Multiple JN.1* branches with S:F456X : 4 Ongoing Unproposed Branches as 7/25

[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,26 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
• [*] 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

• [x] Branch 17, JN.1.4+S:F456L, Designated JN.1.4.9, (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, Designated JN.1.4.9

  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
• [x] Branch 22, Designated MD.2,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

• [*] 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

• [*] Branch 26, Designated JN.1.67.1, 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
• [*] 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 , Proposed in https://github.com/cov-lineages/pango-designation/issues/2547
• [*] 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

• [*] 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
• [*] 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

• [x] FLiRT Branch 71, Designated MD.1, 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, Dead Proposed in https://github.com/cov-lineages/pango-designation/issues/2693

  JN.1.7+C28849T+S:F456L,Orf1a:A3497V, Query: C28849T,T22928C,C10755T, 23 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, not monophyletic proposed in https://github.com/cov-lineages/pango-designation/issues/2682

  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, dead

  JN.1+Orf3a:A103T+S:R346T,F456L, Query: T22928C, G22599C, C1612T,G25770A, 36 seqs, Lithuania, 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

• [*] Branch 86, Dead 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, Dead

  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
• [x] Branch 94, Designated JN.1.65.1 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

• [x] FLiRT Branch 99, Designated LF.6, 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

• [x] Branch 105, Designated JN.1.7.9 JN.1.7+Orf1a:V28I+S:F456L(T22930A),Query: T22930A, G347A, C1057T, 14 seqs, France, USA, Qatar, Iceland
• [*] Branch 106, Dead 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, 49 seqs, Japan, South Korea, Canada, China, most with additional S:S60P, https://github.com/cov-lineages/pango-designation/issues/2688
• [P] Branch 111, JN.1+S:N960S+S:F456L, Query: A24441G, T22928C, C21219T, 11 seqs, USA, Spain, Ireland, France, Italy, https://github.com/sars-cov-2-variants/lineage-proposals/issues/1304
• [x] FLiRT Branch 112,Designated JN.1.48.3, https://github.com/cov-lineages/pango-designation/issues/2547
• [x] Branch 113, dead

  JN.1.19+S:F456L, Query: C9598T, C15216T, T22928C, 9 seqs, Russia

• [ ] Branch 114, By @FedeGueli , JN.1 > > > C5956T >> S:F456L (T22928C) >C24418T Query: C5956T, C24418T,T22928C, 14 seqs.Brazil, Canada, Argentin, USA, Japan,Spain, Denmark
• [x] Branch 115, Designated JN.1.16.5JN.1+S:T22N.F456L,Q493E, Query: C23039G, T22928C, C21627A,-17334,-24872, 5 seqs, Sweden, Turkey, USA
• [P] FLiRT Branch 116, designated LZ.2

  Proposed in https://github.com/cov-lineages/pango-designation/issues/2653,JN.1.18.2+Orf1a:K1226E+S:F456L, Query: T22928C, A3941G, C4331T, 31 seqs, USA, Mexico, Japan, China, Spain, New Zealand, Germany, Singapore, UK, Australia

• [ ] FLiRT Branch 117, JN.1+Orf1a:K399R+S:R346T,F456L,R59S(Can be JN.1.55 or JN.1.18 or JN.1.16 descendants), Query: A1461G, C2644T, G15906A, 5 seqs, USA, Dominician Republic, Venezuela, Netherlands
• [ ] FLiRT Branch 118, JN.1.18+S:F59S+C18348T+S:F456L(T22930A), Query: T22930A, C18348T, T21738C, 9 seqs, USA, UK, Spain
• [ ] Branch 119, JN.1.18+S:F59S+C18348T+Orf1b:M809L,Orf7a:T11K+S:F456V, Query: T22928G, A15892T, C27425A, 7 seqs, USA, Switzerland, Netherlands, Canada

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

[aviczhl2]

The larger branch with A3647T (ORF1a:I1128F) is KU.2 > A3647T,C7113T,C27813A (KU.2 is JN.1.30.1 > T22928C (S:F456L)) and is well-supported (13 sequences from 7 countries). Then there are only two sequences (both India/MH_BJCOG_INSACOG) placed at JN.1.30.1 > A3647T. I will prune & replace those and see what happens.

The JN.1.30.1 > A3647T branch also have S:S31del which is not shown on usher.

[Memorablea]

G1126A,T11928C

[FedeGueli]

G1126A,T11928C

@Memorablea thank you, please for the next time add an explanation to your comment cause me and @aviczhl2 are already quite jammed by queries/singlets/symmetric convergence/mirror issues ;) now i will look at this anyway!

[FedeGueli]

G1126A,T11928C i dont find anything with this @Memorablea

[FedeGueli]

One more samples for Branch 66/KU.2 with S:G252S . interestingly another KU.2 got S:S31F too in a Welsh sample uploaded today

[FedeGueli]

branch 43 combo now 15

[FedeGueli]

Branch 48 up to 18 seems fast

[FedeGueli]

Branch 43 designated JN.1.7.4 via https://github.com/cov-lineages/pango-designation/commit/be7e6050c28e86974272f98124c5a5f6ae9bd5f3

[FedeGueli]

Branch 34 has a little cluster with S:V407I

[FedeGueli]

branch 20 (T22930A) jumped to 51 it seems very fast growing please propose it. EDITED Scratch that, i think the query needs some adjiustment: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_264ad_ffcb70.json?f_userOrOld=uploaded%20sample&label=id:node_6918554

T22930A, T3565C, T22926C,-C1762A,-C774T,-G25552T,-A6705G,-T23031C,-T24364C,-C2061T,-G18756T,-C26684T,-A4005G,-A720G,-G16377T,-C14724T,-C2574T Gives 25 please @aviczhl2 check it!

[FedeGueli]

branch 20 (T22930A) jumped to 51 it seems very fast growing please propose it. EDITED Scratch that, i think the query needs some adjiustment:
T22930A, T3565C, T22926C,-C1762A,-C774T,-G25552T,-A6705G,-T23031C,-T24364C,-C2061T,-G18756T,-C26684T,-A4005G,-A720G,-G16377T,-C14724T,-C2574T Gives 25 please @aviczhl2 check it!

Branch 20 got now two FLiRT sample one from Uk and one from France:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice7_genome_test_4cd70_e9cb0.json?label=id:node_6965842

[FedeGueli]

Branch 47 one more FLirt sample adding it to 1089

[aviczhl2]

Add branch 77-79

[FedeGueli]

Flirt Branch 55 went to 4 one sample from South Korea

[FedeGueli]

Jn.1.26 FLiRT branch 30 went to 9

[FedeGueli]

Branch 54 went FLiRT in India one sample with also S:V70I

[FedeGueli]

Branch 58 now 9 one with FLiRT

[FedeGueli]

Branch 30 JN.1.26 FLirt went to 15

[FedeGueli]

branch 73 (now 9) got FLirt now 4 samples from Ireland : Query: C3244T, A18432T,G22599C tracked as Br.112 of #1089

[FedeGueli]

Branch 17 now 94 please propose it.

[FedeGueli]

Casually found a south korean branch with S:F456L placed as sibling of #2567

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice9_genome_150f8_c372b0.json?label=id:node_6966023 JN.1> C27143T > C13806T > Orf1a:T882I (C2910T), T>C3565A, C7573G, ORF9b:P10F (C28312T) > S:F456L (T22930A), T27143C rev Query: C7573G,T22930A,C13806T

Very. interestingly it has 3565A changing one of the hallmarks of JN.1 T3565C

[aviczhl2]

Casually found a south korean branch with S:F456L placed as sibling of #2567 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice9_genome_150f8_c372b0.json?label=id:node_6966023 JN.1> C27143T > C13806T > Orf1a:T882I (C2910T), T>C3565A, C7573G, ORF9b:P10F (C28312T) > S:F456L (T22930A), T27143C rev Query: C7573G,T22930A,C13806T

Very. interestingly it has 3565A changing one of the hallmarks of JN.1 T3565C

Recombinant?

[FedeGueli]

Casually found a south korean branch with S:F456L placed as sibling of #2567 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice9_genome_150f8_c372b0.json?label=id:node_6966023 JN.1> C27143T > C13806T > Orf1a:T882I (C2910T), T>C3565A, C7573G, ORF9b:P10F (C28312T) > S:F456L (T22930A), T27143C rev Query: C7573G,T22930A,C13806T Very. interestingly it has 3565A changing one of the hallmarks of JN.1 T3565C

Recombinant?

I didnt check, what do you make think to recomb?

[aviczhl2]

I didnt check, what do you make think to recomb?

reversion? Or just misplacement

[FedeGueli]

I didnt check, what do you make think to recomb?

reversion? Or just misplacement

Yes you are right maybe Recomb, misplacement hard to believe cause it has that T>C3565A very peculiar mutation

[aviczhl2]

I didnt check, what do you make think to recomb?

reversion? Or just misplacement

Yes you are right maybe Recomb, misplacement hard to believe cause it has that T>C3565A very peculiar mutation

I checked and it seems that the whole C27143T branch is buggy and very few seqs in this branch actually have this mutation. @AngieHinrichs

[aviczhl2]

I didnt check, what do you make think to recomb?

reversion? Or just misplacement

Yes you are right maybe Recomb, misplacement hard to believe cause it has that T>C3565A very peculiar mutation

Given 27143T branch is buggy, this one may be sub-lineage of branch 20. Don't know where it is going to be re-placed.

[FedeGueli]

Branch 70 is expanding now 6 with a FLiRT singlet ( that i will add to 1089) https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_1b8fb_26cb10.json?label=id:node_7054202

[FedeGueli]

Branch 62 Flirt with G17562T,T3565C, T22928C,-8716,G22599C has now 13 and the 456L parent is 27. but looking at the tree i suggest to modify query of this to G17562T,T3565C, T22928C,-8716,-G18186T,-C21145T,-T2548C that gives back 20 samples

Trees:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_4b07f_34b410.json?f_userOrOld=uploaded%20sample&label=id:node_7020105

[DoropFan]

G22309C, C21762T, T22930G JN.1>C9298T>S:L249F(G22309C)>S:A67V(C21762T), S:F456L(T22930G) https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_31278_46a020.json?c=gt-nuc_22930&gmax=23930&gmin=21930&label=id:node_6961025

[FedeGueli]

G22309C, C21762T, T22930G JN.1>C9298T>S:L249F(G22309C)>S:A67V(C21762T), S:F456L(T22930G)

thank you @DoropFan 2 seqs 2 countries 2 continents

[FedeGueli]

branch update on Branch 20 /T22930A : this is the new query i suggest to use: T22930A, T3565, T22926C,-A2543G,-C4455T,-T8862C,-C25658T,-G260A,-A6705G,-A2251G,-C1762A,-C774T,-G25552T,-A6705G,-T23031C,-T24364C,-C2061T,-G18756T,-C26684T,-A4005G,-A720G,-G16377T,-C14724T,-C2574T

it should keep only the branch 20 and the misplaced SOuth Korean linegae previously discussed in te comments here.

cc @aviczhl2

Before the update of the query the tree resulting from the current query was this one:

the FLiRT branch of it: 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 is 8 now

[aviczhl2]

Add branch 83,84,

Branch 9 becomes 55.

[aviczhl2]

Branch 15 becomes 116 due to massive upload from South Korea.

[FedeGueli]

branch 15 Please propose it.

[FedeGueli]

Branch 24 is now 16 and with a FLiRT sample (from UK via gbw with a quite long branch)

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_19b6d_65e0b0.json?f_userOrOld=uploaded%20sample&label=id:node_6993460

Query:T1368C, C9803T, C19269T

[FedeGueli]

Hi @aviczhl2 just to match things Br. 81 is proposed in #2567 Br.84 here was Branch 98 in #1089

and

Br.87 is the one we discussed as possible recomb? ( see br.113 of #1089] yes checked it was there, i ve took your query much better than the original

Br.120 of #1089 is another JN.1.1.5 FVIRT [edited]

Branch 120 FViRT JN.1.1.5 > T6095C,C6541T, C21911T, S:L176F (C22088T), S:F456V (T22928G ) Query: T6095C,C6541T,C21911T,T3565C Samples: 9 (Canada, US)

[aviczhl2]

Hi @aviczhl2 just to match things Br. 81 is proposed in #2567 Br.84 here was Branch 98 in #1089

and

Br.87 is the one we discussed as possible recomb? ( see br.113 of #1089] yes checked it was there, i ve took your query much better than the original

Br.120 of #1089 is another JN.1.1.5 FVIRT [edited]

Branch 120 FViRT JN.1.1.5 > T6095C,C6541T, C21911T, S:L176F (C22088T), S:F456V (T22928G ) Query: T6095C,C6541T,C21911T,T3565C Samples: 9 (Canada, US)

Branch 87 seems not a recomb, it can be explained by JN.1.1.5+T22930A, just misplaced to other places.

[aviczhl2]

Branch 32 becomes 101.

[FedeGueli]

Hi @aviczhl2 just to match things Br. 81 is proposed in #2567 Br.84 here was Branch 98 in #1089 and Br.87 is the one we discussed as possible recomb? ( see br.113 of #1089] yes checked it was there, i ve took your query much better than the original Br.120 of #1089 is another JN.1.1.5 FVIRT [edited]

Branch 120 FViRT JN.1.1.5 > T6095C,C6541T, C21911T, S:L176F (C22088T), S:F456V (T22928G ) Query: T6095C,C6541T,C21911T,T3565C Samples: 9 (Canada, US)

Branch 87 seems not a recomb, it can be explained by JN.1.1.5+T22930A, just misplaced to other places.

agree

[FedeGueli]

Br.32

Please propose it

[aviczhl2]

update seq count for many lineages.

[FedeGueli]

update seq count for many lineages. Thank you @aviczhl2 i see many that could be potentially worth proposing.

[FedeGueli]

Branch 12 (JN.1.15) went to 33 and it has now its own FLiRT singlet.

[FedeGueli]

Please propose any of these Branches: 9 12 18 20 36 45 52 58 62 64 once any of them reaches 45 seqs

[FedeGueli]

Branch 83 by @DoropFan now 6 all very recent 5 with H445P and 1 with FLiRT.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice13_genome_test_22ce3_ce3600.json?c=gt-S_249&gmax=25384&gmin=21563&label=id:node_6964265

Suggested query for 445P: G22309C, C4456T,C9298T Suggested query for 346T: G22309C, C4456T,C9298T,G22599C

I suggest to propose it @aviczhl2 or @DoropFan once it reaches 10.

[FedeGueli]

Flirt Branch 30 now reached 21 from 15 (updated) please propose it

[FedeGueli]

br.84 is now 7

[FedeGueli]

Br.55 now 7

[FedeGueli]

@AngieHinrichs it is for sure misplacement cause the orf6:i60T lineage has T22930G and not A

New revolution in the tree of Branch 20 :

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_1e741_ea7b60.json?c=userOrOld&label=id:node_6981547

Now it has been broadened and it became alike a JN.1.16 but for T22930A: so we now found that the lineage at the top after Orf6:I60T is https://github.com/cov-lineages/pango-designation/issues/2567 instead before it is what we called Branch 20 FLirt. While at the bottom we see also the south korean sublineage with Orf1a:T882I that we discussed before.