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

aviczhl2 commented 7 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, 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 commented 5 months ago

Branch 31 seems to be an artefact, see #1466.

aviczhl2 commented 5 months ago

Branch 35 designated KU.2

FedeGueli commented 5 months ago

Branch 36 is now 14 one sample from France , in January one Brazilian sample of this lineage had also S:A67V

FedeGueli commented 5 months ago

There is a new (old) branch of JN.1 with S:F456L with one single FLirt sample. JN.1 > Orf1a:K4483R (A13712G) > Orf1a:K1407N (G4486T) > A3058G > S:F456L (T22928C) > S:R346T(G22599C) Query: G4486T,A3058G, T22928C Samples: 3 Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_df38_29efa0.json?label=id:node_6945640

aviczhl2 commented 5 months ago

@FedeGueli Add branch 46 for JN.1->C4777T->S:F456L misplaced under JN.1.16 and JN.1.16.1.

FedeGueli commented 5 months ago

@FedeGueli Add branch 46 for JN.1->C4777T->S:F456L misplaced under JN.1.16 and JN.1.16.1.

thank you i write to Angie

FedeGueli commented 5 months ago

combo branch 29 with 572I and 456L reached 13

FedeGueli commented 5 months ago

One of the branches of JN.1.21(1058Y) with 572I got also 456L query: C13378T, T22912C, G25775T . A singlet that i put here for remainder to check it.

Also a JN.1.11.1 branch got 572I in a singlet from Uk query: G2265A, G3483T, A5641G

FedeGueli commented 5 months ago

There could be a JN.1.16 branch misplaced as follows: JN.1 > A18093G > S:F456L (T22928C) then > Orf3a:R122S (A25758T) > G18093A > S:A688V (C23625T)

more clear here:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice8_genome_test_2c170_3e05a0.json?label=id:node_6917593

cc @angiehinrichs @aviczhl2 Note that hCoV-19/Ecuador/GENSBIO-INSPI-105123/2024 Accession ID: | EPI_ISL_18967534 has not A18093G even if USher places it before the reversion driving the tree misplacement

aviczhl2 commented 5 months ago

cc @AngieHinrichs @aviczhl2 Note that hCoV-19/Ecuador/GENSBIO-INSPI-105123/2024 Accession ID: | EPI_ISL_18967534 has not A18093G even if USher places it before the reversion driving the tree misplacement

That's branch 12 detected by you. But usher is now misplacing it elsewhere.

FedeGueli commented 5 months ago

New 456L > Flirt Branch JN.1 > S:H1101Y ( C24863T )>S:F456L (T22928C) > S:R346T (G22599C )

Query for 456L : C24863T, T22928C, T3565C finds 3 samples Query for 346T :C24863T, G22599C, T3565C finds 1 sample

Apparently it doesnt belong to Jn.1.16.1 (aka JN.1.18 plus 456L) but could be instead that way being H1101Y highly homoplasic

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice4_genome_test_5395a_3ef790.json?label=id:node_6934100

FedeGueli commented 5 months ago

Two new samples of JN.1.16.1 with S:F456V

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_5395a_3ef790.json?label=id:node_6971769

@angiehinrichs could you look at this? @aviczhl2 (and i agree) thinks that it is more likely to be JN.1.18 > S:F456V than this

FedeGueli commented 5 months ago

Two new samples of JN.1.16.1 with S:F456V https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_5395a_3ef790.json?label=id:node_6971769

@AngieHinrichs could you look at this? @aviczhl2 (and i agree) thinks that it is more likely to be JN.1.18 > S:F456V than this

7 now @aviczhl2 i siggest to detach this one and propose it in Pango. with the two alternative placements

aviczhl2 commented 5 months ago

3/28: Add branch 50 (FLiRT+S:60P)

FedeGueli commented 5 months ago

3/28: Add branch 50 (FLiRT+S:60P)

it is the sibling of Branch 66 of #1089 that branch was quite messy with some samples failing to appear in Usher , lets see if maybe they will be joined in one such as S:R346T > S:F456L S:R346T>S:Q183H or not.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2ad9b_533510.json?label=id:node_6967372

aviczhl2 commented 5 months ago

Add branch 52. 53. 54. new branches of T22930A-S:F456L

FedeGueli commented 5 months ago

There may be another JN.1.7 combo lineage with 456L in UK just two samples one only on Gisaid but worth tracking it for a bit: JN.1.7>C28849T > Orf1a:A3497V (C10755T), S:K304K(A22474G),S:F456L (T22928C), ORF9b:R58K (G28456A) Query : A22474G, G28456A,C10755T, T22928C

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice31_genome_3f26f_94c790.json?label=id:node_7012994

FedeGueli commented 5 months ago

Another FViRT (456V) singlet misplaced by Usher under the JN.1.9 FLirt Branch instead it belongs to the big undesignated branch with G17562T query: T22928G, C18657T

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice10_genome_test_313d4_94d190.json?c=gt-S_346,456&gmax=25384&gmin=21563&label=id:node_6947429

FedeGueli commented 4 months ago

worth proposing branch 11 also to soleve the JN.1.39 thing.

aviczhl2 commented 4 months ago

Add branch 55. Branch 22 revives.

FedeGueli commented 4 months ago

Add branch 55.

it was singlet 11 of #1089 already doubled thx

FedeGueli commented 4 months ago

Flirt branch 50 +1 England

KQ.1 seems to have now a singlet with 456L Query : G25555T,A25582G from Hawaii

FedeGueli commented 4 months ago

Flirt branch 50 +1 England

Branch 50 up to 5 with two new GBW samples plkease propose it when it reaches 10.

FedeGueli commented 4 months ago

Flirt branch 50 +1 England

Branch 50 up to 5 with two new GBW samples plkease propose it when it reaches 10.

wait it is already 8! New query : C8092T, T21740C, G22599C Epi- set: EPI_ISL_18874336, EPI_ISL_18999269, EPI_ISL_18999314, EPI_ISL_19019175, EPI_ISL_19025924, EPI_ISL_19028032-19028033, EPI_ISL_19028035

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_3acf3_d18670.json?label=id:node_6971728 Please propose it @aviczhl2

aviczhl2 commented 4 months ago

Flirt branch 50 +1 England

Branch 50 up to 5 with two new GBW samples plkease propose it when it reaches 10.

wait it is already 8! New query : C8092T, T21740C, G22599C Epi- set: EPI_ISL_18874336, EPI_ISL_18999269, EPI_ISL_18999314, EPI_ISL_19019175, EPI_ISL_19025924, EPI_ISL_19028032-19028033, EPI_ISL_19028035

The tree seems a little bit messy. 2 Having the Orf3a reversion and one having S:456 reversion. What's shown on usher tree may not be the correct order. Maybe some form of recomb?

aviczhl2 commented 4 months ago

Flirt branch 50 +1 England Please propose it @aviczhl2

I got it. The correct order shall be 18471->25688->3913->8092+S:S60P,R346T+25378 (Texas S:456F seq ends here)->S:F456L->recomb with JN.1+25571(and remove 25378+25688) branch (2 GBW)

So actual toll is 1(S:60P+346T)+5(S:60P+346T+456L)+2(S:60P+346T+456L+recomb)

aviczhl2 commented 4 months ago

Branch 29 designated KW.1.1

aviczhl2 commented 4 months ago

4/4: Add branch 56-63

Branch 61 is FLiRT. Branch 62 has serious misplacement issue, some placed under JN.1.16 and FLiRT sub-branch placed under JN.1.9(Flip-Flop reversion)

FedeGueli commented 4 months ago

Flirt branch 55 now went to three the last sample is the oldest and it has no S:272H so maybe the query could be changed in: ,T22928C,C14220T,C22311A that finds all the samples of it.

tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_656fa_ffd010.json?label=id:node_6979757

aviczhl2 commented 4 months ago

4/8: Add branch 65

Branch 46 reaches 69.

FedeGueli commented 4 months ago

4/8: Add branch 65

Branch 46 reaches 69.

propose br 46

aviczhl2 commented 4 months ago

Add FLiRT branch 66, shall be separated from KU.2.

aviczhl2 commented 4 months ago

Branch 34 revives and becomes 10. Add branch 68.

FedeGueli commented 4 months ago

Add FLiRT branch 66, shall be separated from KU.2.

why do you think it should be separated? C7113T is quite homoplasic so i dont see evidences to be a separated lineage. Maybe a recombinant with JN.1.11.1 ? that but hard to prove

FedeGueli commented 4 months ago

Re Br.66 i mean it could be but unless we have evidences of it i think we should not complicate things. as JN.1.16 and JN.1.18 are not for sure monophyletic but hence we cant distinguish we take them as good as long it doesnt appear to be possible and plausible a different placement, no?

aviczhl2 commented 4 months ago

Re Br.66 i mean it could be but unless we have evidences of it i think we should not complicate things. as JN.1.16 and JN.1.18 are not for sure monophyletic but hence we cant distinguish we take them as good as long it doesnt appear to be possible and plausible a different placement, no?

There is a JN.1.30.1+Orf1a:I1128F+S:S31del branch(which usher doesn't show the S:S31del). So I think Orf1a:I1128F shall be the first step here.

BTW it is unlikely to gain C7113T from recombinant as it needs multiple breakpoints.

FedeGueli commented 4 months ago

Re Br.66 i mean it could be but unless we have evidences of it i think we should not complicate things. as JN.1.16 and JN.1.18 are not for sure monophyletic but hence we cant distinguish we take them as good as long it doesnt appear to be possible and plausible a different placement, no?

There is a JN.1.30.1+Orf1a:I1128F+S:S31del branch(which usher doesn't show the S:S31del). So I think Orf1a:I1128F shall be the first step here.

BTW it is unlikely to gain C7113T from recombinant as it needs multiple breakpoints.

ah ok thx, good catch, even if we cant be completely sure that is convergence, maybe an intermediate sequence will shape the tree better.

@angiehinrichs what do you think: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2ee43_7934e0.json?c=userOrOld&label=id:node_6922569

aviczhl2 commented 4 months ago

Branch 30 revives in Canada

aviczhl2 commented 4 months ago

Add branch 70 and 71.

aviczhl2 commented 4 months ago

4/12: Add branch 72-75.

FedeGueli commented 4 months ago

26894T, C7732T,G22599C, T22928C

3 continents with 5 sequences

FedeGueli commented 4 months ago

Branch 30 FliRT is expanding

FedeGueli commented 4 months ago

about new >>FliRT branch 71 i doubt it is JN.1.18 there is a much bigger branch in JN.1 with Orf1a:N2147S , just attracted in JN.1.18 by S:R346T

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e6bb_973690.json?label=id:node_6958337

aviczhl2 commented 4 months ago

about new >>FliRT branch 71 i doubt it is JN.1.18 there is a much bigger branch in JN.1 with Orf1a:N2147S , just attracted in JN.1.18 by S:R346T

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e6bb_973690.json?label=id:node_6958337

Also branch 22 shall be this.

aviczhl2 commented 4 months ago

about new >>FliRT branch 71 i doubt it is JN.1.18 there is a much bigger branch in JN.1 with Orf1a:N2147S , just attracted in JN.1.18 by S:R346T

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e6bb_973690.json?label=id:node_6958337

Maybe you shall propose the Orf1a:N2147S+ S:R346T branch, clearly sth. misplaced under JN.1.18. (And has FLiRT and FViRT sub-branches)

G22599C,A6705G,C18894T gets 58.

FedeGueli commented 4 months ago

about new >>FliRT branch 71 i doubt it is JN.1.18 there is a much bigger branch in JN.1 with Orf1a:N2147S , just attracted in JN.1.18 by S:R346T https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e6bb_973690.json?label=id:node_6958337

Maybe you shall propose the Orf1a:N2147S+ S:R346T branch, clearly sth. misplaced under JN.1.18. (And has FLiRT and FViRT sub-branches)

G22599C,A6705G,C18894T gets 58.

yeah i will!

FedeGueli commented 4 months ago

branch 73 has a singlet with FLiRT : BR73>C3244T, A18432T> G29383A > C17373T, S:R346T (G22599C), G29383A Query: G29383A,C17373T, G22599C

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_16090_97a730.json?c=userOrOld&label=id:node_6936865

FedeGueli commented 4 months ago

Also branch 22 shall be this.

ok i ll propose everything in one

FedeGueli commented 4 months ago

Also branch 22 shall be this.

ok i ll propose everything in one

now both BR.22 and BR.71 proposed in https://github.com/cov-lineages/pango-designation/issues/2560

AngieHinrichs commented 4 months ago

There is a JN.1.30.1+Orf1a:I1128F+S:S31del branch(which usher doesn't show the S:S31del). So I think Orf1a:I1128F shall be the first step here. BTW it is unlikely to gain C7113T from recombinant as it needs multiple breakpoints.

ah ok thx, good catch, even if we cant be completely sure that is convergence, maybe an intermediate sequence will shape the tree better.

@AngieHinrichs what do you think: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2ee43_7934e0.json?c=userOrOld&label=id:node_6922569

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.

sars-cov-2-variants / lineage-proposals

Multiple JN.1* branches with S:F456X : 4 Ongoing Unproposed Branches as 7/25 #1253