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
• [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

• [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 , 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

• [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, JN.1.7+C28849T+S:F456L,Orf1a:A3497V, Query: C28849T,T22928C,C10755T, 22 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, dead

  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
• [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

• [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

• [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
• [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
• [P] 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, 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
• [ ] Branch 113, 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
• [ ] Branch 115, JN.1+S:T22N.F456L,Q493E, Query: C23039G, T22928C, C21627A,-17334, 3 seqs, Sweden, Turkey, USA

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

[FedeGueli]

Putative spanish branch in a messy part of the tree showing reversions at S:505 and also at nuc 3565 this query: C775T,C9979T, T22928C catches all the three samples so might be real,

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_35c51_1c01d0.json?c=gt-ORF1ab_170&gmax=21555&gmin=266&label=id:node_6927730

[FedeGueli]

Branch 9 now at 8 with also a S:t572I recent sample

[aviczhl2]

Putative spanish branch in a messy part of the tree showing reversions at S:505 and also at nuc 3565 this query: C775T,C9979T, T22928C catches all the three samples so might be real, https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_35c51_1c01d0.json?c=gt-ORF1ab_170&gmax=21555&gmin=266&label=id:node_6927730

This shall actually be a branch of JN.1.16?

[FedeGueli]

Putative spanish branch in a messy part of the tree showing reversions at S:505 and also at nuc 3565 this query: C775T,C9979T, T22928C catches all the three samples so might be real, https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_35c51_1c01d0.json?c=gt-ORF1ab_170&gmax=21555&gmin=266&label=id:node_6927730

This shall actually be a branch of JN.1.16?

Right , likely it is

[aviczhl2]

We haven't seen 22930A or 22930G branches though.

[FedeGueli]

We haven't seen 22930A or 22930G branches though.

Yeah noticed that too i m.actively search for them ;)

[FedeGueli]

Branch 37 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089 further gained S:F456L

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice6_genome_test_17e23_3457a0.json?label=id:node_6895543

not sure it is a real branch or sequences put together by Usher

[FedeGueli]

while branch 41 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1089 is JN.1.16 + 346T.

[FedeGueli]

SInglet from England today with 346T+456L: JN.1.4 > C25710T > C28312T > T19896C > C20178T, S:R346T (G22599C), S:F456L (T22928C), C27791T Query: C27791T,C20178T, G22599C, T22928C

[FedeGueli]

Another singlet with 456L+346T this time in JN.1.6.1 query: G1156T, C10416T, T22928C, JN.1.6.1 > Orf1a:M297I (G1156T), Orf1:G2941S (G9086A),Orf1a:S3384L (C10416T), S:F456L (T22928C), (G23604A rev, not sure if real)

[aviczhl2]

2/25: Add branch 17-21

[FedeGueli]

2/25: Add branch 17-21

Thank you so now we could see if T22930A is more fit as apparently observed in the past 456L wave.

[FedeGueli]

There is a branch of two seqs by GBW but likely from only one patient (h10/h20) from Japan with T22930A as well Query: T22930A, C26684T,T18471C Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_58d07_b47a30.json?label=id:node_11304311

[FedeGueli]

Putative spanish branch in a messy part of the tree showing reversions at S:505 and also at nuc 3565 this query: C775T,C9979T, T22928C catches all the three samples so might be real, https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_35c51_1c01d0.json?c=gt-ORF1ab_170&gmax=21555&gmin=266&label=id:node_6927730

4 now of this

[FedeGueli]

Another putative 572I 456L branch occuring in the lineage proposed in https://github.com/cov-lineages/pango-designation/issues/2500 JN.1.4 > Orf1a:P971L (C3177T)> C11956T, S:T572I (C23277T) > C2005T > C1188T , 7981G, Orf1b:P2313T (C20404A), S:F456L (T22928C) Query: C2005T ,C1188T , 7981G Samples: 2 MS state US

[aviczhl2]

3/1: Add branch 21-25

[FedeGueli]

Branch 14 parental is now designated JN.1.1.5 . I just saw that Branch 14 it is propose in https://github.com/cov-lineages/pango-designation/issues/2492 i dunno if you want to add the link to the proposal to the chart or not so i dont edit directly not to mess things , while i ve edited JN.1.1.5 as parent to easy your workload cc @aviczhl2 .

[aviczhl2]

Branch 14 parental is now designated JN.1.1.5 . I just saw that Branch 14 it is propose in cov-lineages/pango-designation#2492 i dunno if you want to add the link to the proposal to the chart or not so i dont edit directly not to mess things , while i ve edited JN.1.1.5 as parent to easy your workload cc @aviczhl2 .

Okay let's use your proposal

[FedeGueli]

There should be another branch of JN.1 with S:F456L: JN.1 > M:L46F (G26660T) > G4162A > S:F456L (T22928C) Query:G26660T, G4162A ,T22928C,T3565C Samples: 5 The tree is splitted in two branches one with G1126A and the other without it , i think they are the same lineage cause they all come from Hubei(but one from Henan) and the sample keeping the tree splitted is from Hong Kong and has dropout in the 456 region (cc @angiehinrichs)

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_402c7_5c0460.json?c=gt-M_46&gmax=27191&gmin=26523&label=id:node_6975373

[FedeGueli]

Branch 17 seems fast jumped to 12 today

[FedeGueli]

Branch 37 of #1089 further gained S:F456L https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice6_genome_test_17e23_3457a0.json?label=id:node_6895543

not sure it is a real branch or sequences put together by Usher

This is now JN.1.24 + 346T +456L still two but maybe worth adding to branches Quwery:G22599C, T22928C, G25290T,T3565C tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice9_genome_test_1c512_6dc880.json?label=id:node_6903691

[FedeGueli]

Branch 6 expanded to 23 with two lineages with 346T as highlighted by @krosa1910 in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1421

[aviczhl2]

3/6: Add branch 26-32

Branch 30,31 are R346T+F456L combo branches Branch 32 seems to be growing fast.

[FedeGueli]

• C4795T, T22928C, T3565C

thank you great work

[FedeGueli]

3/6: Add branch 26-32

Branch 30,31 are R346T+F456L combo branches Branch 32 seems to be growing fast.

Also branch 23 went to 5 with a sample from Turkey one to watch likely

cc @corneliusroemer a lot on the move.

[aviczhl2]

I highlight the R346T+F456L combo branches. (23,30,31)

[FedeGueli]

Combo brach 23 went to 6 today traveller from Qatar

[FedeGueli]

branch 17 up to 20

[aviczhl2]

3/9, Add branch 33-34, Branch 7 becomes 39 Branch 26 becomes 10.

[krosa1910]

@aviczhl2 Why do you define JN.1.16* (as branch 3 in 1253) with -A18093G? I know it can seem like a separate branch but A18093G is also not mentioned in the issue.

[aviczhl2]

@aviczhl2 Why do you define JN.1.16* (as branch 3 in 1253) with -A18093G? I know it can seem like a separate branch but A18093G is also not mentioned in the issue.

Only 2 so not listed. Only listing branches with >=3 seqs.

[aviczhl2]

Branch 6 designated JN.1.1.6 via https://github.com/cov-lineages/pango-designation/commit/3475c5b74932201f63da86ab52862c074be31bcd

[FedeGueli]

Hi @aviczhl2 Branch 33 is the one i highlighted in # 2500 of Pango repo, while the reference to pango #2500 previously has been assigned to branch 29 mistakenly ( maybe by me) . So now there is the need to find back the query for branch 29.

Branch 29 is a sublineage of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1244

added there too

[aviczhl2]

Update for branch 11. Although usher put it under JN.1.16 it shall be independently emerged from the G2782T branch of JN.1 39 seqs in 7 countries now. @corneliusroemer @AngieHinrichs

[FedeGueli]

Putative spanish branch in a messy part of the tree showing reversions at S:505 and also at nuc 3565 this query: C775T,C9979T, T22928C catches all the three samples so might be real, https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_35c51_1c01d0.json?c=gt-ORF1ab_170&gmax=21555&gmin=266&label=id:node_6927730

4 now of this

now 6 now Branch 44

[aviczhl2]

3/13: Add branch 36 and branch 37, branch 7 becomes 52

[FedeGueli]

3/13: Add branch 36 and branch 37, branch 7 becomes 52

• T18453C, C12525T,T22928C

Please propose Branch 7

[aviczhl2]

Branch 23 designated KS.1 via https://github.com/cov-lineages/pango-designation/commit/f7585ae3af9545ec713d951d45fa140a8588db05

[aviczhl2]

Add Branch 37 for the JN.1+346T+456V branch misplaced under JN.1.16.1

[FedeGueli]

Branch 37 of #1089 further gained S:F456L https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice6_genome_test_17e23_3457a0.json?label=id:node_6895543 not sure it is a real branch or sequences put together by Usher

This is now JN.1.24 + 346T +456L still two but maybe worth adding to branches Quwery:G22599C, T22928C, G25290T,T3565C tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice9_genome_test_1c512_6dc880.json?label=id:node_6903691

This was massuploaded to 10 yesterday i m proposing it from #1089 Branch 37

[aviczhl2]

3/18: Add branch 42

[FedeGueli]

I have added a comment fast slow dead to the line for the remaining undesignated branches , In my view Branch 9 11 20 32 are the ones to watch with some more still to understand if local or with potential to spread .

[HynnSpylor]

Branch 26 reaches 22

[aviczhl2]

Branch 26 is 28 now. 26 from GISAID query and 2 Hong Kong seqs with no coverage on S:456 but overlapping mutation with the 1126 branch , including GBW from South Korea and Singapore,

The Hong Kong seqs are causing the tree to mistakenly split.

[aviczhl2]

Add branch 43, JN.1.7+S:F456L

[aviczhl2]

@FedeGueli Branch 18 gets FLiRT.

[aviczhl2]

3/23: Add branch 44,45. Branch 9 becomes 24. Branch 17 becomes 25.

[FedeGueli]

Branch 26 is 28 now. 26 from GISAID query and 2 Hong Kong seqs with no coverage on S:456 but overlapping mutation with the 1126 branch , including GBW from South Korea and Singapore,

The Hong Kong seqs are causing the tree to mistakenly split.

propose it please!

[FedeGueli]

• C2644T,A9935G,T22928C

Thank you adding it to 346X

[FedeGueli]

JN.1.18 +456V doubled to 4 , one to watch.