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

xz-keg · 2024-01-04T10:55:08Z

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, JN.1.1.2 (S:G181E ) with S:F456L (14 seqs 7 countries) #1147 DEAD
[*] Branch 2: JN.1.1+C9142T+S:F456L, Another JN.1.1+S:F456L(7 seqs, 4 countries) #1249 DEAD
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
Branch 4: Designated JN.1.11.1 > JN.1.11+Orf1a:T2283I,S:F456L (JN.1+S:V1104L emerging in India(Designated JN.1.11, 16 and 5 countries with Orf1a:T2283I and S:F456L ) cov-lineages/pango-designation#2446)
Branch 5: Designated JN.1.12 > JN.1+Orf7a:A8T+S:F456V, Query: T22928G,G27415A, 13 seqs, Italy, Netherlands, Poland,Spain,France, Greece
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 JN.1.4+Orf1a:T4087I,Orf1b:S1512N+S:F456L(304 seqs, 19 countries, 22 with S:T572I, 10 with S:R346T) cov-lineages/pango-designation#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 cov-lineages/pango-designation#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 JN.1.39+S:F456L mostly misplaced under JN.1.16 (456 seqs, 250 with S:R346T(designated JN.1.39.1), 16 with S:T572I and S:478Q) cov-lineages/pango-designation#2543
Branch 12: Designated JN.1.15.1

Now proposed in cov-lineages/pango-designation#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

FLiRT Branch 14, Designated KR.1 JN.1.1.5 (Original proposal) with a S:F456L /Orf9b:T72I sublineage (9 samples) cov-lineages/pango-designation#2492
[*] Branch 15: by @FedeGueli JN.1 > C23683T > S:F456L (JN.1+S:F456L on C23683T branch(136 seqs, 9 countries) cov-lineages/pango-designation#2578)
[ *] Branch 16, Dead

Proposed in cov-lineages/pango-designation#2595 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, Designated JN.1.4.9, (JN.1.4+S:F456L(298 seqs) cov-lineages/pango-designation#2577)
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

Branch 20, JN.1+S:F456L(T22930A), the S:R346T sub-branch designated JN.1.18.5 JN.1+S:F456L via T22930A (257 seqs, 172 with S:R346T designated JN.1.18.5) cov-lineages/pango-designation#2588
[P] Branch 21, JN.1.4.5+S:F456L, JN.1.4.5 + S:F456L with C28201T branch (96 seqs) cov-lineages/pango-designation#2607
Branch 22, Designated MD.2,JN.1+Orf1a:N2147S+S:R346T+T2800I,S:F456V Proposed in JN.1.18 + Orf1a:N2147S (280) with three FLiRT sublineages (FLiRT1+S:K679R= 69 / FliRT2 = 46) and one FViRT sublineage(50) cov-lineages/pango-designation#2560
FLiRT Branch 23, Designated KS.1, JN.1.13.1+S:F456L, Query: T21738C, T22928C, G24821T, 6 seqs, Singapore, USA, Turkey, Qatar
Branch 24, Designated Jn.1.55.2

JN.1+Orf1a:K399R+Orf1b:P2321H+S:F456L, cov-lineages/pango-designation#2612

[*] Branch 25, proposed in JN.1.3+S:F456L with Orf8:Q18* (16 seqs) cov-lineages/pango-designation#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 JN.1+M:L46F+S:F456L(1922 seqs, 38 countries, 28% China, 22 with S:R346T, 51 with S:S31F, 6 with S:T22N) cov-lineages/pango-designation#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

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,JN.1.26 + S:F456L on C7732T branch (72 seqs) cov-lineages/pango-designation#2605
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,Designated JN.1.51.1, JN.1+S:F456L on C4795T branch (114 seqs, 14 countries) cov-lineages/pango-designation#2581
Branch 33, By @FedeGueli KV.2 > C2005T > C1188T , 7981G, Orf1b:P2313T (C20404A), S:F456L (T22928C), KV.2 (JN.1.4.5 + S:T572I ) with S:F456L (5,Mississippi) cov-lineages/pango-designation#2500
Branch 34, JN.1+A9085G+S:F456L, Designated JN.1.54.1 JN.1 + S:F456L + S:V407i (37 seqs, Spain) cov-lineages/pango-designation#2584
FLiRT Branch 35, Designated KU.2, JN.1.30.1 > S:F456L (T22928C) KU.2 (JN.1.30.1 + S:F456L) FLiRT sublineage got S:G213E and Orf1a:P2739L(19) in Uk, France, NZL cov-lineages/pango-designation#2514
[P] Branch 36, JN.1+Orf10:P10S+S:F456L, JN.1+S:F456L with Orf10:P10S (107 seqs) cov-lineages/pango-designation#2613
Branch 37, JN.1.18+S:F456V,Designated JN.1.18.3, Proposed in JN.1.18+S:F456V misplaced as JN.1.16.1+S:L456V(109 seqs, 19 countries) cov-lineages/pango-designation#2538.
[ *] FLiRT Branch 38, JN.1.24.1+S:F456L, JN.1.24.1 (346T) > FLiRT with S:F456L (101 seqs) emerged in Texas (NOTE: unreliable query) cov-lineages/pango-designation#2520
FLiRT Branch 39, JN.1.1.7+S:R346T+Orf1a:R1464L+S:F456L, Dead, JN.1.1+S:S31F+S:R346T(Designated LC.1)+S:F456L(3 seqs, 2 countries) cov-lineages/pango-designation#2490
Branch 40 JN.1.4.7 > S:R346T (G22599C) > S:F456V (T22928G), Designated LE.1.1 JN.1.4.7 (Orf3a:G18D) with S:R346T, 144 Sequences, 19 countries including 5 different African countries(20% in DRC-Congo in 2024, 5% in South Africa in March) with S:F456V (21) cov-lineages/pango-designation#2493
[P] Branch 41 now proposed in JN.1+S:L176F+S:F456L with C18894T branch (16 seqs) cov-lineages/pango-designation#2632 JN.1+S:L176F+S:F456L, Query: C22088T,C18894T,T22928C,-17562 14 seqs, Germany,Australia, USA, UAE, South Korea,China
FLiRT Branch 42 JN.1.9+S:R346T+S:F456L, Designated LB.1, Query: G22111T, G22599C, T22928C,T3565C Proposed in LB.1 (JN.1.9 + FLiRT) with S:S31del (339) with a singlet with S:A475V (this subbranch spotted by @hynnspylor) cov-lineages/pango-designation#2546
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 cov-lineages/pango-designation#2633 >JN.1+C9979T+C775T,S:F456L, Query: T22928C, C775T, C9979T, 9 seqs, Spain

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
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 JN.1+C4777T+S:F456L(84 seqs, 16 countries) with S:R346T(36 seqs) and S:R346I( 20 seqs) misplaced under JN.1.16 and JN.1.16.1 cov-lineages/pango-designation#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 JN.1+S:F456L with C21911T branch (38 seqs) cov-lineages/pango-designation#2634 >JN.1+C10078T,T14526C,C21911T+S:F456L, Query: T22928C,C10078T,T14526C, 22 seqs, Australia, UK, Germany,New Zealand
[*] Branch 49, proposed in New FLiRT JN.1 with 4 spike mutations (S:S71F,R346T,F456L H1101Y), 19 sequences Uk, Canada cov-lineages/pango-designation#2565 By @FedeGueli ,

JN.1 > S:H1101Y ( C24863T )>S:F456L (T22928C) Query:C24863T, T22928C, T3565C 32 samples, China, UK,Canada,Salvador

FLiRT Branch 50, JN.1+T18471C+Orf3a:A99V+S:S60P,R346T+S:F456L,Designated JN.1.48.1 , Proposed in JN.1.48+S:F456L branches, one designated JN.1.48.1 and LD.1, the other with Orf3a:S60F (43 seqs, 13 countries) cov-lineages/pango-designation#2547
[*] Branch 51, Proposed in JN.1 + S:F456L with C26873T branch (409 seqs) cov-lineages/pango-designation#2622

JN.1+C26873T+S:F456L, Query: T22928C, C26873T, C18894T, 21 seqs, China, Netherlands, Germany, Singapore,USA,Canada, New Zealand

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 cov-lineages/pango-designation#2621
JN.1+Orf3a:A54S+S:F456L(T22930A), Query: G25552T,T22930A,C18894T, 13 seqs, USA

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, Designated LQ.1 JN.1.18.1+S:F456L, Proposed in JN.1.18.1 + S:F456L (FLiRT) with S:P272H (14 sequences 8+ countries) cov-lineages/pango-designation#2596 Query: T22928C,C14220T,C22311A, 13 seqs, USA, UK,India,South Korea
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 JN.1+S:F456L with C28603T branch (267 seqs) cov-lineages/pango-designation#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, JN.1+S:F456L with C12781T branch (83 seqs) cov-lineages/pango-designation#2614
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

FLiRT Branch 61, KY.1+S:F456L,Dead Query: T22928C, A11585G, G22599C, 3 seqs, Nigeria
[*] Branch 62, now proposed in JN.1+S:F456L with G17562T branch (311 seqs) cov-lineages/pango-designation#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 JN.1.4.5+S:F456L with C20823T branch (24 seqs) cov-lineages/pango-designation#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 JN.1+S:F456L with C22858T branch (37 seqs) cov-lineages/pango-designation#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

FLiRT Branch 66, it is likely KU.2 , anyway Proposed in JN.1.30.1+S:F456L with Orf1a:I1128F (97 seqs) cov-lineages/pango-designation#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, JN.1+2-nuc Orf1b:I2273S(65 seqs, 13 countries, 35 with S:R346T, 27 with additional S:F456L) #1503
[*] Branch 68, Now proposed in JN.1+S:F456L with Orf1b:L2560F (75 seqs) cov-lineages/pango-designation#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 JN.1+S:Q677L+S:F456L with C14676T branch (67 seqs) cov-lineages/pango-designation#2650

JN.1+C14676T+S:Q677L+S:F456L, Query: C14676T, A23592T, T22928C, 20 seqs, USA, Netherlands,Spain, UK

FLiRT Branch 71, Designated MD.1, JN.1+Orf1a:N2147S+S:R346T+S:F456L(T22930A), Proposed in JN.1.18 + Orf1a:N2147S (280) with three FLiRT sublineages (FLiRT1+S:K679R= 69 / FliRT2 = 46) and one FViRT sublineage(50) cov-lineages/pango-designation#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 JN.1+S:F456L with C27110T branch (22 seqs) cov-lineages/pango-designation#2645

JN.1+C27110T+S:F456L, Query: T22928C, C27110T, T22926C, 35 seqs, Ireland, Canada, USA, India

[ *] Branch 74, now propose in JN.1.34+S:F456L with C8802T branch (32 seqs) cov-lineages/pango-designation#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 JN.1.7+S:F456L with C10755T branch (28 seqs) cov-lineages/pango-designation#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 JN.1+S:F456L with C6968T branch (169 seqs) cov-lineages/pango-designation#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

FLiRT Branch 81, Designated JN.1.18.4, JN.1.18+Orf6:I60T,S:F456L(T22930G),JN.1.18.4 (JN.1.18+FLiRT+S:L492L+Orf6:I60T) sublineages : one with S:F1103S (22 on Gisaid) , one with Orf8:Q29* (28, Vaud Switzerland) cov-lineages/pango-designation#2567
[*] Branch 82, dead JN.1 + S:K679R emerged in Malaysia(162 samples) with a sublineage with S:F456L in South Korea (29) cov-lineages/pango-designation#2571
Branch 83,Designated JN.1.50 By @DoropFan JN.1>C9298T>S:L249F(G22309C)>S:A67V(C21762T), S:F456L(T22930G), JN.1.50(JN.1 + S:A67V, S:L249F, S:V445P, S:F456L) + S:R346T(6 seq, 3 countries) cov-lineages/pango-designation#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 JN.1+S:F456L with C17119T branch (58 seqs) cov-lineages/pango-designation#2637

JN.1+C17119T+A2251G+S:F456L(T22930A), Query: T22930A, C17119T, A2251G, 20 seqs, South Korea

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

Branch 93, Designated KR.2 JN.1.1.5 > T6095C,C6541T, C21911T, S:L176F (C22088T), S:F456V (T22928G ), Jn.1.1.5 FViRT lineage with S:L176F (13, mostly US) cov-lineages/pango-designation#2586
Branch 94, Designated JN.1.65.1 JN.1 +Orf3a:L85F + ORF1a:T2152I +S:T572I (650 ). With a S:F456L sub-branch (384) with Multiple branches of interest: 1) R346T Branch (62) 2) S:S60P,S:W64L branch (23) 3) Orf9b:E7V branch (44) cov-lineages/pango-designation#2461
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

FLiRT Branch 99, Designated LF.6, Proposed in Another JN.1 + FLiRT lineage emerged in the Iberian Peninsula (Now LF.6) with a S:Q493E branch (2, Spain) cov-lineages/pango-designation#2589

JN.1+T17859C+C3172T+S:R346T,F456L, Query: T17859C,T22928C,T3172G,T3565C, 30 seqs, Spain, Portugal

[*] Branch 100, proposed in JN.1.4+S:S640F+S:F456L with Orf1a:P361L (16 seqs, 2 countries) cov-lineages/pango-designation#2620 >JN.1.4+S:S640F+S:F456L,Orf1a:P361L,H417Y,Orf3a:T24I, Query: C774T,C23481T, T22928C, 16 seqs, Canada, South Korea
FLiRT Branch 101, Designated LN.1.1
FLiRT Branch 102, Designated LM.1, JN.1.25.1 FLirt (15) with a S:S31del sub branch (3) cov-lineages/pango-designation#2608
[ *] FLiRT Branch 103, JN.1.52+S:R346T,S:F456L+S:F59S, Jn.1.52 + FLiRT( placed as JN.1.16.1+Orf1a:K3353R ) with S:F59S in Spain, Sweden (26) #1579
[*] Branch 104, dead

JN.1.30.1+S:F456V, Query: G21255T,T22928G,G22599C, 6 seqs, USA, UK ,France

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 JN.1.7+S:F456L with C14931T branch (33 seqs) cov-lineages/pango-designation#2685

JN.1.7+Orf3a:V97I+S:F456L, Query: T22928C, G25681A,C14931T, 25 seqs, Canada

FLiRT Branch 107, LE.1+Orf1a:T866I, Orf1b:K82R, S:F456L, N:Q409K, Merged to branch 109, Query: T22928C, G25445A,A13712G, 3 seqs, Canada
FLiRT Branch 108, Designated LZ.1,JN.1.18.2+Orf1a:I740V, N:A152T, S:F456L(T22930A),
[P]FLiRT Branch 109, LE.1 (JN.1.4.7.1) got FLiRT (43 , 8 countries) cov-lineages/pango-designation#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, JN.1+S:F456L with C19374T branch (26 seqs) cov-lineages/pango-designation#2688
[P] Branch 111, JN.1+S:N960S+S:F456L, Query: A24441G, T22928C, C21219T, 11 seqs, USA, Spain, Ireland, France, Italy, JN.1+ORF1ab:S2242F+S:F456L+S:N960S(18 sequences, mainly in Europe) #1304
FLiRT Branch 112,Designated JN.1.48.3, JN.1.48+S:F456L branches, one designated JN.1.48.1 and LD.1, the other with Orf3a:S60F (43 seqs, 13 countries) cov-lineages/pango-designation#2547
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
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 cov-lineages/pango-designation#2653, 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.

FedeGueli · 2024-01-04T11:52:45Z

please name the lineages Branch 1 branch 2 branch 3 etc

xz-keg · 2024-01-05T00:09:52Z

JN.1+Orf1a:T2283I,S:F456L,V1104L Query: C7113T,T22928C,T3565C, India

This one is detected in another India state and becomes a branch.

FedeGueli · 2024-01-05T07:55:20Z

JN.1+Orf1a:T2283I,S:F456L,V1104L Query: C7113T,T22928C,T3565C, India

This one is detected in another India state and becomes a branch.

agree already in my tracking list it seems v interesting.

xz-keg · 2024-01-05T07:56:31Z

JN.1+Orf1a:T2283I,S:F456L,V1104L Query: C7113T,T22928C,T3565C, India
This one is detected in another India state and becomes a branch.

agree already in my tracking list it seems v interesting.

They are placed in different branches on usher but that's due to artefacts of India-KA seqs around S:16. KA seqs seem to artefact the ins16MPLF to some other things on all its JN.1* seqs.
@AngieHinrichs @yatisht

FedeGueli · 2024-01-05T08:30:46Z

V1104L

I managed to get a tree and a query for the parental lineage of Branch 4 with S:V1104L:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice7_genome_test_3aa55_7b6bc0.json?label=id:node_6827336

Query: G24872T, G17334T,C897A finds 11

Samples: EPI_ISL_18682687 (Recomb), EPI_ISL_18683064, EPI_ISL_18694660,
EPI_ISL_18694669, EPI_ISL_18694672, EPI_ISL_18704304,
EPI_ISL_18704343, EPI_ISL_18704350, EPI_ISL_18718937,
EPI_ISL_18718979, EPI_ISL_18718993

FedeGueli · 2024-01-05T08:32:24Z

V1104L

I managed to get a tree and a query for the parental lineage with S:V1104L: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice7_genome_test_3aa55_7b6bc0.json?label=id:node_6827336

Query: G24872T, G17334T,C897A finds 11

Samples: EPI_ISL_18682687, EPI_ISL_18683064, EPI_ISL_18694660, EPI_ISL_18694669, EPI_ISL_18694672, EPI_ISL_18704304, EPI_ISL_18704343, EPI_ISL_18704350, EPI_ISL_18718937, EPI_ISL_18718979, EPI_ISL_18718993

i think i ll propose (or you as you want ) the parental branch so Branch 4 could be defined as #XYZ + 456L, what do you think?

xz-keg · 2024-01-05T09:07:05Z

i think i ll propose (or you as you want ) the parental branch so Branch 4 could be defined as #XYZ + 456L, what do you think?

Yes sure.

FedeGueli · 2024-01-05T11:19:57Z

i think i ll propose (or you as you want ) the parental branch so Branch 4 could be defined as #XYZ + 456L, what do you think?

Yes sure.

#1262

FedeGueli · 2024-01-06T15:12:23Z

branch 3 goes to 11

xz-keg · 2024-01-06T15:41:39Z

Add doublet 1 from USA.

There seems to be also S:F456V and S:F456I branches. Include them for branch 5 and singlet 7.

xz-keg · 2024-01-10T01:37:24Z

1/10:
Add doublet 2,3, Singlet 7,8.

Branch 4 Goes to 6 and spread to UK

FedeGueli · 2024-01-10T10:57:50Z

C7113T,T22928C,T3565C,

@aviczhl2 i would ask you to propose it together with the parental in the main page (closing my side proposal) , so @corneliusroemer could track it too . If you can keep it updated also here it would be great.
6 seqs from India could hint to a huge numbers of infections. tell me if you are ok with that.

xz-keg · 2024-01-10T11:32:27Z

C7113T,T22928C,T3565C,

@aviczhl2 i would ask you to propose it together with the parental in the main page (closing my side proposal) , so @corneliusroemer could track it too . If you can keep it updated also here it would be great. 6 seqs from India could hint to a huge numbers of infections. tell me if you are ok with that.

5 in India and 1 in UK actually. Discovered in 2 India states.

You can propose that as your proposal is more focused? If you want me to propose that's also fine.

FedeGueli · 2024-01-10T11:59:58Z

C7113T,T22928C,T3565C,

@aviczhl2 i would ask you to propose it together with the parental in the main page (closing my side proposal) , so @corneliusroemer could track it too . If you can keep it updated also here it would be great. 6 seqs from India could hint to a huge numbers of infections. tell me if you are ok with that.

5 in India and 1 in UK actually. Discovered in 2 India states.

You can propose that as your proposal is more focused? If you want me to propose that's also fine.

as you prefer! you discovered the whole thing! but if u have no time i will! u can copy paste it and then add the analysis of the 456 branch

xz-keg · 2024-01-12T15:20:11Z

1/12:
Branch 5 becomes 10
A previous Indian doublet spread to France and becomes branch 6.

FedeGueli · 2024-07-31T14:27:12Z

branch 115 now 5 with last samples coming from Israel and Netherlands. @aviczhl2 please propose , it seems relevant, too much to be buried in a multiple lineages issue.

DailyCovidCases · 2024-08-03T16:34:07Z

Branch 15,51,57,62 and 110 might be dying off, please close it (denote it with [*] instead of [P])

FedeGueli · 2024-08-03T22:44:40Z

Branch 15,51,57,62 and 110 might be dying off, please close it (denote it with [*] instead of [P])

done

DailyCovidCases · 2024-08-03T23:35:56Z

Branch 21,36,41,48,58,67 and 73 might be dying off, please close it now (denote it with [*] instead of [P])

xz-keg · 2024-08-06T06:58:27Z

Branch 8 grows to 26, reopen.

xz-keg · 2024-08-13T08:46:11Z

I think this one can be closed now. Almost everything now has S:456X. The proportion of S:456F seqs is around 1% and 99% of the seqs belong to 456X lineages.

For new 456X lineages pls make separate issues @FedeGueli @ryhisner

xz-keg · 2024-08-15T07:46:14Z

Branch 110 is 49 now, with many recent samples @FedeGueli

xz-keg · 2024-08-15T07:51:11Z

I think we shall get rid of those DailyCovidCases proposals that are never updated correctly, and re-propose some of the branches if they are still there. @FedeGueli

FedeGueli · 2024-08-15T10:15:22Z

Branch 110 is 49 now, with many recent samples @FedeGueli

it should be 46 with -G17334T,-T3913A,-G1126A,C19374T, T22928C, T3565C,-C1762A,-17334,-7113 ,

yeah agree with multiple branches opened and closed it has been a chaos, maybe next week i will have some time to check all the branches and verify if we lost something on the road. in the meanwhile propose BR.110 here on this repo(if still monophyletic)

FedeGueli · 2024-08-16T15:59:20Z

BR.115 Designated JN.1.16.5 via cov-lineages/pango-designation@56fe08a

FedeGueli · 2024-08-18T22:17:08Z

JN.1.4 + 456L + 475V from China:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice64_genome_test_27cee_265aa0.json?label=id:node_7176682

xz-keg · 2024-08-19T03:49:33Z

-G17334T,-T3913A,-G1126A,C19374T, T22928C, T3565C

This is 54 seqs now, most come from July, and a South Korean branch gets additional S:S60P, S:T572I and S680P

FedeGueli · 2024-08-19T06:35:30Z

-G17334T,-T3913A,-G1126A,C19374T, T22928C, T3565C

This is 54 seqs now, most come from July, and a South Korean branch gets additional S:S60P, S:T572I and S680P

re propose it please

FedeGueli · 2024-08-19T06:54:38Z

-G17334T,-T3913A,-G1126A,C19374T, T22928C, T3565C

This is 54 seqs now, most come from July, and a South Korean branch gets additional S:S60P, S:T572I and S680P

i think the query has to be adjusted again also the tree is not super clear with two branches with 456l:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_3817c_2e95a0.json?f_userOrOld=uploaded%20sample&label=id:node_6948437

FedeGueli · 2024-08-19T06:59:11Z

@aviczhl2 i suggest to propose only the fast growing S:S60P ( also convergent with XDV.1.1) starting from S:S60P and orf1a:Y1734H (PLPRO_Y171H)
Query: T5465C ,T21740C,C9988T
Samples: 29
TRee:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3817c_2e9580.json?label=id:node_7001412

xz-keg · 2024-08-19T07:02:00Z

-G17334T,-T3913A,-G1126A,C19374T, T22928C, T3565C

This is 54 seqs now, most come from July.

@aviczhl2 i suggest to propose only the fast growing S:S60P ( also convergent with XDV.1.1) starting from S:S60P and orf1a:Y1734H (PLPRO_Y171H) Query: T5465C ,T21740C,C9988T Samples: 29 TRee: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3817c_2e9580.json?label=id:node_7001412

Yeah I was about to propose that branch but some Chinese July seqs seem on the lower branch.

FedeGueli · 2024-08-19T07:07:21Z

-G17334T,-T3913A,-G1126A,C19374T, T22928C, T3565C

This is 54 seqs now, most come from July.

@aviczhl2 i suggest to propose only the fast growing S:S60P ( also convergent with XDV.1.1) starting from S:S60P and orf1a:Y1734H (PLPRO_Y171H) Query: T5465C ,T21740C,C9988T Samples: 29 TRee: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3817c_2e9580.json?label=id:node_7001412

Yeah I was about to propose that branch but some Chinese July seqs seem on the lower branch.

SO lets start from C9988T, those chinese cluster seems quite interesting

Over-There-Is · 2024-08-25T06:37:27Z

Flirt branch 84 is 35 now, a Lithuanian imported case is also detected by US

FedeGueli · 2024-08-25T07:30:14Z

Flirt branch 84 is 35 now, a Lithuanian imported case is also detected by US

Please @aviczhl2 (only you) extract it from here to this repo, maybe worth tracking for a bit being quite widespread in Russia ( so we will tag with undersampled area label and let it open for a while)

xz-keg · 2024-08-25T10:09:07Z

Flirt branch 84 is 35 now, a Lithuanian imported case is also detected by US

Please @aviczhl2 (only you) extract it from here to this repo, maybe worth tracking for a bit being quite widespread in Russia ( so we will tag with undersampled area label and let it open for a while)

Last upload from 8-12 and last Russian upload at 7-30. Waiting for the next Russian upload to decide.

DailyCovidCases · 2024-08-26T15:04:17Z

Branch 7 now 308 seqs, this branch got significant proportion between February and April in Canada, so I think it should be designated:

DailyCovidCases · 2024-09-03T13:31:29Z

Branch 116 designated LZ.2 please update the title

DailyCovidCases · 2024-10-07T18:01:43Z

Branch 8,110,114,117,118,119 are dying off, please denote it with [*]

FedeGueli · 2024-10-08T07:49:40Z

Branch 8,110,114,117,118,119 are dying off, please denote it with [*]

Thx but this is closed and dusted!

xz-keg changed the title ~~Multiple JN.1 branches with S:F456L~~ Multiple JN.1* branches with S:F456L Jan 4, 2024

FedeGueli added Multiple lineages JN.1 SLip labels Jan 4, 2024

FedeGueli mentioned this issue Jan 5, 2024

JN.1 with S:V1104L parental of SLip Branch 4 of #1253 emerged in India ( 16 seqs) #1262

Closed

xz-keg changed the title ~~Multiple JN.1* branches with S:F456L~~ Multiple JN.1* branches with S:F456L or F456V or F456I Jan 6, 2024

xz-keg added the S:456 label Jan 6, 2024

FedeGueli added S:455 and removed SLip labels Jan 6, 2024

FedeGueli changed the title ~~Multiple JN.1* branches with S:F456L or F456V or F456I~~ Multiple JN.1* branches with S:F456L or F456V or F456I : 5 Branches as O1/06 Jan 6, 2024

xz-keg changed the title ~~Multiple JN.1* branches with S:F456L or F456V or F456I : 5 Branches as O1/06~~ Multiple JN.1* branches with S:F456L or F456V or F456I : 5 Branches as 1/10 Jan 10, 2024

xz-keg mentioned this issue Jan 10, 2024

JN.1+S:V1104L emerging in India(Designated JN.1.11, 16 and 5 countries with Orf1a:T2283I and S:F456L ) cov-lineages/pango-designation#2446

Closed

FedeGueli added designated partially designated labels Jan 11, 2024

xz-keg changed the title ~~Multiple JN.1* branches with S:F456L or F456V or F456I : 5 Branches as 1/10~~ Multiple JN.1* branches with S:F456L or F456V or F456I : 6 Branches as 1/12 Jan 12, 2024

xz-keg mentioned this issue Jul 31, 2024

JN.1+S:T22N,F456L,Q493E(Designated JN.1.16.5)+S:S31P( 120 seqs, 10 countries, 12 with S:T1273I) cov-lineages/pango-designation#2705

Closed

DailyCovidCases mentioned this issue Aug 2, 2024

JN.1.4+Orf1a:T4087I,Orf1b:S1512N+S:F456L(297 seqs, 19 countries, 20 with S:T572I, 8 with S:R346T) #1818

Closed

xz-keg mentioned this issue Aug 10, 2024

JN.1+S:F456L+S:R346T+S:M153I+S:S31F+S:T22N (10 seqs, 6 countries) #1863

Closed

xz-keg closed this as completed Aug 13, 2024

xz-keg mentioned this issue Aug 23, 2024

JN.1+S:F456L+Orf1a:Y1734H,S:S60P starting and still circulating in Vietnam(65 seqs, 12 countries with two S:T572I branches 9 and 6 seqs ) cov-lineages/pango-designation#2745

Closed

DailyCovidCases mentioned this issue Aug 31, 2024

JN.1.4.5+S:F456L with C28948T branch (29 seqs) cov-lineages/pango-designation#2757

Closed

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

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

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