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Multiple JN.1 + S:R346X + FliRT + Trio : 155 branches as July 30 #1089
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I'm not convinced that the French sequence in that tree is from the same parent. since I believe all of the mutations prior to its S:346i are actually pretty common in JN.1. However, the Sweden, Australia, and Italy sequences appear to be related, despite that they contain a different mutation on S:346. At least the Australia and Italy sequences must represent onwards transmission of an S:346 mutation. Also notable - the Italy sequence has a reversion on S:408, which is allegedly covered. |
4th sequence for the query C11747T, C20629T -- France, R346T. As it stands, the 3 of them with R346T are... Australia - Nov 4 |
Up to 6 seqs now with C11747T, C20629T. All but one are with S:R346T. This should be moved to the main page, imo. EDIT: I'm mistaken. One of the French sequences doesn't have S:R346T or S:R346i, so the query I'm using here isn't perfect now. Correct list with R346T is Australia - Nov 4 |
@HynnSpylor please propose it |
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Other S:R346T popping up: 2 3 all the trees from :https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_13bf8_214840.json?c=userOrOld&label=id:node_4467536 |
It seems that several branches get S:R346T. I decide to arrange it and change the title as "Multiple JN.1+R346X Branches" |
Ok thank you. in the comments you cna find some query i found for the other branches/singlets. |
Transferred from #1118 There are around 40 JN.1 that have S:R346T, but most of them are poor quality sequences with lots of XBB mixed in. When filtering out those pretty clear artefacts, we're left with 11-12 BA.2.86 that may actually have 346T. These are shown in the screenshot, where mutations are shown with respect to BA.2.86 parent, that's why there are so few mutation markers: Interestingly, most of the 346T are within JN.1 (9 out of 11), much more concentrated than we'd expect by chance (around 1/4 of total BA.2.86 are JN.1 in GISAID). Within JN.1, 8 out of 9 are on the JN.1 branch with C1762A (ORF1a:F499L) and C11747T. Again more concentrated than one would expect by chance (around 40% of JN.1 are on that branch). 4 out of those 8 share another mutation that's seen only once elsewhere within JN.1: C20629T (ORF1b:H2388Y). Thus, it looks like at least these 4 sequences form a proper monophyletic lineage that could get designated. Though the numbers are still a bit small and there's a contamination issue as evidenced by the 3/4 of BA.2.86 + 346T being likely artefacts:
GISAID query: It's also possible that the 8 sequences are a single event - better wait for sequence numbers to double before making a decision. Due to the way the other 4 are scattered around, they look like independent events for now, though. On Usher, things are a bit messy: Here's how Nextclade arranges things with just the 346T sequences on the JN.1 branch: |
Let's just track this one here for now, these collection issues can get overwhelming. This one is the biggest and clearest and most likely to be conclusive soon. I think this is a fifth one for the 20629T cluster: Further ones compatible with a single 346T even preceding C20629T rather than following:
So we are at 5 (7) sequences for this cluster. The biggest question now is whether to designate broadly (not requiring 20629T) or narrowly (requiring it). We should know within a week. |
Thank you @corneliusroemer ! |
Yes they are the ones i couldnt find a query for, i think they could be really one same lineage. |
Thx @corneliusroemer @FedeGueli ! |
@corneliusroemer |
New 20629T: Extra ones compatible with event directly on polytomy:
Making it 10 for that case. If it keeps going like this, we'll designate directly on the polytomy. Let's wait a few more days. |
What is the correct query of branch 57 on Covspectrum? |
Branch 73,74,98,107,117,118,119 and 121 must be dying off now, please update this |
most were already flagged as dead thx for theothers. kept open the SA one. |
|
Branch 61,71,123,130,146,147 and 152 might be dying off, please update this |
done |
Added branch 155, it is JN.1.7.8 FLirt + S:T95I 5 recent samples |
|
154 is not dead and proposing it, i kept 73 open too because from an undersampled area. Thank u for pointing me at the others. |
Br.154 was already designated MJ.1 (likely before i added it here in the period Usher was not updated withnew lineages) |
Branch 155 proposed i think this could be archived definitively @aviczhl2 @DailyCovidCases @Over-There-Is @NkRMnZr @HynnSpylor if something new happens please propose it directly. |
Branch 71,84,85,86,87 and 88 on the FLIRT Singlets must be dying off, please close this |
this is archived won't be updated no more. |
LZ.2 got designated (br.147) via cov-lineages/pango-designation@2c6deaf |
branch 98 is 35 now, a Lithuanian imported case is also detected by US |
Br.111 designated KP.2.27 via cov-lineages/pango-designation@986687e |
Br.61 designated JN.1.11.2 starting with 59L sublineage via cov-lineages/pango-designation@608685e |
Intro
**i think the original proposal should be updated in this way** (_Edited and Updated_ BY MOD): I would like to recapitulate current situation looking at the downsampled tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_19c8e_3c4600.json?label=id:node_6806774I can determine as separate branches:
Branch 1: Now designated JN.1.1.3
Branch 2 : Now designated JN.1.1.5 from cov-lineages/pango-designation#2492
Branch 3: Broadened to JN.1.1.3 via cov-lineages/pango-designation@0c19ec3
Branch 4 : canceled it is not monophyletic
Branch 5: now designated JN.1.6.1
Branch 6: now designated JN.1.18
Branch 7: Designated JN.1.44.1
Branch 8: dead
Branch 9: Designated JN.1.8.2 from cov-lineages/pango-designation#2495
Branch 10: dead
Branch 11: Dead
Branch 12 : Dead
Branch 13 : Dead
Branch 14 : Designated JN.1.13.1
Branch 15: Designated JN.1.7.3
Branch 16: now proposed in cov-lineages/pango-designation#2601
Branch 17: Slow
Branch 18: Dead
Branch 19: Dead
Branch 20: designated JN.1.7.1 from #1371
Branch 21 : Designated KQ.1
Branch 22 : Dead
Branch 23: Designated LE.1 and LE.1.1
Branch 24: Now proposed in cov-lineages/pango-designation#2602
Branch 25: Dead
Branch 26 : Dead
Branch 27: Dead
FLiRT Branch 28:Designated JN.1.30.1
from cov-lineages/pango-designation#2514
With further FLIRT S:F456L branch Designated KU.2
Branch 29 :Dead
Branch 30 Dead
Branch 31 Dead
Branch 32 FLIRT now proposed in cov-lineages/pango-designation#2557
Branch 33 Dead
Branch 34 :Now Designated JN.1.26
Branch 35 : Designated JN.1.42.2
Branch 36: Designated JN.1.48.2
Branch 37 designated JN.1.24.1 from cov-lineages/pango-designation#2520
Branch 38 Dead
Branch 39: REMOVED
Branch 40: designated LC.1
FLIRT Branch 41: Designated JN.1.16.1
Branch 42: Dead
Branch 43 : Dead
Branch 44 : Dead
Branch 45 : REMOVED:
FLIRT Branch 46 : Designated KP.1.1 spotted by @aviczhl2
from in cov-lineages/pango-designation#2510
Branch 47: dead
Branch 48: Dead
Branch 49 : Excluded
Branch 50: Dead
Branch 51: Designated JN.1.39.1
FLIRT Branch 52: designated KP.4.2 from cov-lineages/pango-designation#2523
FLIRT Branch 53: desingated KP.4.1 from cov-lineages/pango-designation#2521
FLIRT Branch 54: Designated KP.2
Branch 55 found by @corneliusroemer designated JN.1.25.1
Branch 56 spotted by @krosa1910 FLIRT designated KZ.1.1 from #2548
Designated KZ.1.1.1
Branch 57 thx to @DailyCovidCases i noticed that this is not monophyletic at all, among the lineages caught by query
the most interesting is this one JN.1.4 >> T18453C > C7732T>> Orf1a:D4117N (G12614A) > G22111A > C27944T >S:T22N (C21627A ) > S:R346T (G22599C) > A17256G, S:F58L (T21734C )
Query: A17256G, T21734C
Samples: 12 (US)
Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_601bd_fe5200.json?label=id:node_7136106
Original:
Branch 58 now designated JN.1.4.4
thx to @aviczhl2 that highlighted me the new JN.1.4 tree.
Branch 59 Dead
Branch 60: Dead
Branch 61 Designated JN.1.11.2
FLIRT Branch 62 Designated JN.1.9.2 & LB.1 from cov-lineages/pango-designation#2546
Branch 63 FLiRT first spotted by @aviczhl2 now proposed in cov-lineages/pango-designation#2562
Branch 64: Duplicate
it was KZ.1.1.1
Branch 65: FLiRT spotted and proposed by @aviczhl2 in #1445 (cov-lineages/pango-designation#2530)
Branch 66 Dead
FLiRT branch 67 Dead
FLiRT Branch 68 dead
Branch 69 Dead
Branch 70 : Dead
Branch 71 : Tracked now in #1462
Branch 72 dead
Branch 73 FLiRI> dead
Branch 74 : Undersampled area needed to check if dead
Branch 75 : Dead
Branch 76 FLiRI Designated LA.2 from cov-lineages/pango-designation#2555
Branch 77 dead
Branch 78 FLiRT: dead
Branch 79 Dead
Branch 80 Dead
Branch 81 Dead
Branch 82 Dead
Branch 83 Dead
Branch 84 Designated LQ.1 and LQ.1.1
Branch 85 FLiRT now proposed in cov-lineages/pango-designation#2606
Branch 86 DEAD
Branch 87 JN.1.18.4
Branch 88 dead
Branch 89 Designated JN.1.56.1
Branch 90 spotted and proposed by @aviczhl2 in #1503 #2679
Branch 91 : Designated KW.1.1.1 and LG.1
Branch 92 : Dead
Branch 93 DEAD
Branch 94 FLiRT Now proposed in cov-lineages/pango-designation#2565
Branch 95 Dead
Branch 114 Now designated KP.2.9 TRIO former Singlet 22 = Branch 96
Branch 97 proposed in #1682
Branch 98
Branch 99 FLiRT now proposed in #1648
Branch 100 FliRT now proposed in cov-lineages/pango-designation#2583
Branch 101 JN.1.18.5
Branch 102 Dead
Branch 103 Dead
Branch 104 Dead
Branch 105 Dead
Branch 106 Dead
Branch 107 MP.1 and MP.1.1
Branch 108 now proposed in cov-lineages/pango-designation#2605
Branch 109 Spotted and proposed by @aviczhl2 As branch 62 of #1253
Branch 110 Dead
Branch 111 now designated Kp.2.27
Branch 112: Proposed in cov-lineages/pango-designation#2645
Branch 113 KR.3 see branch 87 of # 1253
Branch 114 Duplicate now KP.2.9
Branch 115 Dead
Branch 116 Dead
Branch 117 Dead
Branch 118 Dead
Branch 119 Dead
Branch 120 Designated KR.2
Branch 121 Dead
Branch 122 : Dead
Branch 123 dead
Branch 124 Designated LF.3
Branch 125: Designated LV.2 it is a MOV lineage- intercontinental
Branch 126: It has now split in two: one proposed in #1623 with A22108C, C23277T, T23599C and the other tracked as Branch 149
Branch 127: Dead
Branch 128 Dead
Branch 129 TRIO duplicate of Branch 126
Branch 130 Dead R346T
Branch 131 Dead
Branch 132 dead
Branch 133 designated LF.6
Branch 134 Proposed in cov-lineages/pango-designation#2659
Branch 135 FLIRT NOW DESIGNATED JQ.2.1.1 VIA cov-lineages/pango-designation@1ff69c9
Branch 136 designated MH.1
Branch 137 designated MF.1
proposed in cov-lineages/pango-designation#2461
Branch 138 now designated LU.1
Branch 139 Designated LM.1
Branch 140 dead
Branch 141 ex singlet 50 dead
Branch 142: dead
Branch 143 Dead
Branch 144 dead
Branch 145 dead
Branch 146 proposed in cov-lineages/pango-designation#2677
Branch 147 Designated LZ.2 via cov-lineages/pango-designation@2c6deaf
Branch 148: dead
Branch 149 (ex branch 126) now proposed in #1755
Branch 150 ex singlet 25 Fvirt designated MB.1
Branch 151 Dead
Branch 152 dead
Branch 153 Now proposed in #1773
Branch 154 Designated MJ.1
JN.1.29.1 > S:R346T > Orf1a:E2070K (G6473A), T17364C, S:S31P ( T21653C)
Query: G6473A, T21653C,A9935G
Samples: 19 (Likely from Latin America)
BRANCH 155 now designated MQ.1
FLIRT Singlets (also FVIRT or FLIRI or FLIRS):
16)Dead
32)Dead
XDK/JN.1.11.1 recombinant spotted by @JosetteSchoenma Query: T2950A, C18115T, G24872T
Now Branch 144
Dead
JN.1.11.1 > Orf1a:T4087I (C12525T) > ORF1a:S2030L (C6354T), A13237T, Orf1b:K2557R (A21137G), A21694G, S:R346T(G22599C), S:Q675H (G23587C), S:D1146E (T25000G)
Query: C6354T, A13237T,T3565C (Scotland)
Dead
Dead
FViRT JN.1 > Orf1a:G519S (G1820A) > S:A288S (G22424T) > S:R346T (G22599C) > A13992G, G17562T, C19524T S:F456V (T22928G) Query: A13992G, G17562T, C19524T (UAE)
Proposed in JN.1.55.2 became FLiRT with S:Q677H and Orf3a:L52F in South America (95, >8 places ) with very high recent prevalence in Pernambuco, Brazil ( after July 1 = 65%) #1678
Now Branch 136
DelTRIO (First ever) LB.1+S:S31Del > S:T572I (C23277T)
Query:C23277T,G22111T , G22599C , T22928C,del21653 (Israel)
Now Branch 138
73)Dead
JN.1.11.1 > C29095T > G18816T, S:R346T (G22599C), S:N641S (A23484G), T24073C
Query: G18816T, A23484G, T24073C (Spain)
JN.1 > A871G, T3172G,C1170T, T17859C, S:R346T (G22599C), S:F456L (T22928C) Query:A871G, T3172G,C1170T (Spain)
now proposed in KP.3.1 with G22599T(S:R346I)singlet(1seqs from France) #1571
FLiRI JN.1.29 > S:F456L(T22928C) > T8053C > Orf1b:1588C (A18230G), S:R346I (G22599T), Orf3a:D155H (G25855C) Query: A18230G, G25855C (Finland)
JN.1.4> C5284T >S:F456L (T22928C) > S:R346T(G22599C), Query: C6433A, T22928C, T18453C,G22599C S.Korea
likelyy misplaced under br.89 of Multiple JN.1* branches with S:F456X : 4 Ongoing Unproposed Branches as 7/25 #1253
Now Branch 147
Singlets will be no more tracked since May 21.
Interesting Singlets:
1) Dead >sibling of branch 79 JN.1.4 > T18453C > T4342C, C5869T, T17154C, Orf1b:A1662V (C18452T) > S:R346T (G22599C) Query: T4342C, C5869T, T17154C,G22599C NY Now **2** 2)Dead >JN.1 > C23896G > C186T > A19782G > C829T, Orf1a:T2093I (C6543T), S:L293I (C22439A), S:R346K (G22599A), S:S884F (C24213T) Query: C829T, C6543T, G22599A NY 3)Dead >JN.1.4 > C25710T > C28312T +346T +456L UK Query: C27791T ,C20178T, G22599C, T22928C 4)Dead >JN.1.33 > Orf1a:Y1846C (A5802G)> C3092T, S:R346K (G22599A) Query: C3092T ,G22599A,T3565C 5) Proposed in # 2560 PANGO >JN.1> Orf1a:N2147S (A6705G) > T24892C > Orf1a:S135R>K (G669A), Orf1a:I368T (T1368C), C4189T, Orf1a:Y1619H (T5120C), S:R346T (G22599C), A24241G, N:N192D(A28847G) Query:G669A, T1368C, C4189T:::::::::::::::::::::::::::::::
Original proposal
Branch 1
Defining mutations:
JN.1>T3565C>T27810C(ORF7b:F19L)>C1762A (ORF1a:F499L)>C11747T>G22599T (S:R346I), then further >C20629T> (ORF1b:H2388Y)>T22599C (S:I346T)
for R346I GISAID query: A6183G, G22599T
for R346T GISAID query: C20629T, G22599C, T22926C
Alternative query by Cornelius for 346T: G22599C,C20629T,C11747T,C1762A (edited)
Earliest seq: 2023-10-02 (France- EPI_ISL_18412591)
Most recent seq: 2023-11-06 (Italy- EPI_ISL_18510429)
Countries detected:
R346I seqs: France (1), Sweden (1)
R346T seqs: Italy (1), Australia (1)
Usher Tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_293e4_7364f0.json?c=gt-S_346
S:R346 is a key site and S:R346T was successful in BF.7*, BQ.1.1*, CH.1* and recently XBB* lineages.
Nowadays JN.1* is the fastest growing lineage, while this JN.1* branch has a two-step evolution as S:R346I>T. We can see how the R346I/R346T work on the JN.1 seqs.
Genomes:
R346I: EPI_ISL_18412591, EPI_ISL_18489980
R346T: EPI_ISL_18510429, EPI_ISL_18513742
****************************+
Branch 2
Defining :
JN.1.1 > C11747T > C9142T > S:R346T (G22599C) then A18600G , S:Q173H (G22081T)
Query: C11747T, C9142T ,G22599C,C1762A
Samples: 5
IDs: EPI_ISL_18552979, EPI_ISL_18553493, EPI_ISL_18577478,
EPI_ISL_18577484, EPI_ISL_18577493
Tree
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