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Published 20 hours ago • verified publisher icon sars-cov-2-variants

Multiple JN.1* branches with S:F456X : 67 Ongoing Branches as 5/7

Open xz-keg opened this issue 1 year ago • 224 comments

It seems that S:F456L is very convergent in JN.1 now.

General query excluding already proposed/designated ones: T3565C,C18894T,T22926C, -12525,-17334,-27415,-G2782T,-G4162A, -T10084A,-C8092T,-28498,-25445,-7981,-22111, Spike_F456

  • [x] Branch 1: JN.1.1.2+S:F456L, #1147 DEAD
  • [x] 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
  • [ ] Branch 7: JN.1.4+Orf1a:T4087I,Orf1b:S1512N+S:F456L Proposed in https://github.com/cov-lineages/pango-designation/issues/2517
  • [x] Branch 8: JN.1.4.5+C28948T+S:F456L, dead Query: C28201T, T22928C, T22926C, C28948T,3 seqs, Singapore 2 has S:ins186TQM dead
  • [ ] Branch 9: JN.1+C6145T+S:F456L https://github.com/cov-lineages/pango-designation/issues/2585
  • [ ] Branch 10: JN.1.4+C9979T+S:F456L Query: T18453C, T22928C,C9979T, 18 seqs, Sweden, Norway
  • [ ] 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
  • [ ] Branch 12: 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
  • [x] Branch 13: JN.1+C3589T+A25102G+S:F456L,Dead 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, By @FedeGueli JN.1.22 > Orf1a:G445V (G1599T) > C11704T > S:F456L (T22928C), Query: G1599T, C11704T ,T22928C, 37 seqs, USA, Spain
  • [ ] Branch 17, JN.1.4+S:F456L, (https://github.com/cov-lineages/pango-designation/issues/2577)
  • [ ] Branch 18, JN.1.29+S:F456L, Query: C2644T,A9935G,T22928C, 29 seqs, Brazil, Canada,UK
  • [x] Branch 19, JN.1+S:F456L, Orf1a:R560C, T2846I,Dead Query: C8802T, C21904T, T22928C, 3 seqs, USA, New Zealand
  • [ ] Branch 20, JN.1+S:F456L(T22930A),https://github.com/cov-lineages/pango-designation/issues/2588
  • [ ] Branch 21, JN.1.4.5+S:F456L, Query: C28201T, T22928C, T22926C, -C28948T,-G2654A,-C3177T,-20823, 25 seqs, Greece, Sweden,China,USA, Spain, Australia, Italy, Switzerland,
  • [ ] Branch 22, JN.1+Orf1a:N2147S+S:R346T+T2800I,S:F456V Proposed in https://github.com/cov-lineages/pango-designation/issues/2560
  • [x] FLiRT Branch 23, Designated KS.1, JN.1.13.1+S:F456L, Query: T21738C, T22928C, G24821T, 6 seqs, Singapore, USA, Turkey, Qatar
  • [ ] Branch 24, JN.1+Orf1a:K399R+Orf1b:P2321H+S:F456L, Query: C20429A, C18894T,T22928C,16 seqs, USA, France, Brazil, Ireland, UK, Australia
  • [ ] Branch 25, JN.1.3+S:F456L, Query: T3565C,T22928C,C27945T,-C4777T, 27 seqs, South Korea,Israel, Canada, Spain, USA,France, Australia, Singapore
  • [ ] Branch 26, By @FedeGueli ,JN.1 > M:L46F (G26660T) > G4162A > S:F456L (T22928C), Proposed in https://github.com/cov-lineages/pango-designation/issues/2531
  • [x] Branch 27, JN.1.1+C9142T+Orf1a:T1589I+S:F456L,Dead Query: T22928C,C1762A,C5031T,C9142T,-10440, 5 seqs, USA, UAE,India
  • [x] Branch 28, JN.1.1+Orf1b:T2165M+Orf1a:S2635L,S:F456L,Dead 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, Query: C26894T, C7732T,G22599C, T22928C 21 seqs, USA, UAE, New Zealand,Canada
  • [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
  • [ ] Branch 32, JN.1+C4795T+S:F456L,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
  • [ ] Branch 34, JN.1+A9085G+S:F456L 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
  • [ ] Branch 36, JN.1+Orf10:P10S+S:F456L, Query: T22928C,C26753T,C18894T, 35 seqs, Brazil, USA,Colombia, France, Singapore, Netherlands, UK, Denmark, New Zealand, Spain
  • [ ] Branch 37, JN.1.18+S:F456V, 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
  • [ ] Branch 41 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, 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, By @FedeGueli , JN.1 > Orf1a:K4483R (A13712G) > Orf1a:K1407N (G4486T) > A3058G > S:F456L (T22928C) Query: G4486T,A3058G, T22928C,4 seqs, UK,Canada
  • [ ] Branch 48, JN.1+C10078T,T14526C,C21911T+S:F456L, Query: T22928C,C10078T,T14526C, 22 seqs, Australia, UK, Germany,New Zealand
  • [ ] Branch 49, By @FedeGueli , JN.1 > S:H1101Y ( C24863T )>S:F456L (T22928C) Query:C24863T, T22928C, T3565C 17 samples, China, UK,Canada
  • [ ] FLiRT Branch 50, JN.1+T18471C+Orf3a:A99V+S:S60P,R346T+S:F456L,Designated JN.1.48.1 and a related recomb, Proposed in https://github.com/cov-lineages/pango-designation/issues/2547
  • [ ] Branch 51, JN.1+C26873T+S:F456L, Query: T22928C, C26873T, C18894T, 21 seqs, China, Netherlands, Germany, Singapore,USA,Canada, New Zealand
  • [ ] Branch 52, JN.1.4.2+S:S680F+S:F456L(T22930A), Query: T22930A, C23601T, A22115G, 29 seqs, USA, New Zealand, Italy, Netherlands
  • [ ] Branch 53, 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
  • [ ] FLiRT Branch 55, JN.1.18.1+S:F456L, Query: T22928C,C14220T,C22311A, 5 seqs, USA, UK,India,South Korea
  • [ ] Branch 56, JN.1+S:V62F,R681H+S:F456L, Query: G21746T, C4586T,T22928C, 5 seqs, Israel, South Korea,USA, France
  • [ ] Branch 57, JN.1+C28603T+S:F456L, Query: T22928C, C28603T, T3565C,-17334,-T565A 10 seqs, UK, South Korea, Chile,Japan, China, Australia
  • [ ] Branch 58, JN.1+C16269A+C12781T+S:F456L, Query: G16269A,C12781T,T22928C 35 seqs, Canada, USA,UK, South Africa
  • [x] Branch 59, JN.1+C4093T+N:A119D,S:F456L,Dead Query: C4093T, T22928C, C186T 4 seqs, USA
  • [ ] Branch 60, JN.1+C27389T+S:F456L, Query: C27389T,T22928C,T3565C, 5 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, 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, JN.1.4.5+C20823T+C9073T,A21417G+S:F456L, Query: T18453C,C9073T,T22928C, 10 seqs, USA, Australia,New Zealand
  • [ ] Branch 64, JN.1+C22858T+S:F456L, Query: C22858T,T22928C,C18894T,-7113, 28 seqs, South Korea,Australia, USA, UK,Finland
  • [ ] Branch 65, JN.1+C25566T+S:F456L, Query: C25566T,T22928C,T22926C,-23277,-C2106T, 5 seqs, Portugal, Luxembourg,Germany,China
  • [ ] FLiRT Branch 66, 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,
  • [ ] FLiRT Branch 67, #1503
  • [ ] Branch 68, JN.1+Orf1b:L2560F+S:F456L, Query: C21145T, T22928C, C18894T,-18453, -4795, 6 seqs, France, India, Singapore,China,USA
  • [x] Branch 69. JN.1+C25521T+C24904T+S:F456L,Dead, Query: C24904T,C25521T,T22928C,C18894T, 6 seqs, USA
  • [ ] Branch 70, JN.1+C14676T+S:Q677L+S:F456L, Query: C14676T, A23592T, T22928C,7 seqs, USA, Netherlands,Spain, UK
  • [ ] FLiRT Branch 71, JN.1+Orf1a:N2147S+S:R346T+S:F456L(T22930A), Proposed in https://github.com/cov-lineages/pango-designation/issues/2560
  • [x] Branch 72, JN.1.4+Orf1a:A2001V+Orf1a:T1040I,S:F456L,Dead, Query: C6267T,T18453C,T22928C, 3 seqs, UK
  • [ ] Branch 73, JN.1+C27110T+S:F456L, Query: T22928C, C27110T, T22926C, 10 seqs, Ireland, Canada, USA, India
  • [ ] Branch 74, JN.1.34+Orf1a:T2846R, S100R, E386D+S:F456L, Query: C23673T,T22928C, C8802T,T565A, 8 seqs, UK, Denmark,USA,Sweden,Hungary
  • [x] Branch 75, JN.1.33+Orf1a:D2060N+Orf1b:T76I,S:F456L,Dead Query: T22928C, G5992A, G6443A, 4 seqs, Australia, France
  • [ ] Branch 76, JN.1+Orf1b:P1427L+S:F456L, Query: C17747T, T22928C, C18894T and C17747T, -T22928C, C18894T,C12786T(sum of the 2), 3 seqs, South Korea
  • [ ] Branch 77, JN.1.7+C28849T+S:F456L,Orf1a:A3497V, Query: C28849T,T22928C,C10755T, 4 seqs, USA, UK
  • [ ] Branch 78, JN.1.7+Orf1a:V1025L+S:F456L,Orf1b:F2173L,Query: G3338T, T10546C, T22928C, 3 seqs, Canada
  • [ ] Branch 79, JN.1+C6968T+S:F456L, Query: C6968T, T22928C, C18894T, 2 seqs, France, Sweden
  • [ ] Branch 80, JN.1+Orf1a:R550H+Orf1a:F1028Y,S:F565L+S:F456L, Query: T3348A,T23257G,T22928C, 3 seqs, Japan
  • [ ] FLiRT Branch 81, JN.1.18+Orf6:I60T,S:F456L(T22930G),https://github.com/cov-lineages/pango-designation/issues/2567
  • [ ] Branch 82, https://github.com/cov-lineages/pango-designation/issues/2571
  • [x] Branch 83,Designated JN.1.50 By @DoropFan JN.1>C9298T>S:L249F(G22309C)>S:A67V(C21762T), S:F456L(T22930G), https://github.com/cov-lineages/pango-designation/issues/2587
  • [ ] FLiRT Branch 84, JN.1+Orf3a:A103T+S:R346T,F456L, Query: T22928C, G22599C, C1612T,G25770A, 4 seqs, Russia, Sweden, USA
  • [ ] Branch 85, JN.1.9+Orf1b:V1402I,A1620V+Orf1a:T3032I,I3758V,S:A376S,F456L, Orf3a:Y141H, Query: T22928C, G17671A, C18326T, 4 seqs, USA
  • [ ] Branch 86, JN.1+C17119T+A2251G+S:F456L(T22930A), Query: T22930A, C17119T, A2251G, 13 seqs, South Korea
  • [ ] FLiRT Branch 87, JN.1.1.5+S:F456L(T22930A), Query: T22930A, C9142T, G22599C,T3565C, 4 seqs, USA, Australia , UK
  • [ ] Branch 88, JN.1.4+C11020T+S:F456L, Query: C11020T, T22928C, T18453C, 6 seqs, USA, South Korea, South Africa
  • [ ] Branch 89, JN.1.4+C5284T+S:F456L, Query: C5284T, T22928C, T18453C, 5 seqs, South Korea, USA
  • [ ] Branch 90, JN.1.4+C22450T+Orf1a:T2274I, S:F456L, Query: C22450T, T22928C, T18453C, 4 seqs, South Korea
  • [ ] Branch 91, JN.1.4+Orf1b:P1342S+S:A123S, F456L, Query: T22928C, C17491T,T18453C, 4 seqs, South Korea
  • [ ] Branch 92, JN.1.4+Orf1a:T602I+Orf1b:H714Y+Orf6:L29P,S:F456L, Query: C2070T, C15613T,T22928C, 3 seqs, China
  • [ ] Branch 93, JN.1.1.5 > T6095C,C6541T, C21911T, S:L176F (C22088T), S:F456V (T22928G ), https://github.com/cov-lineages/pango-designation/issues/2586
  • [ ] Branch 94, https://github.com/cov-lineages/pango-designation/issues/2461
  • [ ] Branch 95, JN.1+Orf1a:K399R+Orf1a:T1017I+S:F456L, Query: T22928C, C3315T, G10255A, 16 seqs, Thailand, USA, Japan, South Korea, Australia, China
  • [ ] Branch 96, 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, JN.1+C14178T+S:F456L,Q613H,Orf1a:V2783F, Query: C14178T,T3565C,T22928C,G23401T, 3 seqs, USA
  • [ ] Branch 98, JN.1+C4048T+S:F456L, Query: C4048T, T22928C, T3565C, 10 seqs, USA, New Zealand, China, Australia
  • [ ] FLiRT Branch 99, JN.1+T17859C+C3172T+S:R346T,F456L, Query: T17859C,T22928C,T3172G,T3565C, 8 seqs, Spain, Portugal
  • [ ] Branch 100, JN.1.4+S:S640F+S:F456L,Orf1a:P361L,H417Y,Orf3a:T24I, Query: C774T,C23481T, T22928C, 16 seqs, Canada, South Korea

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

xz-keg avatar Jan 04 '24 10:01 xz-keg