Multiple JN.1* branches with S:F456X : 9 Ongoing Unproposed Branches as 7/1

[aviczhl2]

It seems that S:F456L is very convergent in JN.1 now. (last complete update June 19)

• [*] Branch 1: JN.1.1.2+S:F456L, #1147 DEAD
• [*] Branch 2: JN.1.1+C9142T+S:F456L, #1249 DEAD
• [x] Branch 3: JN.1+S:F456L, Designated JN.1.16 Query: T22928C, T3565C, T22926C, -C1762A, -18453, -18093, -2782, -3589,-7113,-7967,-1779,-8578,-6145,-16260,-29614,-29700 28 seqs, UK, Canada, Denmark,Netherlands,Singapore, Sweden, USA,Luxembourg
• [x] Branch 4: Designated JN.1.11.1 > JN.1.11+Orf1a:T2283I,S:F456L (https://github.com/cov-lineages/pango-designation/issues/2446)
• [x] Branch 5: Designated JN.1.12 > JN.1+Orf7a:A8T+S:F456V, Query: T22928G,G27415A, 13 seqs, Italy, Netherlands, Poland,Spain,France, Greece
• [x] Branch 6: Designated JN.1.1.6, JN.1.1+S:F456L Query: T22928C,C1762A,C11747T,-9142,-22104,-4720,-25463,-20762,-22227,-21654 28 seqs, India, USA,Singapore,Canada, France,Spain, UK
• [P] Branch 7: JN.1.4+Orf1a:T4087I,Orf1b:S1512N+S:F456L Proposed in https://github.com/cov-lineages/pango-designation/issues/2517
• [ ] Branch 8: JN.1.4.5+C28948T+S:F456L, further gets R346T and S31F, Query: C28201T, T22928C, T22926C, C28948T,15 seqs, Thailand, Singapore, China, Italy, Denmark, South Korea, Japan,
• [* ] Branch 9: DEad

  JN.1+C6145T+S:F456L https://github.com/cov-lineages/pango-designation/issues/2585

• [*] Branch 10: Dead

  JN.1.4+C9979T+S:F456L Query: T18453C, T22928C,C9979T, 18 seqs, Sweden, Norway

• [P] Branch 11: JN.1.39+S:F456L, Usher merges it to JN.1.16 but shall be independent Proposed in https://github.com/cov-lineages/pango-designation/issues/2543
• [x] Branch 12: Designated JN.1.15.1

  Now proposed in https://github.com/cov-lineages/pango-designation/issues/2604 Detected by @FedeGueli JN.1.15+S:F456L,Orf3a:R122S Query: T22928C, C23625T, T22926C, 34 seqs, Switzerland,Ecuador,USA,France, UAE, UK, South Korea, Netherlands, Canada, Spain, Singapore

• [*] Branch 13: Dead

  JN.1+C3589T+A25102G+S:F456L, Query: C3589T,A25102G,T22928C, 4 seqs, Germany, France dead

• [x] FLiRT Branch 14, Designated KR.1 https://github.com/cov-lineages/pango-designation/issues/2492
• [P] Branch 15: by @FedeGueli JN.1 > C23683T > S:F456L (https://github.com/cov-lineages/pango-designation/issues/2578)
• [ *] Branch 16, Dead

  Proposed in https://github.com/cov-lineages/pango-designation/issues/2595 By @FedeGueli
  JN.1.22 > Orf1a:G445V (G1599T) > C11704T > S:F456L (T22928C), Query: G1599T, C11704T ,T22928C, 37 seqs, USA, Spain

• [P] Branch 17, JN.1.4+S:F456L, (https://github.com/cov-lineages/pango-designation/issues/2577)
• [x] Branch 18, JN.1.29+S:F456L,Designated JN.1.29.1 Query: C2644T,A9935G,T22928C, 29 seqs, Brazil, Canada,UK
• [*] Branch 19, JN.1+S:F456L, Orf1a:R560C, T2846I,Dead Query: C8802T, C21904T, T22928C, 3 seqs, USA, New Zealand
• [x] Branch 20, JN.1+S:F456L(T22930A), the S:R346T sub-branch designated JN.1.18.5 https://github.com/cov-lineages/pango-designation/issues/2588
• [P] Branch 21, JN.1.4.5+S:F456L, https://github.com/cov-lineages/pango-designation/issues/2607
• [P] Branch 22, JN.1+Orf1a:N2147S+S:R346T+T2800I,S:F456V Proposed in https://github.com/cov-lineages/pango-designation/issues/2560
• [x] FLiRT Branch 23, Designated KS.1, JN.1.13.1+S:F456L, Query: T21738C, T22928C, G24821T, 6 seqs, Singapore, USA, Turkey, Qatar
• [x] Branch 24, Designated Jn.1.55.2

  JN.1+Orf1a:K399R+Orf1b:P2321H+S:F456L, https://github.com/cov-lineages/pango-designation/issues/2612

• [P] Branch 25, proposed in https://github.com/cov-lineages/pango-designation/issues/2655

  JN.1.3+S:F456L, Query: T3565C,T22928C,C27945T,-C4777T, 44 seqs, South Korea,Israel, Canada, Spain, USA,France, Australia, Singapore

• [P] Branch 26, By @FedeGueli ,JN.1 > M:L46F (G26660T) > G4162A > S:F456L (T22928C), Proposed in https://github.com/cov-lineages/pango-designation/issues/2531
• [*] Branch 27, Dead

  JN.1.1+C9142T+Orf1a:T1589I+S:F456L, Query: T22928C,C1762A,C5031T,C9142T,-10440, 6 seqs, USA, UAE,India

• [*] Branch 28, dead

  JN.1.1+Orf1b:T2165M+Orf1a:S2635L,S:F456L, Query: C19961T,T22928C,G4720A,A28795G, 4 seqs, Spain, France, USA

• [x] Branch 29, KW.1+Orf1b:R2009K+S:F456L,Designated KW.1.1 Query: T10084A, C5184T, T22926C,T22928C,14 seqs, Australia, USA
• [P] FLiRT Branch 30, JN.1.26+S:F456L,https://github.com/cov-lineages/pango-designation/issues/2605
• [x] FLiRT Branch 31 artefact,

  shall be JN.1.16.1, JN.1.18+Orf1a:F536V+S:F456L, Query: G22599C,T22928C, T1871G,T3565C, 5 seqs, Nigeria

• [x] Branch 32, JN.1+C4795T+S:F456L,Designated JN.1.51.1, https://github.com/cov-lineages/pango-designation/issues/2581
• [x] Branch 33, By @FedeGueli KV.2 > C2005T > C1188T , 7981G, Orf1b:P2313T (C20404A), S:F456L (T22928C), https://github.com/cov-lineages/pango-designation/issues/2500
• [x] Branch 34, JN.1+A9085G+S:F456L, Designated JN.1.54.1 https://github.com/cov-lineages/pango-designation/issues/2584
• [x] FLiRT Branch 35, Designated KU.2, JN.1.30.1 > S:F456L (T22928C) https://github.com/cov-lineages/pango-designation/issues/2514
• [P] Branch 36, JN.1+Orf10:P10S+S:F456L, https://github.com/cov-lineages/pango-designation/issues/2613
• [x] Branch 37, JN.1.18+S:F456V,Designated JN.1.18.3, Proposed in https://github.com/cov-lineages/pango-designation/issues/2538.
• [ *] FLiRT Branch 38, JN.1.24.1+S:F456L, https://github.com/cov-lineages/pango-designation/issues/2520
• [x] FLiRT Branch 39, JN.1.1.7+S:R346T+Orf1a:R1464L+S:F456L, Dead, https://github.com/cov-lineages/pango-designation/issues/2490
• [x] Branch 40 JN.1.4.7 > S:R346T (G22599C) > S:F456V (T22928G), Designated LE.1.1 https://github.com/cov-lineages/pango-designation/issues/2493
• [P] Branch 41 now proposed in https://github.com/cov-lineages/pango-designation/issues/2632 JN.1+S:L176F+S:F456L, Query: C22088T,C18894T,T22928C,-17562 14 seqs, Germany,Australia, USA, UAE, South Korea,China
• [x] FLiRT Branch 42 JN.1.9+S:R346T+S:F456L, Designated LB.1, Query: G22111T, G22599C, T22928C,T3565C Proposed in https://github.com/cov-lineages/pango-designation/issues/2546
• [x] Branch 43, Designated JN.1.7.4 (S:F456L), Query: T22928C, C23277T,G25012T,T27810C,-16985 11 seqs, USA, UK, France
• [*] Branch 44, Dead

  proposed in https://github.com/cov-lineages/pango-designation/issues/2633 >JN.1+C9979T+C775T,S:F456L, Query: T22928C, C775T, C9979T, 9 seqs, Spain

• [x] Branch 45, JN.1.1+S:F456L(T22930A)+S:H445P,Orf1a:S2083I, designated JN.1.1.8 Query: T22930A, C11747T, C1762A,T22926C,-9142, 33 seqs, USA, Canada, Qatar,UK, Singapore, Spain, Australia
• [x] Branch 46, designated JN.1.16.2 (LA.1 and LA.2) JN.1->C4777T->S:F456L, has R346T and R346I branches, misplaced in JN.1.16 and JN.1.16.1, Proposed in https://github.com/cov-lineages/pango-designation/issues/2555
• [*] Branch 47, DEAD

  By @FedeGueli , JN.1 > Orf1a:K4483R (A13712G) > Orf1a:K1407N (G4486T) > A3058G > S:F456L (T22928C) Query: G4486T,A3058G, T22928C,4 seqs, UK,Canada

• [P] Branch 48, proposed in https://github.com/cov-lineages/pango-designation/issues/2634 >JN.1+C10078T,T14526C,C21911T+S:F456L, Query: T22928C,C10078T,T14526C, 22 seqs, Australia, UK, Germany,New Zealand
• [*] Branch 49, proposed in https://github.com/cov-lineages/pango-designation/issues/2565 By @FedeGueli ,

  JN.1 > S:H1101Y ( C24863T )>S:F456L (T22928C) Query:C24863T, T22928C, T3565C 32 samples, China, UK,Canada,Salvador

• [x] FLiRT Branch 50, JN.1+T18471C+Orf3a:A99V+S:S60P,R346T+S:F456L,Designated JN.1.48.1 and a related recomb, Proposed in https://github.com/cov-lineages/pango-designation/issues/2547
• [P] Branch 51, Proposed in https://github.com/cov-lineages/pango-designation/issues/2622

  JN.1+C26873T+S:F456L, Query: T22928C, C26873T, C18894T, 21 seqs, China, Netherlands, Germany, Singapore,USA,Canada, New Zealand

• [x] Branch 52, Designated LL.1, JN.1.4.2+S:S680F+S:F456L(T22930A), Query: T22930A, C23601T, A22115G, 29 seqs, USA, New Zealand, Italy, Netherlands
• [*] Branch 53,Dead

  proposed in https://github.com/cov-lineages/pango-designation/issues/2621 JN.1+Orf3a:A54S+S:F456L(T22930A), Query: G25552T,T22930A,C18894T, 13 seqs, USA

• [x] Branch 54, JN.1+Orf3a:T89I+S:F456L(T22930A),Designated JN.1.49.2, Query: C25658T,T22930A,C18894T, 7 seqs, France, Germany,India, UK,USA
• [x] FLiRT Branch 55, Designated LQ.1 JN.1.18.1+S:F456L, Proposed in https://github.com/cov-lineages/pango-designation/issues/2596 Query: T22928C,C14220T,C22311A, 13 seqs, USA, UK,India,South Korea
• [x] Branch 56, Designated JN.1.62

  JN.1+S:V62F,R681H+S:F456L, Query: G21746T, C4586T,T22928C, 10 seqs, Israel, South Korea,USA, France

• [P] Branch 57, proposed in https://github.com/cov-lineages/pango-designation/issues/2641

  JN.1+C28603T+S:F456L, Query: T22928C, C28603T, T3565C,-17334,-T565A 26 seqs, UK, South Korea, Chile,Japan, China, Australia

• [P] Branch 58, JN.1+C16269A+C12781T+S:F456L, https://github.com/cov-lineages/pango-designation/issues/2614
• [x] Branch 59, JN.1+C4093T+N:A119D,S:F456L,Dead Query: C4093T, T22928C, C186T 4 seqs, USA
• [* ] Branch 60, DEAD

  JN.1+C27389T+S:F456L, Query: C27389T,T22928C,T3565C, 11 seqs, USA, South Korea, Malaysia,Singapore, Canada

• [x] FLiRT Branch 61, KY.1+S:F456L,Dead Query: T22928C, A11585G, G22599C, 3 seqs, Nigeria
• [P] Branch 62, now proposed in https://github.com/cov-lineages/pango-designation/issues/2636

  JN.1+G17562T+S:F456L, Query: G17562T,T3565C, T22928C,-8716, 33 seqs, Spain, USA, Singapore, Germany, France, UK, India,Canada, China, Denmark, South Korea, Kenya, Japan, Australia,Singapore, 16 has FLiRT, misplaced under JN.1.16 for normal branch and JN.1.9 for FLiRT branch.

• [*] Branch 63, Proposed in https://github.com/cov-lineages/pango-designation/issues/2629

  JN.1.4.5+C20823T+C9073T,A21417G+S:F456L, Query: T18453C,C9073T,T22928C, 10 seqs, USA, Australia,New Zealand

• [*] Branch 64, now proposed in https://github.com/cov-lineages/pango-designation/issues/2638

  JN.1+C22858T+S:F456L, Query: C22858T,T22928C,C18894T,-7113, 28 seqs, South Korea,Australia, USA, UK,Finland

• [* ] Branch 65, DEAD

  JN.1+C25566T+S:F456L, Query: -C7113T,-A4911T,-A11947G,-T5120C,C25566T,T22928C,T22926C,-23277,-C2106T (Edited in June), 4 seqs, Portugal, Luxembourg,Germany,China

• [x] FLiRT Branch 66, it is likely KU.2 , anyway Proposed in https://github.com/cov-lineages/pango-designation/issues/2640

  JN.1.30.1+Orf1a:I1128F+Orf1a:T2283I,Orf7b:L20I,S:F456L, misplaced under KU.2, Query: A3647T, T22928C, G21255T, 28 seqs, Singapore, USA, Malaysia, Thailand, Canada, Australia, UK, India,Sweden, USA, Pakistan,

• [P] FLiRT Branch 67, #1503
• [*] Branch 68, Now proposed in https://github.com/cov-lineages/pango-designation/issues/2639

  JN.1+Orf1b:L2560F+S:F456L, Query: C21145T, T22928C, C18894T,-18453, -4795, 19 seqs, France, India, Singapore,China,USA

• [*] Branch 69. DEAD

  JN.1+C25521T+C24904T+S:F456L,Dead, Query: C24904T,C25521T,T22928C,C18894T, 6 seqs, USA

• [*] Branch 70, dead proposed in https://github.com/cov-lineages/pango-designation/issues/2650

  JN.1+C14676T+S:Q677L+S:F456L, Query: C14676T, A23592T, T22928C, 20 seqs, USA, Netherlands,Spain, UK

• [P] FLiRT Branch 71, JN.1+Orf1a:N2147S+S:R346T+S:F456L(T22930A), Proposed in https://github.com/cov-lineages/pango-designation/issues/2560
• [*] Branch 72, Dead

  JN.1.4+Orf1a:A2001V+Orf1a:T1040I,S:F456L,Dead, Query: C6267T,T18453C,T22928C, 3 seqs, UK

• [P] Branch 73, proposed in https://github.com/cov-lineages/pango-designation/issues/2645

  JN.1+C27110T+S:F456L, Query: T22928C, C27110T, T22926C, 35 seqs, Ireland, Canada, USA, India

• [ *] Branch 74, now propose in https://github.com/cov-lineages/pango-designation/issues/2651

  JN.1.34+Orf1a:T2846R, S100R, E386D+S:F456L, Query: C23673T,T22928C, C8802T,T565A, 21 seqs, UK, Denmark,USA,Sweden,Hungary

• [*] Branch 75, Dead

  JN.1.33+Orf1a:D2060N+Orf1b:T76I,S:F456L,Dead Query: T22928C, G5992A, G6443A, 5 seqs, Australia, France

• [ *] Branch 76, Dead

  JN.1+Orf1b:P1427L+S:F456L, Query: C17747T, T22928C, C18894T and C17747T, -T22928C, C18894T,C12786T(sum of the 2), 13 seqs, South Korea

• [ ] Branch 77, JN.1.7+C28849T+S:F456L,Orf1a:A3497V, Query: C28849T,T22928C,C10755T, 17 seqs, USA, UK, France
• [*] Branch 78, Dead

  JN.1.7+Orf1a:V1025L+S:F456L,Orf1b:F2173L,Query: G3338T, T10546C, T22928C, 4 seqs, Canada

• [ ] Branch 79, JN.1+C6968T+S:F456L, Query: C6968T, T22928C, C18894T,36 seqs, France, Sweden, China, Spain, UK, USA, Australia, Singapore
• [*] Branch 80, Dead

  JN.1+Orf1a:R550H+Orf1a:F1028Y,S:F565L+S:F456L, Query: T3348A,T23257G,T22928C, 4 seqs, Japan

• [x] FLiRT Branch 81, Designated JN.1.18.4, JN.1.18+Orf6:I60T,S:F456L(T22930G),https://github.com/cov-lineages/pango-designation/issues/2567
• [*] Branch 82, dead https://github.com/cov-lineages/pango-designation/issues/2571
• [x] Branch 83,Designated JN.1.50 By @DoropFan JN.1>C9298T>S:L249F(G22309C)>S:A67V(C21762T), S:F456L(T22930G), https://github.com/cov-lineages/pango-designation/issues/2587
• [ ] FLiRT Branch 84, JN.1+Orf3a:A103T+S:R346T,F456L, Query: T22928C, G22599C, C1612T,G25770A, 18 seqs, Russia, Sweden, USA, UK, Australia
• [ *] Branch 85, Dead

  JN.1.9+Orf1b:V1402I,A1620V+Orf1a:T3032I,I3758V,S:A376S,F456L, Orf3a:Y141H, Query: T22928C, G17671A, C18326T, 5 seqs, USA

• [P] Branch 86, proposed in https://github.com/cov-lineages/pango-designation/issues/2637

  JN.1+C17119T+A2251G+S:F456L(T22930A), Query: T22930A, C17119T, A2251G, 20 seqs, South Korea

• [x] FLiRT Branch 87, Designated KR.3 JN.1.1.5+S:F456L(T22930A), Query: T22930A, C9142T, G22599C,T3565C, 4 seqs, USA, Australia , UK
• [ *] Branch 88, dead

  JN.1.4+C11020T+S:F456L, Query: C11020T, T22928C, T18453C, 7 seqs, USA, South Korea, South Africa

• [ ] Branch 89,JN.1.4+C5284T+S:F456L, Query: C5284T, T22928C, T18453C, 9 seqs, South Korea, USA,Netherlands
• [*] Branch 90, dead JN.1.4+C22450T+Orf1a:T2274I, S:F456L, Query: C22450T, T22928C, T18453C, 5 seqs, South Korea
• [*] Branch 91, Dead

  JN.1.4+Orf1b:P1342S+S:A123S, F456L, Query: T22928C, C17491T,T18453C, 4 seqs, South Korea

• [*] Branch 92,Dead

  JN.1.4+Orf1a:T602I+Orf1b:H714Y+Orf6:L29P,S:F456L, Query: C2070T, C15613T,T22928C, 3 seqs, China

• [x] Branch 93, Designated KR.2 JN.1.1.5 > T6095C,C6541T, C21911T, S:L176F (C22088T), S:F456V (T22928G ), https://github.com/cov-lineages/pango-designation/issues/2586
• [P] Branch 94, https://github.com/cov-lineages/pango-designation/issues/2461
• [ x] Branch 95, Designated JN.1.55.1

  JN.1+Orf1a:K399R+Orf1a:T1017I+S:F456L, Query: T22928C, C3315T, G10255A, 16 seqs, Thailand, USA, Japan, South Korea, Australia, China

• [*] Branch 96, dead

  By @FedeGueli ,JN.1.4 >>> T18453C > C27297T > S:L249F (G22309T), S:F456L (T22930A ) Query: G22309T ,T22930A,T3565C, 5 seqs but only 3 seqs on GISAID, UK

• [* ] Branch 97, Dead JN.1+C14178T+S:F456L,Q613H,Orf1a:V2783F, Query: C14178T,T3565C,T22928C,G23401T, 4 seqs, USA
• [*] Branch 98, Dead

  JN.1+C4048T+S:F456L, Query: C4048T, T22928C, T3565C, 10 seqs, USA, New Zealand, China, Australia

• [P] FLiRT Branch 99, Proposed in https://github.com/cov-lineages/pango-designation/issues/2589

  JN.1+T17859C+C3172T+S:R346T,F456L, Query: T17859C,T22928C,T3172G,T3565C, 30 seqs, Spain, Portugal

• [*] Branch 100, proposed in https://github.com/cov-lineages/pango-designation/issues/2620 >JN.1.4+S:S640F+S:F456L,Orf1a:P361L,H417Y,Orf3a:T24I, Query: C774T,C23481T, T22928C, 16 seqs, Canada, South Korea
• [x] FLiRT Branch 101, Designated LN.1.1
• [x] FLiRT Branch 102, Designated LM.1, https://github.com/cov-lineages/pango-designation/issues/2608
• [ *] FLiRT Branch 103, JN.1.52+S:R346T,S:F456L+S:F59S, https://github.com/sars-cov-2-variants/lineage-proposals/issues/1579
• [*] Branch 104, dead

  JN.1.30.1+S:F456V, Query: G21255T,T22928G,G22599C, 6 seqs, USA, UK ,France

• [ ] Branch 105, JN.1.7+Orf1a:V28I+S:F456L(T22930A),Query: T22930A, G347A, C1057T, 14 seqs, France, USA, Qatar, Iceland
• [P] Branch 106, proposed in https://github.com/cov-lineages/pango-designation/issues/2685

  JN.1.7+Orf3a:V97I+S:F456L, Query: T22928C, G25681A,C14931T, 25 seqs, Canada

• [x] FLiRT Branch 107, LE.1+Orf1a:T866I, Orf1b:K82R, S:F456L, N:Q409K, Merged to branch 109, Query: T22928C, G25445A,A13712G, 3 seqs, Canada
• [x] FLiRT Branch 108, Designated LZ.1,JN.1.18.2+Orf1a:I740V, N:A152T, S:F456L(T22930A),
• [P]FLiRT Branch 109, https://github.com/cov-lineages/pango-designation/issues/2663
• [ ] Branch 110, JN.1+C19374T+S:F456L, Query: C19374T, T22928C, T3565C,-17334,-7113, 20 seqs, Japan, South Korea, Canada, China, most with additional S:S60P
• [ ] Branch 111, JN.1+S:N960S+S:F456L, Query: A24441G, T22928C, C21219T, 11 seqs, USA, Spain, Ireland, France, Italy
• [ ] Branch 112, https://github.com/cov-lineages/pango-designation/issues/2547
• [ ] Branch 113, JN.1.19+S:F456L, Query: C9598T, C15216T, T22928C, 9 seqs, Russia

Doublets and Singlets no longer tracking. Only track >=3 branches, or branches with seqs from multiple countries now.

[FedeGueli]

please name the lineages Branch 1 branch 2 branch 3 etc

[aviczhl2]

JN.1+Orf1a:T2283I,S:F456L,V1104L Query: C7113T,T22928C,T3565C, India

This one is detected in another India state and becomes a branch.

[FedeGueli]

JN.1+Orf1a:T2283I,S:F456L,V1104L Query: C7113T,T22928C,T3565C, India

This one is detected in another India state and becomes a branch.

agree already in my tracking list it seems v interesting.

[aviczhl2]

JN.1+Orf1a:T2283I,S:F456L,V1104L Query: C7113T,T22928C,T3565C, India This one is detected in another India state and becomes a branch.

agree already in my tracking list it seems v interesting.

They are placed in different branches on usher but that's due to artefacts of India-KA seqs around S:16. KA seqs seem to artefact the ins16MPLF to some other things on all its JN.1* seqs. @AngieHinrichs @yatisht

[FedeGueli]

V1104L

I managed to get a tree and a query for the parental lineage of Branch 4 with S:V1104L:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice7_genome_test_3aa55_7b6bc0.json?label=id:node_6827336

Query: G24872T, G17334T,C897A finds 11

Samples: EPI_ISL_18682687 (Recomb), EPI_ISL_18683064, EPI_ISL_18694660, EPI_ISL_18694669, EPI_ISL_18694672, EPI_ISL_18704304, EPI_ISL_18704343, EPI_ISL_18704350, EPI_ISL_18718937, EPI_ISL_18718979, EPI_ISL_18718993

[FedeGueli]

V1104L

I managed to get a tree and a query for the parental lineage with S:V1104L: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice7_genome_test_3aa55_7b6bc0.json?label=id:node_6827336

Query: G24872T, G17334T,C897A finds 11

Samples: EPI_ISL_18682687, EPI_ISL_18683064, EPI_ISL_18694660, EPI_ISL_18694669, EPI_ISL_18694672, EPI_ISL_18704304, EPI_ISL_18704343, EPI_ISL_18704350, EPI_ISL_18718937, EPI_ISL_18718979, EPI_ISL_18718993

i think i ll propose (or you as you want ) the parental branch so Branch 4 could be defined as #XYZ + 456L, what do you think?

[aviczhl2]

i think i ll propose (or you as you want ) the parental branch so Branch 4 could be defined as #XYZ + 456L, what do you think?

Yes sure.

[FedeGueli]

i think i ll propose (or you as you want ) the parental branch so Branch 4 could be defined as #XYZ + 456L, what do you think?

Yes sure.

1262

[FedeGueli]

branch 3 goes to 11

[aviczhl2]

Add doublet 1 from USA.

There seems to be also S:F456V and S:F456I branches. Include them for branch 5 and singlet 7.

[aviczhl2]

1/10: Add doublet 2,3, Singlet 7,8.

Branch 4 Goes to 6 and spread to UK

[FedeGueli]

• C7113T,T22928C,T3565C,

@aviczhl2 i would ask you to propose it together with the parental in the main page (closing my side proposal) , so @corneliusroemer could track it too . If you can keep it updated also here it would be great. 6 seqs from India could hint to a huge numbers of infections. tell me if you are ok with that.

[aviczhl2]

• C7113T,T22928C,T3565C,

@aviczhl2 i would ask you to propose it together with the parental in the main page (closing my side proposal) , so @corneliusroemer could track it too . If you can keep it updated also here it would be great. 6 seqs from India could hint to a huge numbers of infections. tell me if you are ok with that.

5 in India and 1 in UK actually. Discovered in 2 India states.

You can propose that as your proposal is more focused? If you want me to propose that's also fine.

[FedeGueli]

• C7113T,T22928C,T3565C,

@aviczhl2 i would ask you to propose it together with the parental in the main page (closing my side proposal) , so @corneliusroemer could track it too . If you can keep it updated also here it would be great. 6 seqs from India could hint to a huge numbers of infections. tell me if you are ok with that.

5 in India and 1 in UK actually. Discovered in 2 India states.

You can propose that as your proposal is more focused? If you want me to propose that's also fine.

as you prefer! you discovered the whole thing! but if u have no time i will! u can copy paste it and then add the analysis of the 456 branch

[aviczhl2]

1/12: Branch 5 becomes 10 A previous Indian doublet spread to France and becomes branch 6.

[FedeGueli]

Branch 6 went already to 4

[aviczhl2]

1/16: Add singlet 8,9,10,11,12

Branch 3 goes to 18.

[FedeGueli]

@aviczhl2 i suggest to add a count to branches. now JN.1.11 is 15,

[FedeGueli]

2. JN.1.4+T18453C with C28201T（ORF8:S103L）（1272seqs） #1171+S:F456L Query: C28201T, T22928C, T22926C, -6781, Sweden,Singapore

this is now 4 i would convert it in a branch

[FedeGueli]

3. JN.1.4+Orf1a:T4087I+S:F456L Query: T18453C, C12525T,T22928C, USA

this is now 5 same as above

[FedeGueli]

8. JN.1.1+Orf1a:T1589I(15 seqs, 6 countries, mainly India) #1298+S:F456L,S704L,Q836L Query:C5031T,C9142T,T22928C, USA

this is 2

[FedeGueli]

11. JN.1+Orf1a:S505F+Orf1a:D589Y,S:F456L Query: T22928C,C1779T,T3565C, Belgium

2 this one too

[aviczhl2]

1/19: Add branch 7 and 8 Branch 5 becomes 13.

[aviczhl2]

I just realized that Orf1a:E4388K can be illumina induced artefact @AngieHinrichs.

Some singlets are removed, and Branch 6 becomes 5

[FedeGueli]

Here a triplet that could be interesting from SIngapore: JN.4 > Orf8:S103L > C28948T > S:F456L (T22928C) 3 sequences, with 2/3 with S:ins186TQM (Spike_ins186TQM/ ins22120ACACAGATG). Query: C28948T,T22928C,C774T finds 4 , one GBW sample was likely part of this lineage bbut displaced by Usher in a BA..2.86dropout tree.

[aviczhl2]

Here a triplet that could be interesting from SIngapore: JN.4 > Orf8:S103L > C28948T > S:F456L (T22928C) 3 sequences, with 2/3 with S:ins186TQM (Spike_ins186TQM/ ins22120ACACAGATG). Query: C28948T,T22928C,C774T finds 4 , one GBW sample was likely part of this lineage bbut displaced by Usher in a BA..2.86dropout tree.

I think that's branch 8 and 28498T shall not be branch specific.

[FedeGueli]

Here a triplet that could be interesting from SIngapore: JN.4 > Orf8:S103L > C28948T > S:F456L (T22928C) 3 sequences, with 2/3 with S:ins186TQM (Spike_ins186TQM/ ins22120ACACAGATG). Query: C28948T,T22928C,C774T finds 4 , one GBW sample was likely part of this lineage bbut displaced by Usher in a BA..2.86dropout tree.

I think that's branch 8 and 28498T shall not be branch specific.

oh yes thx! why not including 28498T?

[aviczhl2]

oh yes thx! why not including 28498T?

The Swedish seq doesn't have that. Singapore seqs have S:27 and S:484 artefacts so usually not placed in the correct place.

[FedeGueli]

Branch 5 got designated JN.1.12 via https://github.com/cov-lineages/pango-designation/commit/54f733f2ff9ac2a4ad9e13be007059c2fbfe1b38

[FedeGueli]

branch 4 designated JN.1.11.1 via https://github.com/cov-lineages/pango-designation/commit/a6e6ad346c36a4dcf839d8054eea9f7764784c6c

[aviczhl2]

Here a triplet that could be interesting from SIngapore: JN.4 > Orf8:S103L > C28948T > S:F456L (T22928C) 3 sequences, with 2/3 with S:ins186TQM (Spike_ins186TQM/ ins22120ACACAGATG). Query: C28948T,T22928C,C774T finds 4 , one GBW sample was likely part of this lineage bbut displaced by Usher in a BA..2.86dropout tree.

I think that's branch 8 and 28948T shall not be branch specific.

oh yes thx! why not including 28498T?

It seems that 28498T is a branch and there exist lots of seqs with 28948T but without 456. I'll separate them.

[FedeGueli]

Here a triplet that could be interesting from SIngapore: JN.4 > Orf8:S103L > C28948T > S:F456L (T22928C) 3 sequences, with 2/3 with S:ins186TQM (Spike_ins186TQM/ ins22120ACACAGATG). Query: C28948T,T22928C,C774T finds 4 , one GBW sample was likely part of this lineage bbut displaced by Usher in a BA..2.86dropout tree.

I think that's branch 8 and 28498T shall not be branch specific.

oh yes thx! why not including 28498T?

It seems that 28498T is a branch and there exist lots of seqs with 28498T but without 456. I'll separate them.

Yeah it is a branch, so there is more than one 456X in that branch? sorry i didnt get what you mean for"separate them"

[aviczhl2]

Yeah it is a branch, so there is more than one 456X in that branch? sorry i didnt get what you mean for"separate them"

Separate the 28948T+456L branch from 456L branch without 28948T

[FedeGueli]

Yeah it is a branch, so there is more than one 456X in that branch? sorry i didnt get what you mean for"separate them"

Separate the 28948T+456L branch from 456L branch without 28948T

perfect, thx

[aviczhl2]

1/26 Add branch 9 from Japan Branch 3 becomes 28.

[FedeGueli]

please add : https://github.com/sars-cov-2-variants/lineage-proposals/issues/1346

[FedeGueli]

Singlet found via Dave Mcnally's tool: JN.1.4> T4615C, C10537T > Orf1b:A1491V ( C17939T),S:F456L (T22928C), A29700G Query : T4615C, C10537T,C17939T

[FedeGueli]

Triplet Uk (1 on Gisaid) from Dave's McNally JN.1 > ORF1a:K1407N (G4486T) > A3058G, S:F456L (T22928C) Query : A3058G , T22928C, G4486T https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_37bdd_817bd0.json?label=id:node_6888569

[FedeGueli]

Branch 3 now designated JN.1.16 via https://github.com/cov-lineages/pango-designation/commit/d2eec4daaddbbbbe2b7d3d1fde33b87e7872902b

[aviczhl2]

2/6: Add branch 10 and branch 11

[FedeGueli]

@aviczhl2 where is ther uk cluster i cant find it no more?

[FedeGueli]

@aviczhl2 where is ther uk cluster i cant find it no more?

scratch that i got confused with 1058Y sorry! brain going jammed in multiple branch issues

[FedeGueli]

New super recent Suisse branch : JN.1.15 > T18453C > G9220A, C9803T,19443G , S:F456L (T22928C), , Orf3a:R122S (A25758T), C29296T Query: G9220A, C9803T,19443G Samples : 8 Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice7_genome_test_3b7bb_aa18a0.json?c=gt-S_456&label=id:node_6893126

[aviczhl2]

2/13: Add branch 12 and branch 13.

[FedeGueli]

@aviczhl2 yesterday while updating the 346X issue i spotted this one with 346T/456L :

Branch 32 JN.1.1 > C11747T > C11704T, G21641T, S:R346T (G22599C), S:F456L (T22928C),S:A520S (G23120T) Query: C11704T, G21641T,G23120T,C11747T Samples : 2 Singapore

[FedeGueli]

Branch 11 jumped to 16

[FedeGueli]

Branch 2 of #1089 got 456L and now it is 3 seqs from three countries/continents

Branch 2 : JN.1.1 > C11747T > C9142T > S:R346T (G22599C)
Query: C11747T, C9142T ,G22599C,C1762A Samples: 64 fast with a further branch with S:F456L: Branch2 > C28498T > S:F456L (T22928C) / 3 seqs Us,UK, Jap Query:C28498T ,T22928C,G22599C,C1762A

[FedeGueli]

relatively new mini branch with 3 seqs arising from Japan, South Korea:

JN.1 > C23683T > S:F456L (T22928C) Query: C23683T ,T22928C,C897A Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2938_f37a40.json?label=id:node_6895598

[FedeGueli]

New Branch of JN.1.22 with S:F456L in NY: JN.1.22 > Orf1a:G445V (G1599T) > C11704T > S:F456L (T22928C) Query: G1599T, C11704T ,T22928C Samples : 5

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_35c51_1c01d0.json?c=userOrOld&label=id:node_6898163

[FedeGueli]

branch 7 expanding to new american states. branch 11 now in france. updated only these two counts.