Multiple EG.5.1* Lineages with S:T478X #787

NkRMnZr · 2023-09-11T04:55:34Z

Checking Singlets, Doublets, Triplets, Quadruplets and Quintuplets. Query for all EG.5* with S:T478X minus already designated ones: spike_T478, -spike_T478K, C9693T, T22930A, -C1613T, -C1875T, -C2462T, -A27388C, 1195 seqs, 01/12. Checking updates.

Branch 1

Defining Mutations: EG.5.1.3 > G28038A(ORF8:V49I), G28851A(N:S193N) > C24082T > C22995G(S:T478R)
Query: C1889T, C22995G, C24082T
Earliest seq: 2023-06-03 (EPI_ISL_17809720, Arizona)
Latest seq: 2023-08-23 (EPI_ISL_18240921, Arizona)
Sampled Countries: USA (5: AZ)

Genomes:

EPI_ISL_17809720, EPI_ISL_18129977, EPI_ISL_18133578, EPI_ISL_18225105, EPI_ISL_18240921

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20958_e88620.json?c=gt-S_478&label=id:node_6965095

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Branch 2

Defining Mutations: EG.5.1.1 > C541T > C22995G(S:T478R), T27922C(ORF8:I10T)
Query: C541T, C6541T, C22995G
Earliest seq: 2023-08-14 (EPI_ISL_18239149, South Korea)
Latest seq: 2023-08-20 (EPI_ISL_18232626, Shanghai, China)
Sampled Countries: Canada (1, BC), China (1, SH), South Korea

Genomes:

EPI_ISL_18232626, EPI_ISL_18239149, EPI_ISL_18240021

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice5_genome_20958_e88630.json?label=id:node_6964021

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Branch 3: Mostly under `C5178T(ORF1a:T1638I)` sub-branch

Defining Mutations: EG.5.1 > C22995G(S:T478R)
Query: C5178T, A18492G, C22995G
Earliest seq: 2023-08-12 (EPI_ISL_18129969, Vaud, Switzerland)
Latest seq: 2023-09-08 (EPI_ISL_18262746, Vaud, Switzerland)
Sampled Countries: Switzerland (5: VD)

Genomes:

EPI_ISL_18129969, EPI_ISL_18211237, EPI_ISL_18262746, EPI_ISL_18262752-18262753

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_320b3_63f800.json?label=id:node_3460213

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Branch 4

Defining Mutations: EG.5.1.1 > G22918T(S:L452) > C11767T, A22996C(S:K478N)
Query: C11767T, A22996C, G22918T
Earliest seq: 2023-09-28 (EPI_ISL_18398859, Scotland)
Latest seq: 2023-10-05 (EPI_ISL_18398557, England)
Sampled Countries: UK (4: EN/3; SC)

Genomes:

EPI_ISL_18392330, EPI_ISL_18392462, EPI_ISL_18398557, EPI_ISL_18398859

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_5396e_f96f30.json?label=id:node_3459091

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Branch 5

Transferred to main repo

Defining Mutations: HK.30 > C9319T, C22995G(S:T478R) (ignores C27507T flip-flop)
Query: C9319T, C22995G, T26609C, -A2977G
Earliest seq: 2023-09-11 (EPI_ISL_18417620, Tyumen, Russia)
Latest seq: 2023-12-18 (EPI_ISL_18721444, Denmark)
Sampled Countries: Russia (148: SPE/99; ME/19; TYU/6; MOS/4; TA/4; MOW/3; LEN/2; MAG/2; MO/2; NIZ/2; VLG/2; AMU; KLU; SAM), USA (3: ID; IN; TX), Denmark (2), New Zealand (2), China (1: ex. Russia), Ukraine (1)

Genomes:

Transferred to cov-lineages/pango-designation#2458

EPI_ISL_18416868, EPI_ISL_18416917, EPI_ISL_18417066, EPI_ISL_18417075, EPI_ISL_18417084, EPI_ISL_18417086, EPI_ISL_18417313, EPI_ISL_18417371, EPI_ISL_18417374, EPI_ISL_18417574, EPI_ISL_18417620, EPI_ISL_18417639, EPI_ISL_18487069, EPI_ISL_18487203, EPI_ISL_18487207, EPI_ISL_18487290, EPI_ISL_18487328, EPI_ISL_18487348, EPI_ISL_18487448, EPI_ISL_18487451, EPI_ISL_18487654, EPI_ISL_18487657, EPI_ISL_18487678, EPI_ISL_18487691, EPI_ISL_18487762, EPI_ISL_18487769, EPI_ISL_18550560, EPI_ISL_18561244, EPI_ISL_18561291, EPI_ISL_18561369, EPI_ISL_18561395, EPI_ISL_18562139, EPI_ISL_18579945, EPI_ISL_18580191, EPI_ISL_18638598, EPI_ISL_18638600, EPI_ISL_18638641, EPI_ISL_18638775, EPI_ISL_18638787, EPI_ISL_18638789, EPI_ISL_18638841, EPI_ISL_18638851, EPI_ISL_18638888, EPI_ISL_18638896, EPI_ISL_18638965, EPI_ISL_18639024, EPI_ISL_18643646, EPI_ISL_18671614, EPI_ISL_18679983, EPI_ISL_18682690, EPI_ISL_18682713, EPI_ISL_18682716, EPI_ISL_18682739, EPI_ISL_18682770, EPI_ISL_18682786, EPI_ISL_18682815, EPI_ISL_18682832, EPI_ISL_18682849, EPI_ISL_18682853, EPI_ISL_18682858, EPI_ISL_18682863, EPI_ISL_18682893, EPI_ISL_18682927, EPI_ISL_18682975, EPI_ISL_18682992, EPI_ISL_18685398, EPI_ISL_18685506, EPI_ISL_18685554, EPI_ISL_18685557, EPI_ISL_18685569, EPI_ISL_18685578, EPI_ISL_18685612, EPI_ISL_18685616, EPI_ISL_18685697, EPI_ISL_18685727, EPI_ISL_18685749, EPI_ISL_18685786, EPI_ISL_18685798-18685799, EPI_ISL_18685880, EPI_ISL_18685883, EPI_ISL_18685899, EPI_ISL_18685909, EPI_ISL_18685950, EPI_ISL_18685959, EPI_ISL_18685961, EPI_ISL_18685971, EPI_ISL_18685985, EPI_ISL_18685989, EPI_ISL_18686007, EPI_ISL_18686025, EPI_ISL_18686062, EPI_ISL_18686126, EPI_ISL_18686139, EPI_ISL_18686154, EPI_ISL_18686177, EPI_ISL_18686208-18686209, EPI_ISL_18686226, EPI_ISL_18686238-18686239, EPI_ISL_18686245, EPI_ISL_18703850, EPI_ISL_18721444, EPI_ISL_18736049, EPI_ISL_18736052, EPI_ISL_18736143, EPI_ISL_18736157-18736158, EPI_ISL_18736170, EPI_ISL_18736195, EPI_ISL_18736197, EPI_ISL_18736201, EPI_ISL_18736207, EPI_ISL_18736221, EPI_ISL_18736250, EPI_ISL_18736252, EPI_ISL_18736386-18736387, EPI_ISL_18736424, EPI_ISL_18736426, EPI_ISL_18736441, EPI_ISL_18736452, EPI_ISL_18736461, EPI_ISL_18736518, EPI_ISL_18736534, EPI_ISL_18736539, EPI_ISL_18736548, EPI_ISL_18736579, EPI_ISL_18736634, EPI_ISL_18736669, EPI_ISL_18736690, EPI_ISL_18736744, EPI_ISL_18736752, EPI_ISL_18736763, EPI_ISL_18736846, EPI_ISL_18736855, EPI_ISL_18736896, EPI_ISL_18736905, EPI_ISL_18736950, EPI_ISL_18736973, EPI_ISL_18737032, EPI_ISL_18737087, EPI_ISL_18737119, EPI_ISL_18737147, EPI_ISL_18737164, EPI_ISL_18737170, EPI_ISL_18737183, EPI_ISL_18737189, EPI_ISL_18737194, EPI_ISL_18737205, EPI_ISL_18737208, EPI_ISL_18737221, EPI_ISL_18737289, EPI_ISL_18737343, EPI_ISL_18744035, EPI_ISL_18754622

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_22e80_469090.json?label=id:node_3452170

Trivia:

Formerly (mis)placed under either C22995G(S:T478R) branch right under HK.3 polytomy or EG.5.1.1's flip-flop C27507T (aka revoked unclear HK.32)

Historical query for those branches, including the real S:T478R branch right under HK.3 polytomy

C6541T, C22995G, C29625T, -C541T, -C673T, -G2075A, -G2648A, -T3049C, -C3168A, -G3692T, -G4180A, -G5917A, -T6274C, -C6310T, -G6369T, -C6752T, -G7791A, -C7973T, -A8107T, -C9907T, -T11186C, -C11750T, -C11779T, -G12482A, -A13712G, -C13378T, -C13860T, -A14270T, -T14988C, -G15093A, -C18508T, -T20281C, -T20407C, -G22927T, -T23803C, -T24259C, -C24912T, -C25418A, -C25517T, -G25526T, -T26543C, -T28105C, -C29272T

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Branch 6

Defining Mutations: EG.5.1.6 > C28236T(ORF8:R115C) > C16092T > A2151G(ORF1a:D629G), G19872T, C22995G(S:T478R), C23988T(S:P809L)
Query: C5835T, C16092T, C22995G
Earliest seq: 2023-07-20 (EPI_ISL_18264993, Bayern, Germany)
Latest seq: 2023-08-02 (EPI_ISL_18118424, Madrid, Spain)
Sampled Countries: Germany (2: BY), Spain (1)

Genomes:

EPI_ISL_18118424, EPI_ISL_18264993, EPI_ISL_18264995

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice5_genome_27d74_5817c0.json?label=id:node_10885360

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Branch 7

Defining Mutations: EG.5.1.3 > C13806T > C22995G(S:T478R)
Query: C13806T, C22995G, C22570T
Earliest seq: 2023-08-28 (EPI_ISL_18305863, Arkansas, USA)
Latest seq: 2023-09-16 (EPI_ISL_18304509, Virginia, USA)
Sampled Countries: USA (3: AR/2; VA/1) UK (1: EN)

Genomes:

EPI_ISL_18302414, EPI_ISL_18304509, EPI_ISL_18305863, EPI_ISL_18305876

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_29e3_2b4d90.json?c=gt-S_478&gmax=25384&gmin=21563&label=id:node_6980592

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Branch 8: FLiP + T478I

Defining Mutations: JJ.1 (EG.5.1.4.1) > C25624T(ORF3a:H78Y) > C21648T(S:T29I) > C22995T(S:T478I)
Query: C21648T, C22995T, C25624T
Earliest seq: 2023-08-08 (EPI_ISL_18146183, Tokyo)
Latest seq: 2023-09-03 (EPI_ISL_18366160, Shizuoka)
Sampled Countries: Japan (5)

Genomes:

EPI_ISL_18146183, EPI_ISL_18285373-18285374, EPI_ISL_18366127, EPI_ISL_18366160

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d2f8_4f2fe0.json?f_userOrOld=uploaded%20sample&label=id:node_3409522

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Branch 9

Defining Mutations: EG.5.1 > C20759T(ORF1b:A2431V) > A19033G(ORF1b:I1856V) > C2878T, C4794T(ORF1a:S1510F), C22995G(S:T478R)
Query: A19033G, C20759T, C22995G
Earliest seq: 2023-09-07 (EPI_ISL_18309303, Nevada)
Latest seq: 2023-09-20 (EPI_ISL_18370319, California)
Sampled Countries: USA (5: CA/3; NV/2)

Genomes:

EPI_ISL_18309303, EPI_ISL_18309468, EPI_ISL_18327892, EPI_ISL_18341615, EPI_ISL_18370319

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice24_genome_aef2_630250.json?label=id:node_3406369

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Branch 10

Defining Mutations: EG.5.1.1 > C25517T(ORF3a:P42L) > C18981T, C22995G(S:T478R)
Query: C6541T, C22995G, C25517T
Earliest seq: 2023-07-31 (EPI_ISL_18108595, Shanghai, China)
Latest seq: 2023-10-16 (EPI_ISL_18446979, Valenciennes, France)
Sampled Countries: France (5), China (3: SH)

Genomes:

EPI_ISL_18108595, EPI_ISL_18138239, EPI_ISL_18268285, EPI_ISL_18428441, EPI_ISL_18446976-18446979

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4c15a_d6fb0.json?label=id:node_3485840

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Branch 11

Transferred to main repo

Transferred to cov-lineages/pango-designation#2459

Defining Mutations: HK.26 (C25546A/ORF3a:L52I) > T9577C > C22995G(S:T478R)
Query: T9577C, T14988C, C22995G
Earliest seq: 2023-09-19 (EPI_ISL_18452026, Plovdiv, Bulgaria)
Latest seq: 2023-12-28 (EPI_ISL_18754426, Västra Götalands, Sweden)
Sampled Countries: Finland (21), Sweden (11), USA (7: FL/3; NY; OH; OR; UT), Denmark (4), France (2), Bulgaria (1), Italy (1), Lithuania (1), New Zealand (1), Norway (1), Portugal (1), UK (1: EN)

Genomes:

EPI_ISL_18452026, EPI_ISL_18458286, EPI_ISL_18458317, EPI_ISL_18458355, EPI_ISL_18458443, EPI_ISL_18498158, EPI_ISL_18499386, EPI_ISL_18500972, EPI_ISL_18500991, EPI_ISL_18501018, EPI_ISL_18521950, EPI_ISL_18523122, EPI_ISL_18540316, EPI_ISL_18541289, EPI_ISL_18541379, EPI_ISL_18569438, EPI_ISL_18587007, EPI_ISL_18587319, EPI_ISL_18588097, EPI_ISL_18596255, EPI_ISL_18596358, EPI_ISL_18626259, EPI_ISL_18634896, EPI_ISL_18634919, EPI_ISL_18634926, EPI_ISL_18635176, EPI_ISL_18635277, EPI_ISL_18635292, EPI_ISL_18635314, EPI_ISL_18635338, EPI_ISL_18635342, EPI_ISL_18635361, EPI_ISL_18635367, EPI_ISL_18635372, EPI_ISL_18636458, EPI_ISL_18654029, EPI_ISL_18668754, EPI_ISL_18670579, EPI_ISL_18680850, EPI_ISL_18688452, EPI_ISL_18694205, EPI_ISL_18713134, EPI_ISL_18713140, EPI_ISL_18713154, EPI_ISL_18714214, EPI_ISL_18716916, EPI_ISL_18726965, EPI_ISL_18729107, EPI_ISL_18729197, EPI_ISL_18753036, EPI_ISL_18754426, EPI_ISL_18756863

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2ee6f_46f550.json?f_userOrOld=uploaded%20sample&label=id:node_3524511

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Branch 12

Defining Mutations: HK.12 > C22995G(S:T478R)
Query: G13627A, A22629C, C22995G
Earliest seq: 2023-09-10 (EPI_ISL_18313564, Hyogo, Japan)
Latest seq: 2023-10-10 (EPI_ISL_18465051, Heilongjiang, China)
Sampled Countries: UK (3: SC), China (2: GS; HL), Japan (1)

Genomes:

EPI_ISL_18313564, EPI_ISL_18363152, EPI_ISL_18385852, EPI_ISL_18388971, EPI_ISL_18444685, EPI_ISL_18465051

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_10d73_b73ce0.json?f_userOrOld=uploaded%20sample&label=id:node_3506046

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Branch 13

Defining Mutations: HK.3 (EG.5.1.1.3) > C25919T(ORF3a:T176I) > T4468C, C6936T(ORF1a:S2224F), C22995G(S:T478R), T25620C
Query: T4468C, C22995G, C25919T
Earliest seq: 2023-10-03 (EPI_ISL_18404250, Massachusetts, USA)
Latest seq: 2023-10-25 (EPI_ISL_18500862, Örebro, Sweden)
Sampled Countries: Sweden (6), USA (1)

Genomes:

EPI_ISL_18404250, EPI_ISL_18449555, EPI_ISL_18452291, EPI_ISL_18458659, EPI_ISL_18469494, EPI_ISL_18500856, EPI_ISL_18500862

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_40e9a_4bc1f0.json?label=id:node_3515163

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Branch 14

Transferred to main repo

Transferred to cov-lineages/pango-designation#2393

Defining Mutations: HK.3.1 > C19017T > C1288T, T4057C > C22995G(S:T478R)
Query: C1288T, T4057C, C22995G
Earliest seq: 2023-10-13 (EPI_ISL_18435593, Skåne, Sweden)
Latest seq: 2023-11-19 (EPI_ISL_18543800, Noord-Holland, Netherlands)
Sampled Countries: Sweden (16), Denmark (4), Germany (1), Netherlands (1)

Genomes:

EPI_ISL_18435593, EPI_ISL_18435596, EPI_ISL_18472820, EPI_ISL_18494552, EPI_ISL_18500965, EPI_ISL_18500984, EPI_ISL_18500986, EPI_ISL_18501005, EPI_ISL_18501009, EPI_ISL_18501038, EPI_ISL_18501066-18501067, EPI_ISL_18506905, EPI_ISL_18518456, EPI_ISL_18523106, EPI_ISL_18523121, EPI_ISL_18537846-18537847, EPI_ISL_18537882, EPI_ISL_18538323, EPI_ISL_18540321, EPI_ISL_18543800

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3ecda_53ed00.json?f_userOrOld=uploaded%20sample&label=id:node_3534934

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Branch 15

Defining Mutations: HK.6 > C22995G(S:T478R)
Query: G6032A, T14988C, C22995G, -G10046A, -A17984G
Earliest seq: 2023-08-25 (EPI_ISL_18314670, Greece)
Latest seq: 2023-11-10 (EPI_ISL_18530031, Yamanashi, Japan)
Sampled Countries: Japan (3), USA (3: CA; FL; NY), UK (2: EN), Greece (1), Israel (1)

Genomes:

EPI_ISL_18246923, EPI_ISL_18314670, EPI_ISL_18420526, EPI_ISL_18444420, EPI_ISL_18508429, EPI_ISL_18528640, EPI_ISL_18530029-18530031, EPI_ISL_18530288

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3bbf4_407ab0.json?label=id:node_3496801

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Branch 16

Defining Mutations: HK.11.1 > C22995G(S:T478R)
Query: T4789A, T13228C, C22995G
Earliest seq: 2023-10-16 (EPI_ISL_18442797, Denmark)
Latest seq: 2023-11-22 (EPI_ISL_18582940, Ontario, Canada)
Sampled Countries: Finland (4), Canada (3: ON), USA (3: CA; OH; UT), Belgium (1), Denmark (1), Poland (1)

Genomes:

EPI_ISL_18442797, EPI_ISL_18496274, EPI_ISL_18505152, EPI_ISL_18541353, EPI_ISL_18541364, EPI_ISL_18549363, EPI_ISL_18555266, EPI_ISL_18577740, EPI_ISL_18582940, EPI_ISL_18609333, EPI_ISL_18614734, EPI_ISL_18634954, EPI_ISL_18634969

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20b96_c401b0.json?label=id:node_3465023

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Branch 17

Defining Mutations: HK.3.1 > A29700G > C10776T(ORF1a:P3504L/nsp5_P241L), C13384T > T20046C > C22995G(S:T478R) > T6534C(ORF1a:V2090A/nsp3_V1272A)
Query: C10776T, T20046C, C22995G
Earliest seq: 2023-09-20 (EPI_ISL_18409355, Yunnan, China)
Latest seq: 2023-12-08 (EPI_ISL_18662080, Isère, France)
Sampled Countries: France (5), China (1), Netherlands (1)

Genomes:

EPI_ISL_18409355, EPI_ISL_18522308, EPI_ISL_18568701, EPI_ISL_18618262, EPI_ISL_18641813, EPI_ISL_18653326, EPI_ISL_18662080

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_173ce_3d1440.json?label=id:node_3491244

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Branch 18

Defining Mutations: JG.3 > G2516A > T898G > C28708T, G29422T > C22995G(S:T478R), A23494G(S:Q644Q)
Query: C22995G, A23494G, G29422T
Earliest seq: 2023-10-23 (EPI_ISL_18498711, Denmark)
Latest seq: 2023-12-07 (EPI_ISL_18665444, Skåne, Sweden)
Sampled Countries: Sweden (6), Denmark (2)

Genomes:

EPI_ISL_18498711, EPI_ISL_18500963, EPI_ISL_18523065, EPI_ISL_18587144, EPI_ISL_18607521, EPI_ISL_18617665, EPI_ISL_18631624, EPI_ISL_18665444

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1d306_3d3620.json?label=id:node_3518913

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Branch 19

Defining Mutations: EG.5.1.1 > C9907T > C16230T, C22995G(S:T478R) > C11575T
Query: C9907T, G13627A, C22995G
Earliest seq: 2023-09-20 (EPI_ISL_18340130, Illinois, USA)
Latest seq: 2023-12-02 (EPI_ISL_18646910, Utah, USA)
Sampled Countries: USA (17: UT/7; IL/4; CA/3; AZ/2; TX), Costa Rica (1), UK (1: SC)

Genomes:

EPI_ISL_18340130, EPI_ISL_18407821, EPI_ISL_18446667, EPI_ISL_18517562, EPI_ISL_18525612, EPI_ISL_18527917, EPI_ISL_18547790, EPI_ISL_18554980, EPI_ISL_18555028, EPI_ISL_18584021, EPI_ISL_18593152, EPI_ISL_18622528, EPI_ISL_18622634, EPI_ISL_18623669, EPI_ISL_18631653, EPI_ISL_18646689, EPI_ISL_18646886, EPI_ISL_18646910, EPI_ISL_18656938

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_24356_3d5ae0.json?label=id:node_3471285

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Branch 20

Defining Mutations: EG.5.1.2 > T1252C, C3787T > G23621T(S:V687L) > G4255A > C22995G(S:T478R)
Query: T1252C, G4255A, C22995G
Earliest seq: 2023-08-10 (EPI_ISL_18222883, California, USA)
Latest seq: 2023-12-12 (EPI_ISL_18660702, England, UK)
Sampled Countries: UK (7: EN/6; NI), USA (1)

Genomes:

EPI_ISL_18222883, EPI_ISL_18462542, EPI_ISL_18557710, EPI_ISL_18557721, EPI_ISL_18606223, EPI_ISL_18618437, EPI_ISL_18652320, EPI_ISL_18660702

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a594_3d7ce0.json?label=id:node_3415543

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Branch 21

with credit to @FedeGueli who spotted it first

Defining Mutations: EG.5.1.2 > A21788G(S:T76A) > G29041A > C11758T > C832T, G7295A(ORF1a:A2344T), C14230T(ORF1b:P255S), G22021T(S:M153I) > C14724T > C25693T(ORF3a:L101F) > C22995G(S:T478R)
Query: G7295A, C14230T, C22995G
Earliest seq: 2023-10-09 (EPI_ISL_18430166, Québec, Canada; OR EPI_ISL_18440921, Hérault, France)
Latest seq: 2023-12-07 (EPI_ISL_18642830, Stockholm, Sweden)
Sampled Countries: Sweden (5) Belgium (2), France (2), Canada (1), Netherlands (1), Spain (1)

Genomes:

EPI_ISL_18430166, EPI_ISL_18440921, EPI_ISL_18473937, EPI_ISL_18507428, EPI_ISL_18522269, EPI_ISL_18522863, EPI_ISL_18535994, EPI_ISL_18547164, EPI_ISL_18547239, EPI_ISL_18579647, EPI_ISL_18636219, EPI_ISL_18642830

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e402_3d90f0.json?label=id:node_3415342

Trivia:

There's also a S:T478E(A22994G) sub-branch under C25693T(ORF3a:L101F)

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Branch 22

Defining Mutations: HK.13.1 > G4436A(ORF1a:V1391I), A6377G(ORF1a:N2038D), G27708A > C920T, C22995G(S:T478R)
Query: G4436A, C13378T, C22995G
Earliest seq: 2023-10-17 (EPI_ISL_18461972, Sydney, Australia)
Latest seq: 2023-11-25 (EPI_ISL_18623865, Ibaraki, Japan)
Sampled Countries: Australia (7: NSW), Japan (3), New Zealand (1)

Genomes:

EPI_ISL_18461872, EPI_ISL_18461972, EPI_ISL_18513291, EPI_ISL_18513359, EPI_ISL_18513417, EPI_ISL_18561676, EPI_ISL_18566777, EPI_ISL_18623840, EPI_ISL_18623849, EPI_ISL_18623865, EPI_ISL_18633553

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_37a79_3dc6a0.json?label=id:node_3472662

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Branch 23

Defining Mutations: HK.11.1 > C12733T > T6259C, C8895T(ORF1a:T2877I), A17809G(ORF1b:T1448I), T22020C(S:M153T), G23611A(S:R683R) > C3168G(ORF1a:A968G), T18324A(ORF1b:H1619Q), A26234G, A28037G > G21724C(S:L54F), A22996T(S:T478N), A29389T(N:K372N)
Query: C3168G, T18324A, A22996T
Earliest seq: 2023-11-27 (EPI_ISL_18712117, South Korea)
Latest seq: 2023-12-07 (EPI_ISL_18752141, S. Korea)
Sampled Countries: South Korea (10)

Genomes:

EPI_ISL_18712117, EPI_ISL_18712127-18712130, EPI_ISL_18733464, EPI_ISL_18752123, EPI_ISL_18752127-18752128, EPI_ISL_18752141

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_38f44_474530.json?label=id:node_3465900

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Branch 24

Defining Mutations: EG.5.1.1 > T15915C > T3049C > G26959A(M:R146H) > G8796T(ORF1a:S2844I) > C22995G(S:T478R)
Query: T3049C, G8796T, C22995G
Earliest seq: 2023-09-28 (EPI_ISL_18487259, Samara, Russia)
Latest seq: 2023-11-25 (EPI_ISL_18736604, Saint Petersburg, Russia)
Sampled Countries: Russia (10: SAM/8; SPE; TA)

Genomes:

EPI_ISL_18487259, EPI_ISL_18487287, EPI_ISL_18487289, EPI_ISL_18685684, EPI_ISL_18736604, EPI_ISL_18736842, EPI_ISL_18736866, EPI_ISL_18736942, EPI_ISL_18736963, EPI_ISL_18737030

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_436e_47b890.json?label=id:node_3487939

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Branch 25

Defining Mutations: EG.5.1.1 > C27059T > G22927T(S:L455F) > A15271G(ORF1b:N602D) > T27059C_rev > C14928T > C22995G(S:T478R)
Query: C14928T, A15271G, C22995G
Earliest seq: 2023-10-10 (EPI_ISL_18503802, South Korea)
Latest seq: 2023-12-19 (EPI_ISL_18751986, S. Korea)
Sampled Countries: South Korea (22), China (2: ex. S. Korea)

Genomes:

EPI_ISL_18495060, EPI_ISL_18503802, EPI_ISL_18511118, EPI_ISL_18511483, EPI_ISL_18511611, EPI_ISL_18539431, EPI_ISL_18539805, EPI_ISL_18539849, EPI_ISL_18564377, EPI_ISL_18564694, EPI_ISL_18564737, EPI_ISL_18564825, EPI_ISL_18565047, EPI_ISL_18597361, EPI_ISL_18597880, EPI_ISL_18639678, EPI_ISL_18672174, EPI_ISL_18686935, EPI_ISL_18687001, EPI_ISL_18711866, EPI_ISL_18733833, EPI_ISL_18751394, EPI_ISL_18751437, EPI_ISL_18751986

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_8122_47d5e0.json?label=id:node_3457075

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Branch 26

Defining Mutations: HV.1 > C2695T > C26964T(M:H148Y) > C27600T > A25806T > C8476T, C22995T(S:T478I), ins28250CTG, A28254Δ
Query: C2695T, C8476T, C22995T
Earliest seq: 2023-10-23 (EPI_ISL_18481059, Minnesota, USA)
Latest seq: 2023-12-14 (EPI_ISL_18728537, Illinois, USA)
Sampled Countries: USA (7: MN/6; IL)

Genomes:

EPI_ISL_18481059, EPI_ISL_18481090, EPI_ISL_18554159, EPI_ISL_18664947, EPI_ISL_18728537, EPI_ISL_18731044-18731045

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_fc7e_480f80.json?label=id:node_3596169

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Branch 27

Defining Mutations: HV.1 > G11378A(ORF1a:A3705T) > T16224C > C22995G(S:T478R)
Query: G11378A, T16224C, C22995G
Earliest seq: 2023-11-22 (EPI_ISL_18620601, Georgia, USA)
Latest seq: 2023-12-31 (EPI_ISL_18743318, Texas, USA)
Sampled Countries: USA (9: NC/5; DE; GA; TN; TX)

Genomes:

EPI_ISL_18602049, EPI_ISL_18602053, EPI_ISL_18620601, EPI_ISL_18647210, EPI_ISL_18691141, EPI_ISL_18691177, EPI_ISL_18716027, EPI_ISL_18716134, EPI_ISL_18743318

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_17bc4_4846f0.json?label=id:node_3579910

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Branch 28

Defining Mutations: EG.5.1.1 > C29272T > C1057T, C13378T, A22582G(S:E340E) > C22995G(S:T478R), C25904T(ORF3a:S171L), G26144A(ORF3a:G251D)
Query: C1057T, C13378T, C22995G
Earliest seq: 2023-08-27 (EPI_ISL_18417303, Moscow, Russia)
Latest seq: 2023-11-24 (EPI_ISL_18685947, Saint Petersburg, Russia)
Sampled Countries: Russia (9: SPE/4; ME; MOS; MOW; TAM), Norway (1)

Genomes:

EPI_ISL_18417175, EPI_ISL_18417303, EPI_ISL_18417423, EPI_ISL_18499365, EPI_ISL_18561377, EPI_ISL_18580108, EPI_ISL_18685456, EPI_ISL_18685947, EPI_ISL_18686081, EPI_ISL_18736229

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_271bd_48aa90.json?label=id:node_3458687

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Singlets

Canada/AB-ABPHL-106762/2023|EPI_ISL_18493235|2023-10-26
EG.5.1.1 > C11779T > C15720T > C13665T > G25455T(ORF3a:K21N) > C9042T(ORF1a:S2926F), C17999T(ORF1b:T1511I), C29409T(N:T379I) > C10186T, A17892C > G22021A(S:M153I) > A382G, C16675T, G21604A(S:Q14), A22776G(S:D405S), C22995G(S:T478R), A24190G(S:A876), C26339T(E:A32V) [Query: C10186T, A17892C, C22995G, 11/10]
Denmark/DCGC-663875/2023|EPI_ISL_18540339|2023-11-06 (Sub-lineage to Branch 76 of Multiple EG.5.1* Lineages with S:L455F #537)
EG.5.1.1 > T26609C > G22927T(S:L455F) > C16616T(ORF1b:T1050I), C17172A, C22995G(S:T478R), T29341C [Query: G22927T, C22995G, T26609C, 11/24]
Liaoning/LNCDC-398-2/2023|EPI_ISL_18465267|2023-10-10
HK.1.1 > C4276T, G14500T(ORF1b:V345L), C19524T, C21602G(S:Q14E), A22994C(S:T478Q), G25621A(ORF3a:V77I), G27659T(ORF7a:R89I), G27877T(ORF7b:C41F) [Query: G22927T, A22994C, 11/03]
France/ARA-HCL023186076601/2023|EPI_ISL_18605732|2023-11-27
HK.3 (EG.5.1.1.3) > ORF1a:R232S(C959T, G960C) > C3874T > T15912C, A22994G(S:T478E) [Query: G960C, C3874T, A22994G, 12/11]
Malaysia/UNIMAS-B9809/2023|EPI_ISL_18575614|2023-11-09
HK.3 > C3743T(ORF1a:H1160Y) > C2623A(ORF1a:N786K) > T22304C(S:Y248H), C22995G(S:T478R), A27241G(ORF6a:I14V), C28770T(N:T166I) [Query: C2623A, C3743T, C22995G, -G564A, 12/03]
Malaysia/UNIMAS-B9812/2023|EPI_ISL_18575616|2023-10-29
HK.3 > C3923T(ORF1a:P1220S) > A3652G, C11563T, A17344G(ORF1b:I1293V) > G4913A(ORF1a:V1550I), C21658T(S:F32F), G22132T(S:R190S), C22995G(S:T478R) [Query: A3652G, C3923T, C22995G, 12/03]
Malaysia/UNIMAS-B9813/2023|EPI_ISL_18575617|2023-10-29
HK.3 > T4888C > C17119T, A18504G, C27155T > C22995G(S:T478R), C25624T(ORF3a:H78Y) [Query: T4888C, A18504G, C22995G, 12/03]
Sichuan/YBCDC-XGCX479/2023|EPI_ISL_18564308|2023-11-08
HK.3 > G6337T, C6681T(ORF1b:A2139V), T7009A > T18447C > A27899G > C21602A(S:Q14K), C22995G(S:T478R), C28717T [Query: C6681T, T18447C, C22995G, 11/30]
Canada/NB-CHUDGLD-18L-MM00123S/2023|EPI_ISL_18730941|2023-12-18
HK.3 > C8320T > C4012T, T24870C(S:F1103S) > C4754T(ORF1a:P1497S), C22995G(S:T478R), A27675C(ORF7a:Q94H) [Query: C4012T, C8320T, C22995G, 01/08]
Norway/Ahus-5059/2023|EPI_ISL_18402143|2023-09-27
HK.3 > C10369T > G19480T(ORF1b:G2005C), A22994G(S:T478E), C28697T(N:P142S) [Query: C10369T, G19480T, A22994G, 10/18]
Yunnan/YNCDC-3301/2023|EPI_ISL_18602955|2023-10-29
HK.3 > A20262G > C3267T(ORF1a:T1001I) > G3476A(ORF1a:V1071I), C18118A(ORF1b:L1551I), C18348T, C21714T(S:T51I), C22995G(S:T478R), T27206C(ORF6:F2S), G29645T(ORF10:V30L) [Query: C3267T, A20262G, C22995G, 12/08]
Austria/AGES-1141955/2023|EPI_ISL_18485485|2023-10-25
HK.3 > C22264T(S:N234) > ORF1a:R232S(C959T, G960C) > C11902T, C17036T(ORF1b:A1190V) >C14805T, A22994C(S:T478Q) [Query: C959T, G960C, A22994C, 11/09]
Spain/CT-HCB-3849/2023|EPI_ISL_18492361|2023-10-22
HK.3 > C25546A(ORF3a:L52I) > T14988C > C28940T > C22995G(S:T478R), A26811G(M:I97V), G28875T(N:S201I) [Query: T14988C, C22995G, C28940T, 11/10]
Poland/Kce-954/2023|EPI_ISL_18419862|2023-10-13
HK.3 > C26781T(M:L87F) > C1909T > G18960T, T21886C, C22995G(S:T478R), C24130T [Query: C1909T, C22995G, C26781T, 10/23]
Malaysia/UNIMAS-B9798/2023|EPI_ISL_18575611|2023-11-11
HK.3.2 > C22208T(S:L216F), G23222A(S:E554K), A26441G(E:N66S) > C100T, C22995G(S:T478R), A28877T, G28878C [Query: C853T, C22995G, A26441G, 12/03]
Xinjiang/XJCDCALT-158/2023|EPI_ISL_18495105|2023-10-07
HK.3.3 > T13111C > A1291C(ORF1a:E342D), A23665T(S:A701) > G28166A > G22302A(S:S247N), C22995G(S:T478R), C25513T(ORF3a:L41F), C26885T [Query: A1291C, T13111C, C22995G, 11/11]
Canada/NB-CHUDGLD-04J-MM00044R/2023|EPI_ISL_18393315|2023-10-04
HK.3.3 > C25546T(ORF3a:L52F) > C21595T > C16559T(ORF1b:A1031V), A21317G(ORF1b:D2617G), C22995G(S:T478R), C26645T [Query: C21595T, C22995G, C25546T, Oct16]
USA/NJ-CDC-QDX87748018/2023|EPI_ISL_18592804|2023-11-15
HK.3.12 > C27847T(ORF7b:S31L) > A4501C(ORF1a:Q1412H), G12176A(ORF1a:G3971S), T16950C, C22995G(S:T478R), A28111G(ORF8:Y73C) [Query: C10834T, C22995G, C27847T, 12/06]
Spain/VC-CVA_ALIC-121183/2023|EPI_ISL_18543119|2023-09-15
HK.6 > G10046A(ORF1a:V3261I) > A26077G(ORF3a:T229A) > G16396A(ORF1b:G977S) > C8660T(ORF1a:H2799Y), C22995G(S:T478R) [Query: G10046A, G16396A, C22995G, 11/24]
Denmark/DCGC-664867/2023|EPI_ISL_18590940|2023-11-27
HK.13.1 > T6178C, C23086T > C17004T > G17658T(ORF1b:M1397I) > C9967T, C22995G(S:T478R), G29645T [Query: T6178C, G17658T, C22995G, 12/06]
Russia/SPE-RII-MH147877S/2023|EPI_ISL_18487757|2023-10-24
HK.13.1 > C18166T > C22995G(S:T478R), G29134A, C29200T [Query: C13378T, C18166T, C22995G, 11/09]
Spain/AN-PMC-38209/2023|EPI_ISL_18468128|2023-09-22
JG.3 (EG.5.1.3.3) > C1519T, T18164C(ORF1b:V1566A) > C10977T(ORF1a:A3571V), A22996T(S:T478N) [Query: C1519T, T18164C, A22996T, 11/06]
USA/UT-UPHL-1124577645/2023|EPI_ISL_18555007|2023-11-09
JG.3 > C1519T, T18164C(ORF1b:V1566A) > C29362T > C21161T(ORF1a:A2565V) > A22994G(S:T478E), C27002T [Query: C1519T, C21161T, A22994G, 11/28]
USA/UT-UPHL-1124376540/2023|EPI_ISL_18555004|2023-11-08
JG.3 > A27551T(ORF7a:K53I) > T13686C > C22995G(S:T478R) [Query: T13686C, C22995G, A27551T, 11/28]
USA/NJ-CDC-QDX88030744/2023|EPI_ISL_18602575|2023-11-22
JG.3 > C5628T(ORF1a:T1788M) > A5096T(ORF1a:N1611Y) > C12525T(ORF1a:T4087I), C22995G(S:T478R) [Query: A5096T, C5628T, C22995G, 12/08]
USA/HI-H2326233/2023|EPI_ISL_18593098|2023-11-17
JG.3 > C12295T > C5020T, C22995G(S:T478R) [Query: C7086T, C12295T, C22995G, 12/07]
England/CLIMB-CM7YEISO/2023|EPI_ISL_18735707|2023-12-27
JG.3 > A21456G > C3832T, A23614G(S:A684A) > C10681T, C22995G(S:T478R), G27715A(ORF7a:V108M) [Query: C3832T, A21456G, C22995G, -C151T, 01/09]
USA/NJ-GBW-H10-018-9503/2023|EPI_ISL_18615294|2023-12-03
JG.3 > C25378T(S:Y1272Y) > G670A, A2015G(ORF1a:M584V), C9611T(ORF1a:L3116F), G13427A(ORF1a:E4388K), C22995G(S:T478R), C26208T [Query: C7086T, C22995G, C25378T, 12/12]
Scotland/CLIMB-CM7YEDAT/2023|EPI_ISL_18421567|2023-09-28
JG.3.1 > T14418C > A2483G(ORF1a:I740V) > C1973T, A22996T(S:T478N), C25614T [Query: A2483G, T14418C, A22996T, 10/23]
Switzerland/AG-UHB-USB_2023_10_23_511530ad/2023|EPI_ISL_18440344|2023-10-13
JG.3.1 > T14418C > C15810T, C22995G(S:T478R), G29212C [Query: C7932T, T14418C, C22995G, 10/27]
Austria/AGES-1142696/2023|EPI_ISL_18560060|2023-11-15
JG.3.1 > T14418C > C16092T > C28674T(N:A134V) > C21727T(S:F55F) > A2437C(ORF1a:R724S), G18937A(ORF1b:G1824S), C23111T(S:L517F), G23545T(S:E661D) > C22995G(S:T478R) [Query: A2437C, G18937A, C22995G, 11/30]
Denmark/DCGC-664800/2023|EPI_ISL_18590873|2023-11-20
JG.3.1 > G28884A(N:G204Q) > T27328C(ORF6:S43P) > C16915T > C22916T(S:L452L), C22995T(S:T478I), C23981T(S:P807S), A24092G(S:I844V), C28849T [Query: C16915T, C22995T, G28884A, 12/06]
Spain/CL-44679/2023|EPI_ISL_18509432|2023-10-18
HV.1 (EG.5.1.6.1) > C19983T > G6943A > C6539T(ORF1a:H2092Y), A22994G(S:T478E), C26895T(M:H125Y) [Query: G6943A, C19983T, A22994G, 11/16]
Spain/PV-HUD-70073311/2024|EPI_ISL_18746174|2024-01-07
HV.1.1 > A22556G(S:I332V), G22770A(S:R403K) > A22629C(S:K356T), C22995G(S:T478R), C27684T [Query: C12513T, A22556G, C22995G, 01/11]
New_Zealand/23ZA4872/2023|EPI_ISL_18459902|2023-09-26
EG.5.1.8 > C12100G > C27603T > G21809A(S:V83T, V>A>T) > A11002G, C14821T(ORF1b:P452S), T15258C, C22995G(S:T478R), T24565C(S:L1001), A29127G(N:N285S) [Query: C12100G, G21809A, C22995G, 11/02]
England/CLIMB-CM7YMEJO/2023|EPI_ISL_18557574|2023-11-03
EG.5.1.8 > C12100G > C27603T > C28132T(ORF8:T80I) > C10681T, C22995T(S:T478I) [Query: C10681T, C12100G, C22995T, 11/29]

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Doublets

Canada/AB-ABPHL-108235/2023|EPI_ISL_18538835|2023-11-11 and Canada/AB-ABPHL-108239/2023|EPI_ISL_18538838|2023-11-11 (Sub-lineage to Branch 10 of Multiple EG.5.1* Lineages with S:L455F #537)
EG.5.1.1 > C11173T > G22927T(S:L455F) > C10833T(ORF1a:A3523V) > C7765T, C21757T > G4955A(ORF1a:E1564K), C20594A(ORF1:T2376K) > T9445C, A22994G(S:T478E) [Query: G4955A, A22994G, 2 seqs, 11/23]
USA/TX-HMH-M-135832/2023|EPI_ISL_18690586|2023-11-30 and USA/TX-HMH-M-136315/2023|EPI_ISL_18690085|2023-12-15
EG.5.1.1 > C12053T(ORF1a:L3930F) > C503T(ORF1a:P80S), A8116G > C18175T(ORF1b:P1570S), G22927T(S:L455F) > C7732T > G27962A > T26310C > T27713C(ORF7a:I107T) > C8290T > T18632G(ORF1b:F1722C) > T27438C > G1043A(ORF1a:A260T), C4540T, C8964T(ORF1a:S2900L), C9348T(ORF1a:T3028I), C16575T > C8752T, C22995G(S:T478R) [Query: G1043A, C16575T, C22995G, 2 seqs, 12/26]
England/CLIMB-CM7YKPJN/2023|EPI_ISL_18362805|2023-09-25 and England/CLIMB-CM7Y8D18/2023|EPI_ISL_18398144|2023-10-10 FLippeR
HK.3 (EG.5.1.1.3) > C25546A(ORF3a:L52I) > T14988C > G26199T > G12019A, C20544T, C22995G(S:T478R) [Query: T14988C, C22995G, G26199T, 2 seqs, 10/17]
Sweden/D-6546810476/2023|EPI_ISL_18543775|2023-11-12 and Sweden/D-6338981476/2024|EPI_ISL_18754323|2024-01-03
HK.3.1 > C24334T(S:A924A) > C18267T, A22013C(S:S151R), C22995G(S:T478R) [Query: A22013C, C22995G, 2 seqs, 01/12]
Austria/AGES-1143020/2023|EPI_ISL_18596785|2023-11-02 and Austria/AGES-1143108/2023|EPI_ISL_18596866|2023-11-17
JG.3 > G16975T(ORF1b:V1170F) > C29640T(ORF10a:A28V) > A13756C(ORF1b:I97L), C14649T, A21825C(S:D88A), C22995G(S:T478R), G24781C(S:K1073N), C27128T [Query: C7086T, G16975T, C22995G, 2 seqs, 12/08]
Italy/UMB-LAOP-141-2-08-2023/2023|EPI_ISL_18542062|2023-11-17 and Italy/UMB-LAOP-142-2-06/2023|EPI_ISL_18566879|2023-11-25
JG.3.1 > C1973T > G8179T, C17745T, rev_T29625C(rev_ORF10:F23S) > C22995T(S:T478I), C27532T(ORF7a:H47Y) [Query: G8179T, C17745T, C22995T, 2 seqs, 12/01]
Canada/AB-ABPHL-108739/2023|EPI_ISL_18563992|2023-11-13 and Canada/AB-ABPHL-108669/2023|EPI_ISL_18563933|2023-11-14 (Sub-lineage to Branch 77 of Multiple EG.5.1* Lineages with S:L455F #537)
EG.5.1.6 > C925T, C27161T > C14919A > G14559A > G22927T(S:L455F) > C2189A(ORF1a:L642I), C27011T, C27849T(ORF7b:L32F) > C21928T, C22995G(S:T478R), C27092T [Query: C2189A, G14559A, C22995G, 2 seqs, 11/30]
USA/MN-MDH-37267/2023|EPI_ISL_18481059|2023-10-23 and USA/MN-MDH-37268/2023|EPI_ISL_18481090|2023-10-23
HV.1 > C2695T > C26964T(M:H148Y) > C27600T > T28251C(ORF8:F120L), A28254C(ORF8:I121L) > A25806T > C8476T, C22995T(S:T478I) [Query: C2695T, C22995T, C27600T, 2, 11/08]
Belgium/UGent-1576/2023|EPI_ISL_18457889|2023-10-16 and Netherlands/NB-PAMM-K03-0071/2023|EPI_ISL_18522363|2023-11-03
EG.5.1.8 > G10900A > A23523T(S:E654V) > G5950A > G6358A, G10877A(ORF1a:G3538S), T14399C(ORF1b:V311A), T21980C(S:F140L), C22995G(S:T478R), A27921G(ORF8:I10V) [Query: G5950A, G10900A, C22995G, 2 seqs, 11/20]

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Triplets

South_Korea/KDCA267197/2023|EPI_ISL_18382134|2023-09-20 and South_Korea/KDCA269145/2023|EPI_ISL_18439457|2023-09-25, sub-lineage of Branch 62 from Multiple EG.5.1* Lineages with S:L455F #537
EG.5.1.1 > C18559T(ORF1b:L1698F) > T15927C, G22927T(S:L455F) > T2058C(ORF1a:M598T), A2184C(ORF1a:E640A), C22995G(S:T478R) [Query: T15927C, C18559T, C22995G, 2 seqs, 10/27]
USA/IL-S23WGS2068/2023|EPI_ISL_18747446|2023-10-08; USA/IL-S23WGS2070/2023|EPI_ISL_18747448|2023-10-09 and USA/VA-VTVAS3-GSC44320/2023|EPI_ISL_18555655|2023-11-04
HK.31 > C1077T(ORF1a:P271L) > C22995G(S:T478R) [Query: C1077T, G2075A, C22995G, 3 seqs, 01/11]
Lithuania/MB231128_0377/2023|EPI_ISL_18683117|2023-11-20; Lithuania/MB231128_0378/2023|EPI_ISL_18683118|2023-11-20 and France/GES-IPP28184/2023|EPI_ISL_18598614|2023-11-20
EG.5.1.6 > G6404T(ORF1a:V2047F) > C8140T, C26082T > C17481T > G6032A(ORF1a:A1923T), G17334A > C28498T(ORF9b:T72I) > C14220T, C22995G(S:T478R) [Query: G6032A, G17334A, C22995G, 3 seqs, 12/24]
USA/NY-SUNYQB-X7579/2023|EPI_ISL_18681771|2023-12-02; USA/DE-CDC-LC1075182/2023|EPI_ISL_18690967|2023-12-04; USA/DE-DHSS-B1325062/2023|EPI_ISL_18721047|2023-12-09 and USA/NJ-DHSS-B1276678/2023|EPI_ISL_18721014|2023-12-14
HV.1 > G29260T > T18672C > C22995T(S:T478I) [Query: C5835T, T18672C, C22995T, 4 seqs, 01/05]

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Quadruplets

Scotland/CLIMB-CM7YKRJM/2023|EPI_ISL_18444685|2023-09-18; Scotland/CLIMB-CM7YKPO8/2023 | EPI_ISL_18385852 | 2023-09-20; Gansu/PLCDC-0193/2023|EPI_ISL_18388971|2023-09-25 and Scotland/CLIMB-CM7YFMDB/2023 | EPI_ISL_18363152 | 2023-09-25
EG.5.1.1 > A8443G > C3168A(ORF1a:A968D), T7480C, A22023C(S:E154A), A22629C(S:K356T), C22995G(S:T478R), C23802T(S:T747I) [Query: A8443G, G13627A, C22995G, 4, 10/30]
USA/WI-WSLH-2302436/2023|EPI_ISL_18644121|2023-11-09; USA/WI-WSLH-2302474/2023|EPI_ISL_18644158|2023-11-10; USA/WI-WSLH-2302470/2023|EPI_ISL_18644154|2023-11-13 and USA/WI-WSLH-2302585/2023|EPI_ISL_18644260|2023-11-15
HK.31 > A28771G > T1623C(ORF1a:I453T) > G19947T(ORF1b:K2160N) > C3373T > G22927T(S:L455F), C22995G(S:T478R) [Query: C3373T, G19947T, G22927T, 4 seqs, 12/18]
USA/TX-HMH-M-135592/2023|EPI_ISL_18546746|2023-11-14; USA/TX-HMH-M-135650/2023|EPI_ISL_18690389|2023-11-19; USA/TX-HMH-M-135667/2023|EPI_ISL_18690358|2023-11-22 and USA/NC-CDC-LC1076608/2023|EPI_ISL_18699582|2023-12-13
HV.1 > C26801T > C24865G(S:H1101Q) > A22790G(S:I410V) > C13620T, G22567A(S:L335L) > G3431T(ORF1a:V1056L), T27984C(ORF8:Y31H) > T13162C, C22995G(S:T478R) [Query: G3431T, C13620T, C22995G, 4 seqs, 12/28]
USA/HI-TAMC_3007/2023|EPI_ISL_18466067|2023-10-10; USA/HI-H2325654/2023|EPI_ISL_18449171|2023-10-12; USA/HI-H2325713/2023|EPI_ISL_18457029|2023-10-15 and USA/HI-H2325726/2023|EPI_ISL_18457042|2023-10-18
HV.1.4 (EG.5.1.6.1.4) > T6673C, A22001G(S:K147E), C24374T(S:L938F) > T137C > A8848G, C22995G(S:T478R), C25002T(S:S1147L) [Query: T6673C, A8848G, C22995G, 4 seqs, 11/06]

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Quintuplets

ON-PHL-23-43722/2023|EPI_ISL_18583263|2023-11-22; Canada/ON-PHL-23-45584/2023|EPI_ISL_18610758|2023-11-27; Canada/ON-PHL-23-45594/2023|EPI_ISL_18610764|2023-11-27; Canada/ON-PHL-23-45598/2023|EPI_ISL_18610768|2023-11-27 and Canada/ON-PHL-23-45857/2023|EPI_ISL_18610975|2023-11-29
EG.5.1.1 > C11779T > C2395T, C23191T(S:F543F) > C21627A(S:T22N) > C1419T(ORF1a:A385V), C11455T, C15952T, C26625T > C22995G(S:T478R), C26601T [Query: C1419T, C11455T, C22995G, 5 seqs, 12/11]
England/CLIMB-CM7YKD6R/2023|EPI_ISL_18366767|2023-10-02; England/CLIMB-CM7Y8KQN/2023|EPI_ISL_18363003|2023-10-03; England/CLIMB-CM7YGNOI/2023|EPI_ISL_18385839|2023-10-03; Germany/BY-MVP-000021740/2023|EPI_ISL_18526086|2023-10-16 and Germany/BY-MVP-000023296/2023|EPI_ISL_18757834|2023-12-13
HK.11 > C29420T(N:P383S) > T21718C(S:H52H) > C27143T > C22995G(S:T478R), C23785T(S:Y741Y), T26543C [Query: G21718C, C22995G, C27143T, 5 seqs, 01/12]
Belgium/Briant-12314536501/2023|EPI_ISL_18432700|2023-10-08; Belgium/AZDelta-2341-01611/2023|EPI_ISL_18399805|2023-10-09; Belgium/rega-47668/2023|EPI_ISL_18441860|2023-10-09; Belgium/Briant-12315089501/2023|EPI_ISL_18522433|2023-10-18 and Belgium/Briant-12315455101/2023|EPI_ISL_18522425|2023-10-24
EG.5.1.3 > A28769G(N:T166A) > G3083A(ORF1a:E940K), C8650T > A3222G(ORF1a:Q986R), C29409T(N:T379I) > C22995G(S:T478R) [Query: A3222G, C8650T, C22995G, 5 seqs, 11/20] many with follow-up S:T307I/C22482T
USA/IA-SHL-2370298/2023|EPI_ISL_18609224|2023-11-26; USA/IA-SHL-2370303/2023|EPI_ISL_18609229|2023-11-26; USA/IA-SHL-2370302/2023|EPI_ISL_18609238|2023-11-26; USA/IA-SHL-2373162/2023|EPI_ISL_18659295|2023-12-08 and USA/IA-SHL-2374650/2023|EPI_ISL_18651396|2023-12-12
JG.3 > C5365T > C15720T > C22995G(S:T478R), G26350A(E:A36T), G28044T(ORF8:A51S) [Query: C5365T, C7086T, C15720T, C22995G, 5 seqs, 12/20]
USA/MD-CDC-QDX85698963/2023|EPI_ISL_18369414|2023-09-25; France/OCC-HCL023188900901/2023|EPI_ISL_18675871|2023-11-27; France/ARA-HCL023193124501/2023|EPI_ISL_18676055|2023-12-02 and France/ARA-HCL023193125901/2023|EPI_ISL_18676056|2023-12-02
HV.1 > C15579T > C22995G(S:T478R), C28453T(ORF9b:A57V) [Query: C5835T, C15579T, C22995G, 4 seqs, 12/22]
USA/GA-CDC-LC1076715/2023|EPI_ISL_18699419|2023-12-10; USA/GA-CDC-LC1076693/2023|EPI_ISL_18699422|2023-12-10; USA/GA-CDC-LC1076304/2023|EPI_ISL_18699474|2023-12-12; USA/GA-CDC-LC1077272/2023|EPI_ISL_18715749|2023-12-14 and USA/GA-CDC-LC1077421/2023|EPI_ISL_18715998|2023-12-19
HV.1 > T23198C(S:L546L) > G16377T > A25048G(S:P1162P) > C3777T(ORF1a:T1171I), C22995G(S:T478R), G24928A(S:V1122V) [Query: C5835T, G16377T, C22995G, 5 seqs, 01/03]
USA/WA-CDC-UW23101311625/2023|EPI_ISL_18430323|2023-10-13; hCoV-19/USA/IL-CDC-2-7482994/2023|EPI_ISL_18719242|2023-11-12; hCoV-19/USA/IL-CDC-2-7480988/2023|EPI_ISL_18719257|2023-11-16; hCoV-19/USA/WA-CDC-LC1073942/2023|EPI_ISL_18690902|2023-12-03 and USA/AZ-ASPHL-3554/2023|EPI_ISL_18656957|2023-12-13
HV.1 > T23198C(S:L546L) > C29466T(N:A398V) > A12829G > A22994C(S:T478Q) [Query: C5835T, A12829G, A22994C, 5 seqs, 01/04]

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Trivia:

EG.5* with S:T478R acutally started earlier than now dominating FLIP lineages, but went hiatus for a few months (or maybe from places with months delay in sample submission), until it goes active again. Much like what we have found on XBB.1.5.49, S:T478R now scattered on multiple EG.5* branches, especially on the more North American EG.5.1.3 rather than the more East Asian EG.5.1.1. Only 2 bigger active clusters are proposed here, more (singlets, doublets and inactive ones) can be tracked EG.5* Lineage Tracker NkRMnZr/hSC2-Tracking-Log#20 .
Query for all EG.5* with S:T478R: C9693T, T22930A, C22995G, -C1875T, 42 seqs, 09/09. It may not be a big deal as EG.5* is already highly evasive (not to mention the spawning of multiple FLIP lineages), however, there's FL.1.5.1, plus a recombinant EG.5.1.1/XBB.1.16.6 Recombinant (US, Spain, England, 15 seq, Oct 20) #777 (the query is using -C1875T to exclude that said recombinant) indicating S:F456L and S:T478R can still be something to aware of.

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The text was updated successfully, but these errors were encountered:

FedeGueli · 2023-09-11T06:27:38Z

If you compare F456L and T478R without their combo helper mutations S:T478R is bigger and more able in standing alone than 456L:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=S%3AT478R+%26+%21S%3AF456L+%26+%21S%3AL455F+%26+%21S%3AP521S&variantQuery1=S%3AF456L+%26+%21S%3AQ52H+%26+%21S%3AT478R+%26%21S%3AL455F&aaMutations2=S%3AT478R&aaMutations3=S%3AF456L&analysisMode=CompareEquals&

krosa1910 · 2023-09-11T23:28:19Z

Do not think it is fast or major compared with other major mutations we have seen in EG.5.1*. I agree that Its true number is something at about 45 seqs (if excluding the questionable K478Trev), or 70 (counting those reversions).
And even if you want to keep record of mutation here, I suggest that reducing this proposal to S:T478R would suffice. as it is 37/45 of seqs that is not T478K or K478rev, and the remaining seem to be limited to singlets.
And the T478R dominance is in every major clades of XBB*. According to cov-spectrum, only XBB.2.3* seem to harbor a decent bit of minor S:T478 mutations like I,Q,E,N or something. So I recommend focusing on S:T478R if you want to track 478 mutation on EG.5.1 unless a relatively successful mutant appeared (which could be tracked elsewhere)

NkRMnZr · 2023-09-12T05:10:36Z

Thanx @krosa1910 , it's just a copy-paste from other XBB.2.3* tracker, and yes it would be suffice to only track 478R outside XBB.2.3* (and perhaps a bit share of XBB.1.5* and XBB.1.19*), I'll fix that once new seqs coming in.

NkRMnZr · 2023-09-13T09:24:56Z

Tracking updates

09-13, Branch 1, +1 (USA); Branch 2, +4 (China)

Branch 1, +1 (Arizona ) EPI_ISL_18247039
Branch 2, +4 (Heilongjiang) EPI_ISL_18245976, EPI_ISL_18246104, EPI_ISL_18246171, EPI_ISL_18246184

09-15, Branch 1 (+2, USA) EPI_ISL_18256461, EPI_ISL_18260400
09-16, adding Branch 3~6
09-20, update on Branch 1, 2 and 5
09-26, update on branch 1-3, 5-6, adding branch 7
10-10, Adding Branch 8 and 9
10-18, update on Branch 1-2, 7-9
10-25, update on Branch 1 and 5
10-27, update on Branch 3
11-07, Branch 3, +8 (Sweden)
11-09, Branch 5, +13 (Russia)
11-15, Update on Branch 3 and 11; Adding Branch 13 and 14
12-15; 12-20

NkRMnZr · 2023-09-16T11:26:13Z

09-16

Branch 1, +1 (North Carolina) EPI_ISL_18267009

Adding Branch 3 from former doublet with 3 seqs from Vaud
Adding Branch 4 from former doublet with 1 sequence from Shanghai
Adding Branch 5 from former soublet with 2 seqs from China and Denmark
Adding Branch 6 from former singlet with 2 seqs from Bayern

NkRMnZr · 2023-09-20T05:33:03Z

09-20, update on Branch 1, 2 and 5

Branch 1, +1 (Arizona) EPI_ISL_18284027
Branch 2, +1 (S. Korea) EPI_ISL_18271954
Branch 5, +1 (Anhui) EPI_ISL_18277173

NkRMnZr · 2023-09-26T11:37:59Z

09-26, update on branch 1-2, 5-6, adding branch 7; branch 3 is moved to EG.5.1's polytomy and start to pull singlets/doublets under it.

FedeGueli · 2023-09-29T07:49:37Z

Branch 1 : Inactive
Branch 2 : 11 samples
Branch 3: 10 samples
Branch 4: inactive
Branch 5: 12 samples
Branch 6: inactive
Branch 7: 4 (argentina)

i think you can focus on 2 3 5 and 7, but not for long they doesnt seem able to compete

https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&aaMutations1=S%3At478R&nextcladePangoLineage1=EG.5.1*&analysisMode=CompareToBaseline&

NkRMnZr · 2023-10-10T06:50:46Z

10-10

Adding Branch 8 (FLiP + 478I) from former doublet
Adding Branch 9 from former triplet

Branch 6, +8 (Spain) EPI_ISL_18362455, EPI_ISL_18362512, EPI_ISL_18362587, EPI_ISL_18362607, EPI_ISL_18362655, EPI_ISL_18362659-18362660, EPI_ISL_18362702

FedeGueli · 2023-10-10T09:25:21Z

10-10

Adding Branch 8 (FLiP + 478I) from former doublet

is it also in #537 ?

NkRMnZr · 2023-10-11T05:07:59Z

10-10
Adding Branch 8 (FLiP + 478I) from former doublet

is it also in #537 ?

nope, it is sublineage of JJ.1 proposed by @aviczhl2

FedeGueli · 2023-10-11T07:37:18Z

10-10
Adding Branch 8 (FLiP + 478I) from former doublet

is it also in #537 ?

nope, it is sublineage of JJ.1 proposed by @aviczhl2

Yes thx noticed that opening the tree.

NkRMnZr · 2023-10-18T09:31:43Z

10-18

Branch 1 +3 (USA) EPI_ISL_18375676, EPI_ISL_18399900, EPI_ISL_18399952
Branch 2 +4 (China, Japan, S. Korea, USA) EPI_ISL_18382906, EPI_ISL_18383995, EPI_ISL_18384368, EPI_ISL_18400599
Branch 7 +3 (UK, USA) EPI_ISL_18373488, EPI_ISL_18392543, EPI_ISL_18399984
Branch 8 +2 (Japan) EPI_ISL_18402281, EPI_ISL_18402668
Branch 9 +2 (USA) EPI_ISL_18394604, EPI_ISL_18394751

NkRMnZr · 2023-10-25T12:07:07Z

10-25

Branch 1, +3 (USA) EPI_ISL_18416483, EPI_ISL_18424493, EPI_ISL_18424962
Branch 5, +12 (Russia), misplaced under EG.5.1.1 > C27507T > C9319T, C22995G(S:T478R), T26609C where they don't have C27507T: EPI_ISL_18416868, EPI_ISL_18416917, EPI_ISL_18417066, EPI_ISL_18417075, EPI_ISL_18417084, EPI_ISL_18417086, EPI_ISL_18417313, EPI_ISL_18417371, EPI_ISL_18417374, EPI_ISL_18417574, EPI_ISL_18417620, EPI_ISL_18417639

NkRMnZr · 2023-10-28T03:29:06Z

10-27

Branch 3, +4 (Sweden, Switzerland) EPI_ISL_18436143-18436144, EPI_ISL_18436146, EPI_ISL_18440451

FedeGueli · 2023-10-30T12:11:03Z

There could be also an EG.5.1.2 + S:R158G + S:T76A + S:M153I > S:T478R doublet:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2bbdb_f9b790.json?label=id:node_3430687
Query G7295A, C14230T, G22021T,C25693T

NkRMnZr · 2023-11-08T11:51:56Z

11-07 Branch 3, +8 (Sweden) EPI_ISL_18458610, EPI_ISL_18458615, EPI_ISL_18458619, EPI_ISL_18458633, EPI_ISL_18458636, EPI_ISL_18458649, EPI_ISL_18465570, EPI_ISL_18465579

FedeGueli · 2023-11-09T15:36:46Z

No one seems able to compete @NkRMnZr what do you think? i m thinking about closing it

NkRMnZr · 2023-11-10T13:04:10Z

No one seems able to compete @NkRMnZr what do you think? i m thinking about closing it

There are FLippeR branches emerging so I'd keep it open for a week or two

NkRMnZr · 2023-11-10T13:07:33Z

11-09

Branch 5, +13 (Russia), misplaced under EG.5.1.1 > C27507T > C9319T, C22995G(S:T478R), T26609C where they don't have C27507T: EPI_ISL_18487069, EPI_ISL_18487203, EPI_ISL_18487290, EPI_ISL_18487328, EPI_ISL_18487348, EPI_ISL_18487448, EPI_ISL_18487451, EPI_ISL_18487654, EPI_ISL_18487657, EPI_ISL_18487678, EPI_ISL_18487691, EPI_ISL_18487762, EPI_ISL_18487769

FedeGueli · 2023-11-10T16:54:29Z

No one seems able to compete @NkRMnZr what do you think? i m thinking about closing it

There are FLippeR branches emerging so I'd keep it open for a week or two

Please flipper sublineages to be tracked in #537

NkRMnZr · 2023-11-15T13:28:48Z

11-15
Branch 3, +4 (Sweden, USA) EPI_ISL_18500173, EPI_ISL_18500774, EPI_ISL_18500814, EPI_ISL_18501169
Branch 11, +5 (Norway, Sweden, USA) EPI_ISL_18498158, EPI_ISL_18499386, EPI_ISL_18500972, EPI_ISL_18500991, EPI_ISL_18501018

Adding Branch 13 from former quintuplet
Adding Branch 14 from former quadruplet

NkRMnZr · 2023-11-20T19:22:28Z

11-20 adding a few quintuplets

FedeGueli · 2023-11-26T07:52:37Z

Hi @NkRMnZr it is striking most of the samples of this issue are around mid october with two exception Branch 5 and 14 ,
Branch 5 is real or it is just the collection of the emergence of S:T478R direclty from politomy? , Branch 14 seems growing.
Please propose these two and then close the issue.

FedeGueli · 2023-11-26T08:07:10Z

Tree for branch 14 clearly growing:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_a6a9_2f9f90.json?label=id:node_3533478

FedeGueli · 2023-11-26T08:20:15Z

NkRMnZr · 2023-11-28T01:21:58Z

Hi @NkRMnZr it is striking most of the samples of this issue are around mid october with two exception Branch 5 and 14 , Branch 5 is real or it is just the collection of the emergence of S:T478R direclty from politomy? , Branch 14 seems growing. Please propose these two and then close the issue.

Yes, Branch 5 seems to be a collection of 478R as the query suggests.

FedeGueli · 2023-11-28T08:13:23Z

Lets wait for Branch 15 if it grows otherwise we will close this

FedeGueli · 2023-11-28T16:47:53Z

Please check relationship between Branch 5 and HK.30 ( in the original misplacement it was there, but i cannot rewind the whole thing, just a suggestion not urgent nor important)

NkRMnZr · 2023-12-15T12:09:06Z

12-15
Branch 3, +9 (Sweden, USA) EPI_ISL_18587225, EPI_ISL_18587338, EPI_ISL_18587356, EPI_ISL_18587450, EPI_ISL_18588063, EPI_ISL_18588116, EPI_ISL_18588140, EPI_ISL_18595179, EPI_ISL_18614225
Branch 10, +6 (Netherlands) EPI_ISL_18630963, EPI_ISL_18630982, EPI_ISL_18630993-18630994, EPI_ISL_18630996, EPI_ISL_18631012
Branch 11, +18 (Denmark, Finland, France, Sweden) EPI_ISL_18587007, EPI_ISL_18587319, EPI_ISL_18588097, EPI_ISL_18596255, EPI_ISL_18596358, EPI_ISL_18626259, EPI_ISL_18634896, EPI_ISL_18634919, EPI_ISL_18634926, EPI_ISL_18635176, EPI_ISL_18635277, EPI_ISL_18635292, EPI_ISL_18635314, EPI_ISL_18635338, EPI_ISL_18635342, EPI_ISL_18635361, EPI_ISL_18635367, EPI_ISL_18635372
Branch 13, +8 (Sweden) EPI_ISL_18587373, EPI_ISL_18600785, EPI_ISL_18600943, EPI_ISL_18607432, EPI_ISL_18607461, EPI_ISL_18607482, EPI_ISL_18619252, EPI_ISL_18619318
Adding Branch 16 from former quintuplet

NkRMnZr · 2023-12-21T06:45:49Z

12-20

Branch 13, +5 (Sweden) EPI_ISL_18642849, EPI_ISL_18642909, EPI_ISL_18642963, EPI_ISL_18642986, EPI_ISL_18662468
Branch 16, +5 (Canada, Netherlands, US) EPI_ISL_18640031, EPI_ISL_18645545, EPI_ISL_18646997, EPI_ISL_18647246, EPI_ISL_18656581
Adding Branch 17, 18 from former doublets
Adding Branch 19 from former quadruplet
Adding Branch 20 from former singlet
Adding Branch 21 from former quintuplet first spotted by @FedeGueli
Adding Branch 22 from former quintuplet

FedeGueli · 2023-12-28T11:24:32Z

there could be a new JG.3 + S:t478R branch defined by T>G670A it was spotted by @NkRMnZr in : USA/NJ-GBW-H10-018-9503/2023|EPI_ISL_18615294|2023-12-03
JG.3 > C25378T(S:Y1272Y) > G670A, A2015G(ORF1a:M584V), C9611T(ORF1a:L3116F), G13427A(ORF1a:E4388K), C22995G(S:T478R), C26208T [Query: C7086T, C22995G, C25378T, 12/12]

but now the tree has changed leaving only JG.3 > C25378T(S:Y1272Y) > G670A, C22995G(S:T478R) as defining :
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_22d67_d59210.json?c=userOrOld&label=id:node_1000121

FedeGueli · 2023-12-30T01:43:57Z

@NkRMnZr please propose branch 5 , to me it is clearly HK.30 + S:T478R .

it is affected by the mutation A27507T from A27507C defining of XBB.1.9.2 that messes the tree as discussed in #861

BUT it seems very high in prevalence in Russia

the query i found is : A27507,T26609C, 22995G,C9319T

it finds 101 samples (95 in Russia)

Genomes

EPI_ISL_18416868, EPI_ISL_18416917, EPI_ISL_18417066, EPI_ISL_18417075, EPI_ISL_18417084, EPI_ISL_18417086, EPI_ISL_18417313, EPI_ISL_18417371, EPI_ISL_18417374, EPI_ISL_18417574, EPI_ISL_18417620, EPI_ISL_18417639, EPI_ISL_18487069, EPI_ISL_18487203, EPI_ISL_18487290, EPI_ISL_18487328, EPI_ISL_18487348, EPI_ISL_18487448, EPI_ISL_18487451, EPI_ISL_18487654, EPI_ISL_18487657, EPI_ISL_18487678, EPI_ISL_18487691, EPI_ISL_18487762, EPI_ISL_18487769, EPI_ISL_18550560, EPI_ISL_18561244, EPI_ISL_18561291, EPI_ISL_18561369, EPI_ISL_18561395, EPI_ISL_18562139, EPI_ISL_18579945, EPI_ISL_18580191, EPI_ISL_18638598, EPI_ISL_18638600, EPI_ISL_18638641, EPI_ISL_18638775, EPI_ISL_18638787, EPI_ISL_18638789, EPI_ISL_18638841, EPI_ISL_18638851, EPI_ISL_18638888, EPI_ISL_18638896, EPI_ISL_18638965, EPI_ISL_18639024, EPI_ISL_18643646, EPI_ISL_18671614, EPI_ISL_18679983, EPI_ISL_18682690, EPI_ISL_18682713, EPI_ISL_18682716, EPI_ISL_18682739, EPI_ISL_18682770, EPI_ISL_18682786, EPI_ISL_18682815, EPI_ISL_18682832, EPI_ISL_18682849, EPI_ISL_18682853, EPI_ISL_18682858, EPI_ISL_18682863, EPI_ISL_18682893, EPI_ISL_18682927, EPI_ISL_18682975, EPI_ISL_18682992, EPI_ISL_18685398, EPI_ISL_18685506, EPI_ISL_18685554, EPI_ISL_18685557, EPI_ISL_18685569, EPI_ISL_18685578, EPI_ISL_18685612, EPI_ISL_18685616, EPI_ISL_18685697, EPI_ISL_18685727, EPI_ISL_18685749, EPI_ISL_18685786, EPI_ISL_18685798-18685799, EPI_ISL_18685880, EPI_ISL_18685883, EPI_ISL_18685899, EPI_ISL_18685909, EPI_ISL_18685950, EPI_ISL_18685959, EPI_ISL_18685961, EPI_ISL_18685971, EPI_ISL_18685985, EPI_ISL_18685989, EPI_ISL_18686007, EPI_ISL_18686025, EPI_ISL_18686062, EPI_ISL_18686126, EPI_ISL_18686154, EPI_ISL_18686177, EPI_ISL_18686208-18686209, EPI_ISL_18686226, EPI_ISL_18686238-18686239, EPI_ISL_18686245, EPI_ISL_18703850

Tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3b7da_f75010.json?label=id:node_3444384

It represents 7% of samples in Russia in December.

FedeGueli · 2024-01-02T23:50:17Z

I m closing this Branch 17 and branch 22 should be monitored a bit more.

FedeGueli · 2024-01-15T08:40:48Z

Thx for Branch 11, i had an old query that showed it stale, instead is quite fast one.

FedeGueli added S:456 S:478 Multiple lineages Rapid review needed labels Sep 11, 2023

NkRMnZr changed the title ~~Multiple EG.5.1* Lineages with S:T478X~~ Multiple EG.5.1* Lineages with S:T478R Sep 13, 2023

NkRMnZr mentioned this issue Sep 20, 2023

EG.5* Lineage Tracker NkRMnZr/hSC2-Tracking-Log#20

Open

72 tasks

FedeGueli removed the Rapid review needed label Sep 29, 2023

NkRMnZr changed the title ~~Multiple EG.5.1* Lineages with S:T478R~~ Multiple EG.5.1* Lineages with S:T478X Oct 10, 2023

FedeGueli mentioned this issue Oct 30, 2023

EG.5.1.2+S:T76A(100 seqs, 21 countries, 15 with S:M153I) #512

Closed

NkRMnZr mentioned this issue Nov 14, 2023

JG.3+S:478R in USA(18 seqs) #1081

Closed

NkRMnZr mentioned this issue Nov 28, 2023

HK.3.1 with S:T478R (71 seqs, mainly in Sweden, 8 countries) cov-lineages/pango-designation#2393

Closed

NkRMnZr referenced this issue in cov-lineages/pango-designation Nov 29, 2023

Designate HK.32.1 (S:L455F)

6e3305f

FedeGueli referenced this issue in cov-lineages/pango-designation Dec 17, 2023

Designate JG.3.4 (XBB.1.9.2.5.1.3.3.4, S:478R, USA)

f84dfde

FedeGueli mentioned this issue Dec 30, 2023

Potential Usher bug that places unrelated seqs to branches with mutations they don't have. #861

Closed

FedeGueli closed this as completed Jan 2, 2024

Multiple EG.5.1* Lineages with S:T478X #787

Multiple EG.5.1* Lineages with S:T478X #787

Comments

NkRMnZr commented Sep 11, 2023 • edited Loading

Multiple EG.5.1* Lineages with S:T478R or S:T478I

Branch 1

Branch 2

Branch 3: Mostly under C5178T(ORF1a:T1638I) sub-branch

Branch 4

Branch 5

Branch 6

Branch 7

Branch 8: FLiP + T478I

Branch 9

Branch 10

Branch 11

Branch 12

Branch 13

Branch 14

Branch 15

Branch 16

Branch 17

Branch 18

Branch 19

Branch 20

Branch 21

Branch 22

Branch 23

Branch 24

Branch 25

Branch 26

Branch 27

Branch 28

Singlets

Doublets

Triplets

Quadruplets

Quintuplets

FedeGueli commented Sep 11, 2023

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FedeGueli commented Jan 15, 2024

NkRMnZr commented Sep 11, 2023 •

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Multiple `EG.5.1*` Lineages with `S:T478R` or `S:T478I`

Branch 3: Mostly under `C5178T(ORF1a:T1638I)` sub-branch

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