22599C),ORF3a:Q213K (C26029A), ORF7a:T28I (C27476T) Query: A12928G, 17301C, T21973C,
Samples : 3

Branch 10: JN.1 > C2395T, G17562T, S:R346T (G22599C) Query: C2395T, G22599C,C18894T Samples : 3

Branch 11: JN.1 > C5654T, C9763T , C7840T, S:R346T (G22599C) Query: C5654T, C9763T , C7840T Samples: 3

I left out for now the branches under Orf1a:T170I i will add in the following weeks

[FedeGueli]

Many branches now are growing (B1-2-3-5-7)

[aviczhl2]

Branch 1 designated JN.1.1.3 via https://github.com/cov-lineages/pango-designation/commit/f240a76716a6cdf8dcbd15a8f8dbb924f2dd06a1 Branch 5 designated JN.1.6.1 via https://github.com/cov-lineages/pango-designation/commit/5625be4ba186f79501d0700e666ca6af702b0f4e

[FedeGueli]

added branch 12

[FedeGueli]

added branch 13 (that has both JN.1.3 and JN.1.1 defining so it could be either one of them.)

[aviczhl2]

Branch 6 is 89 now

[FedeGueli]

Branch 6 is 89 now

Thanks it unluckily collects all the new samples outside the branches excluded. ping @corneliusroemer maybe a planned designation of mayor reamianing branches could help?

[FedeGueli]

added branch 14 from https://github.com/cov-lineages/pango-designation/issues/2464

[aviczhl2]

Branch 6 is 230 now

[FedeGueli]

Branch 6 is 230 now

thx checking if it collects unrelated sample now.

[FedeGueli]

@aviczhl2 a lot of new things also in combo w 572I stay tuned!

[FedeGueli]

Branch 6 is 230 now

New query excluding multiple lineages found 209. very likely it is around 200 seqs . cc @corneliusroemer

Also Branch 2 and Branch 3 and Branch 14 going up.

[FedeGueli]

Added branch 16: Jn.1.4+346T from Jap/Sing.

[FedeGueli]

Branch 6 at 230 with the query now quite good ( i ve excluded some recombinant with excluding orf8:8*

[FedeGueli]

Added a NZL branch with 346I and 622I from NZL

[FedeGueli]

here the S:R346I trees popping up in JN.1 , highly homoplasic too:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_bb32_e8c2b0.json?f_userOrOld=uploaded%20sample&label=id:node_6875015

[aviczhl2]

Branch 6 designated JN.1.18 from https://github.com/cov-lineages/pango-designation/commit/425fe95872f894f6f168ec62796929defd8bef47

[HynnSpylor]

@FedeGueli proposes the JN.1.7+R346K branch https://github.com/sars-cov-2-variants/lineage-proposals/issues/1371

[FedeGueli]

now 22 branches

[FedeGueli]

I ve added branch 23 : cc @corneliusroemer i ve missed to add this one until today cause i mistook it for another branch with Orf3a:G18D include in the multiple 572I lineages. I count at least 10 countries for it and it has been sampled in Kenya and in a traveller from Ghana this makes me think to a solid prevalence in african continent, hence i suggest direct designation of it.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_19ec3_a35470.json?c=country&f_userOrOld=uploaded%20sample&label=id:node_6876283

Moreover one recent sample from England got also S:K304N that worked well in XBB.1.16

[FedeGueli]

Added branch 28. @corneliusroemer it is a 15ish sequence lineage emerging from India (KA,MH) and already exported to Uk and US.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice21_genome_test_5d3bc_a3ba10.json?c=gt-nuc_7789&gmax=8789&gmin=6789&label=id:node_6887973

[FedeGueli]

Added branch 29 . cc @corneliusroemer and @angiehinrichs could you take. a look at this ? it is misplaced to JN.1.1 but has orf1a:499 reverted, it has S:T22I, S:Q23H and S:Q183R beyond 346T but on Gisaid the nuc query with these mutations fails to catch any , while it works if i take the node from 346T ahead :

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_5d3bc_a3baa0.json?label=id:node_6931126

[FedeGueli]

Added Branch 35 this one is interesting cause coming from Peru'

[FedeGueli]

Deleted branch 39 cause it is part of branch 7 :

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_4de25_c91c40.json?label=id:node_6883378

[FedeGueli]

@corneliusroemer i will propose in the next fe hpours three branches each of them emerged in an under sampled area

[FedeGueli]

Rearranged Branch 9 , the query caught just a singaporean cluster of JN.1.8 while now it is 19 and widespread in different countires added branch 41 456L+346T new query for Branch 37 that gained s:f456L

[AngieHinrichs]

Added branch 29 . cc @corneliusroemer and @AngieHinrichs could you take. a look at this ? it is misplaced to JN.1.1 but has orf1a:499 reverted, it has S:T22I, S:Q23H and S:Q183R beyond 346T but on Gisaid the nuc query with these mutations fails to catch any

The S:T22I and S:Q23H are artefacts and will be masked starting in tomorrow's build (2024-02-20), hopefully that will fix it. Unless you think the S:Q183R is also incorrect?

[FedeGueli]

Added branch 29 . cc @corneliusroemer and @AngieHinrichs could you take. a look at this ? it is misplaced to JN.1.1 but has orf1a:499 reverted, it has S:T22I, S:Q23H and S:Q183R beyond 346T but on Gisaid the nuc query with these mutations fails to catch any

The S:T22I and S:Q23H are artefacts and will be masked starting in tomorrow's build (2024-02-20), hopefully that will fix it. Unless you think the S:Q183R is also incorrect?

Thanks @AngieHinrichs i think it is real , lets see what happens when the update will be up!