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

xz-keg commented 10 months ago

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.

Memorablea commented 5 months ago

please see it:G4162A, T22928C, G26660T

xz-keg commented 5 months ago

please see it:G4162A, T22928C, G26660T

That's branch 26 already proposed.

FedeGueli commented 5 months ago

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.

@aviczhl2 @DoropFan please propose it in the main Pango page : it is now 8 with 6 countries plus one unknown GBW sample seems very fast potentially

FedeGueli commented 5 months ago

Checking Branch 83 i found a similar unrelated variant that arose in England only three samples: JN.1.4 >>> T18453C > C27297T > S:L249F (G22309T), S:F456L (T22930A ) Query: G22309T ,T22930A,T3565C

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1ab27_139320.json?label=id:node_7096449

FedeGueli commented 5 months ago

Not sure if you want to track it here but there is another XDK +456L that emerged recently in Spain: (different from #1511 and #1467)

XDK (572I) > C22388T > S:F456L (T22928C) Query: C5314T, T22928C,C22388T Samples: 20

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_188d1_1fabb0.json?c=userOrOld&label=id:node_7023724

FedeGueli commented 5 months ago

branch 36 has now a flirt singlet, i suggest a revisited query: T22928C,C26753T,C18894T,T19092C to exclude some unrelated flirt sequences. with this query is 33

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice12_genome_test_120f9_24d3e0.json?c=gt-S_346&label=id:node_6973750

FedeGueli commented 5 months ago

+1 FLirt Branch 55

xz-keg commented 5 months ago

Not sure if you want to track it here but there is another XDK +456L that emerged recently in Spain: (different from #1511 and #1467)

XDK (572I) > C22388T > S:F456L (T22928C) Query: C5314T, T22928C,C22388T Samples: 20 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_188d1_1fabb0.json?c=userOrOld&label=id:node_7023724

yeah I was tracking this one. Previously Spain only so not proposed, Now it also exports to USA.

FedeGueli commented 5 months ago

A22474G, G28456A,C10755T, T22928C JN.1.7+456L + orf9b:R58K now 4 from 2 unsure if worth adding or not at this point

xz-keg commented 5 months ago

Branch 54 designated JN.1.49.2 via https://github.com/cov-lineages/pango-designation/commit/3f31249f349fbcb4d67fd194fa23b1cc34e60316

FedeGueli commented 5 months ago

updated br.96 +1 > 3

FedeGueli commented 5 months ago

@aviczhl2 please propose branch 73 it has a FLiRT branch that topped 8 yesterday:

The FLiRT branch is tracked in #1089 as :

Branch 112: FLiRT ( originally spotted in Branch 73 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253 by @aviczhl2 ) JN.1>C27110T>S:F456L(T22928C) >C3244T, A18432T> G29383A > S:R346T (G22599C), Query:C3244T, A18432T,G22599C Samples: 8 (Ireland, Scotland, California) ( 5 with S:M153I Query: C9169T, T12987C)

Last sample from ireland has S:T500N with S:M153I

FedeGueli commented 5 months ago

Branch 12 has now a growing FLiRT branch of 3 samples 2 countries tracked in #1089 as:

Branch 138 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: 3 Spain, US

Worth proposing it too.

FedeGueli commented 5 months ago

Branch 83 by @DoropFan now designated JN.1.50 via https://github.com/cov-lineages/pango-designation/issues/2587

xz-keg commented 5 months ago

sub-branch of branch 45 designated JN.1.1.8.

xz-keg commented 5 months ago

Add branch 97-99

xz-keg commented 5 months ago

Add branch 100, a Canadian cluster

xz-keg commented 5 months ago

I just checked , 90%+ of branch 45 belongs to JN.1.1.8. Shall be a proper designation.

FedeGueli commented 5 months ago

I just checked , 90%+ of branch 45 belongs to JN.1.1.8. Shall be a proper designation.

Do you mean it is ok?

FedeGueli commented 5 months ago

C25566T

Add branch 97-99

Branch 99 is the one proposed in https://github.com/cov-lineages/pango-designation/issues/2589

FedeGueli commented 5 months ago

Branch 95 now 21 seems growing quite fast now

DailyCovidCases commented 5 months ago

Branch 10 is pretty much dead now: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=T18453C%2CT22928C%2CC9979T&nextcladePangoLineage=JN.1.4*&

FedeGueli commented 5 months ago

Br 18 (JN.1.49) is now 44 with multiple FLiRT and FLiRI sublineages

FedeGueli commented 5 months ago

br.16 has been proposed in https://github.com/cov-lineages/pango-designation/issues/2595

DailyCovidCases commented 5 months ago

Branch 10 is likely dying off now: usher Screenshot (49)

FedeGueli commented 5 months ago

I m proposing branch 55 ( aka br.84 of 1089) is now 13 and well distributed in a vast area

FedeGueli commented 5 months ago

@aviczhl2 i m going to propose directly this new spanish branch of JN.1.30 + 456L +572I i think we missed it but seems interesting,

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_36e7f_b21640.json?label=id:node_7073772

wait wait it a XBB.1.16 from Chile misplaced here (EDITED)

proposed in https://github.com/cov-lineages/pango-designation/issues/2598

xz-keg commented 5 months ago

@aviczhl2 i m going to propose directly this new spanish branch of JN.1.30 + 456L +572I i think we missed it but seems interesting, https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_36e7f_b21640.json?label=id:node_7073772

wait wait it a XBB.1.16 from Chile misplaced here (EDITED)

proposed in cov-lineages/pango-designation#2598

That's not a sub-branch of JN.1.30, the usher placement is wrong here. I suspect this being sub-branch of JN.1.16 so didn't listed.

FedeGueli commented 5 months ago

branch 30 now 32 seqs mostly from canadian clusters

FedeGueli commented 5 months ago

[Scartch:Br.62 now 45 27 with FLirt, after verifying the placement i would suggest to propose it]

Branch 62 is now under JN.1.16.1 close it please. ( i would not complicate further with masked nuc thing) https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_35057_c768e0.json?f_userOrOld=uploaded%20sample&label=id:node_7135547

FedeGueli commented 5 months ago

Not sure if you want to track it here but there is another XDK +456L that emerged recently in Spain: (different from #1511 and #1467) XDK (572I) > C22388T > S:F456L (T22928C) Query: C5314T, T22928C,C22388T Samples: 20 test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_188d1_1fabb0.json?c=userOrOld&label=id:node_7023724

yeah I was tracking this one. Previously Spain only so not proposed, Now it also exports to USA.

32 for this worth proposing i think.

FedeGueli commented 5 months ago

Br.51 now 58 worth proposing

FedeGueli commented 5 months ago

Br.52 now 55 worth proposing

FedeGueli commented 5 months ago

Br.58 now 54 worth proposing

FedeGueli commented 5 months ago

Br.12 proposed in https://github.com/cov-lineages/pango-designation/issues/2604

FedeGueli commented 5 months ago

Br.30 proposed in https://github.com/cov-lineages/pango-designation/issues/2605

FedeGueli commented 5 months ago

Br 21 proposed in https://github.com/cov-lineages/pango-designation/issues/2607

FedeGueli commented 5 months ago

Br 18 now proposed in https://github.com/cov-lineages/pango-designation/issues/2609

FedeGueli commented 5 months ago

Not sure if you want to track it here but there is another XDK +456L that emerged recently in Spain: (different from #1511 and #1467) XDK (572I) > C22388T > S:F456L (T22928C) Query: C5314T, T22928C,C22388T Samples: 20 test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_188d1_1fabb0.json?c=userOrOld&label=id:node_7023724

yeah I was tracking this one. Previously Spain only so not proposed, Now it also exports to USA.

32 for this worth proposing i think.

37 now i m proposing it

FedeGueli commented 5 months ago

Br 36 now proposed in https://github.com/cov-lineages/pango-designation/issues/2613

FedeGueli commented 5 months ago

Br.24 now proposed in https://github.com/cov-lineages/pango-designation/issues/2612

FedeGueli commented 5 months ago

Br.52 (JN.1.4.2 with 185D 680F 456L) up to 58 worth proposing it https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2d71c_441b50.json?label=id:node_7103772