xz-keg
commented
1 year ago @AngieHinrichs May I suggest for a slight upgrade on usher, as it always have one branch fully-sampled and other branches downsampled, can it highlight the fully-sampled branch so that we can see more clearly which branch belongs to which?
Currently the biggest problem on analysis EG.5.1.1 samples is that when uploading seqs, there suddenly come up 30+ sub-branches, with each having one fully-sampled branch and other branches downsampled. However, it is really hard to distinguish which branch is fully-sampled and which is downsampled. They look all the same at the first glance.
FedeGueli
NkRMnZr
AngieHinrichs
olias120676
krosa1910
Over-There-Is
S:L455Fin EG.5.1 backbone. Checking updates.C66T,C346T,G598A,G1820A,C4423T,C6843T,A10323G(ORF1a:K3353R),C12651T(ORF1a:T4129I),C13860T,A15159G,C19983T,C22096T(S:D178D),C22264T(S:N234N),C22792T(S:I410I),C22998T(S:P479L),C26681T,C27059T,C27507T,C27884T,A29700GBranch 1:
Transferred to main repo. Designated as HK.8
**Designated as HK.8 (EG.5.1.1.8) via cov-lineages/pango-designation@9527e15** _Transferred to cov-lineages/pango-designation#2230_ **Defining Mutations:** `EG.5.1.1` > `C11779T` > `G22927T(S:L455F)` **Query:** `C6541T, C11779T, G22927T` **Earliest seq:** 2023-06-27 (`EPI_ISL_18060870`, Yibin, Sichuan, China) **Latest seq:** 2023-07-17 (`EPI_ISL_18060877`, Zi'yang, Sichuan, China) **Sampled Countries:** China (2, Sichuan)Genomes:
`EPI_ISL_18060870, EPI_ISL_18060877`Back to Tasklist
Branch 2:
Transferred to main repo:
_Transferred to cov-lineages/pango-designation#2229_ **Defining Mutations:** `EG.5.1.1` > `C12053T(ORF1a:L3930F)` > `C503T(ORF1a:P80S)` > `C7732T, C18175T(ORF1b:P1570S), G22927T(S:L455F)` **Query:** `C503T, C6541T, G22927T` **Earliest seq:** 2023-07-15 (`EPI_ISL_18060497`, Tokyo, Japan) **Latest seq:** 2023-07-18 (`EPI_ISL_18065046`, Miyagi, Japan) **Sampled Countries:** Japan (2)Genomes:
`EPI_ISL_18060497, EPI_ISL_18065046`Back to Tasklist
Branch 3
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2194_ **Defining Mutations:** `EG.5.1.1` > `C11779T` > `C6781T, C17802T, G22927C(S:L455F)` **Query:** `C6781T, C17802T, G22927C` **Earliest seq:** 2023-07-04 (`EPI_ISL_17994488`, Shanghai, China) **Latest seq:** 2023-07-18 (`EPI_ISL_18074754`, Shanghai, China) **Sampled Countries:** China (3, Shanghai)Genomes:
`EPI_ISL_17994488, EPI_ISL_18074751, EPI_ISL_18074754`Back to Tasklist
Branch 4
Transferred to main repo
Transferred to cov-lineages/pango-designation#2224 **Defining Mutations:** `EG.5.1` > `C12100G, G22927T`(**S:L455F**) **Query:** `C12100G, G22927T` **Earliest seq:** 2023-07-09 (`EPI_ISL_18060822`, Shanghai, China) **Latest seq:** 2023-07-31 (`EPI_ISL_18094969`, Washington, USA with Travel History to: Japan) **Sampled Countries:** China (2, Shanghai, 1 ex. Thailand), USA (2, Washington, ex. Japan)Genomes:
`EPI_ISL_18060822, EPI_ISL_18075026, EPI_ISL_18094946, EPI_ISL_18094969`Back to Tasklist
Branch 5
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2250_ **Defining Mutations:** `EG.5.1.1` > `G22927C`(**S:L455F**, different to **HK.3**'s `G22927T`) **Query:** `C6541T, G22927C, -C3653T, -C6317T, -C6327T, -A6659G, -T7111C, -C8074T, -G8768A, -C10702T, -C11779T, -C13968A, -T17811C, -A21137G, -T21748C, -C22482T, -C24023T, -C27741T, -G29734T` **Earliest seq:** 2023-07-08 (`EPI_ISL_18012368`, Sichuan, China) **Latest seq:** 2023-07-27 (`EPI_ISL_18105834`, Shanghai, China) **Sampled Countries:** China (3: Shanghai/2; Sichuan/1)Genomes:
`EPI_ISL_18012368, EPI_ISL_18074450, EPI_ISL_18105834`Back to Tasklist
Branch 6
Many sequences pulled back to HK.3, the reversion probably due to dropout rather than recombinant
**Defining Mutations:** `EG.5.1.1` > _T22480C_Reversion_ > `G22927T`(**S:L455F**) **Query:** `C6541T, G13627A, G22927T, -C7948T, -C22480T` **Earliest seq:** 2023-07-05 (`EPI_ISL_17988079`, Xiangyang, Hubei) **Latest seq:** 2023-08-07 (`EPI_ISL_18105560`, Xiangyang, Hubei) **Sampled Countries:** China (4, Hubei)Genomes:
`EPI_ISL_17988079, EPI_ISL_18105559-18105560, EPI_ISL_18105562`Back to Tasklist
Branch 7
Defining Mutations:
EG.5.1.1>C6627T(ORF1a:T2121I)>T17147C(ORF1b:I1227T)>G22927T(S:L455F) Query:C6627T, T17147C, G22927TEarliest seq: 2023-07-06 (EPI_ISL_18074610, Shanghai) Latest seq: 2023-08-05 (EPI_ISL_18108436, Shanghai, Travel history: Singapore) Sampled Countries: China (3: Shanghai)Genomes:
`EPI_ISL_18074610, EPI_ISL_18108436, EPI_ISL_18108490`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1999b_eabba0.json?f_userOrOld=uploaded%20sample&label=id:node_10741278
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Branch 8
Defining Mutations:
EG.5.1.1>C5284T>T14655C>C15951T, G22927T(S:L455F) Query:C5284T, T14655C, G22927TEarliest seq: 2023-07-23 (EPI_ISL_18105571, Shanghai) Latest seq: 2023-08-11 (EPI_ISL_18114886, Shanghai) Sampled Countries: China (3, Shanghai)Genomes:
`EPI_ISL_18105571, EPI_ISL_18108625, EPI_ISL_18114886`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28a92_b9eb0.json?f_userOrOld=uploaded%20sample&label=id:node_6895881
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Branch 9
Defining Mutations:
EG.5.1.1>C19983T>G22927T(S:L455F) Query:C6541T, G13627A, C19983T, G22927T, -C6695T **Earliest seq:** 2023-06-30 (EPI_ISL_18074254, Liaoning, China) **Latest seq:** 2023-08-27 (EPI_ISL_18239976`, Utah, USA) Sampled Countries: China (3: Liaoning/2; Shanghai/1)Genomes:
`EPI_ISL_18074249, EPI_ISL_18074254`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2cc80_bc030.json?f_userOrOld=uploaded%20sample&label=id:node_6895986
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Branch 10
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2251_ **Defining Mutations:** EG.5.1.1 > C11173T > G22927T(**S:L455F**) **Query:** `C11173T, G13627A, G22927T, -T22228C, -C27406T, -T28157C` **Earliest seq:** 2023-07-16 (`EPI_ISL_18049850`, Qinghai) **Latest seq:** 2023-08-01 (`EPI_ISL_18114762`, Shanghai) **Sampled Countries:** China (3, Qinghai, Shanghai, Xinjiang)Genomes:
`EPI_ISL_18049850, EPI_ISL_18108872, EPI_ISL_18114762`Back to Tasklist
Branch 11
Defining Mutations:
EG.5.1>C9430T>T1939C, C10039T, C20873G(ORF1b:A2469G), G22927T(S:L455F)Query:C9430T, G21718T, G22927T, -C1889T, -G13627A, -C21622AEarliest seq: 2023-07-31 (EPI_ISL_18127303, Tokyo, Japan) Latest seq: 2023-08-07 (EPI_ISL_18127606, Kanagawa, Japan) Sampled Countries: Japan (3: Tokyo/2; Kanagawa/1)Genomes:
`EPI_ISL_18127215, EPI_ISL_18127303, EPI_ISL_18127606`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice4_genome_1293d_792f00.json?f_userOrOld=uploaded%20sample
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Branch 12:
Designated EG.5.1.17
_Designated as **EG.5.1.17** via cov-lineages/pango-designation@5a8103c_ **Defining Mutations:** `EG.5.1` > `G22927C(S:L455F)` **Query:** `C2334T, A18492G, G22927C, -G1069A, -A22106C, -C22570T, -C25572T` **Earliest seq:** 2023-07-09 (`EPI_ISL_18108295`, Anhui, China) **Latest seq:** 2023-08-15 (`EPI_ISL_18138165`, Shanghai, China) **Sampled Countries:** China (4: Shanghai/3; Anhui/1)Genomes:
`EPI_ISL_18108295, EPI_ISL_18114797, EPI_ISL_18138165, EPI_ISL_18138282`Back to Tasklist
Branch 13:
Transferred to main repo
_transferred to cov-lineages/pango-designation#2364_ **Defining Mutations:** `EG.5.1.1` > `C19011T` > `C8991T(ORF1a:A2909V)` > `G22927T(S:L455F)` **Query:** `C8991T, C19011T, G22927T` **Earliest seq:** 2023-08-14 (`EPI_ISL_18146054`, Hubei, China) **Latest seq:** 2023-10-31 (`EPI_ISL_18473645`, Singapore, travel history: India) **Sampled Countries:** China (38: HB/23; SH/4; AH/3; BJ/2; YN/2; GS/1; HA/1; QH/1; XJ/1), Singapore (5: Local/2; ex. China/2; ex. India/1), Netherlands (3), Australia (2: NSW), Austria (1), Croatia (1), France (1), Laos (1)Genomes:
`EPI_ISL_18141179, EPI_ISL_18146054, EPI_ISL_18146087, EPI_ISL_18217222, EPI_ISL_18217236, EPI_ISL_18254205, EPI_ISL_18268148-18268149, EPI_ISL_18268153, EPI_ISL_18268244, EPI_ISL_18284712, EPI_ISL_18284755, EPI_ISL_18306934, EPI_ISL_18313098, EPI_ISL_18313105, EPI_ISL_18313198, EPI_ISL_18313226, EPI_ISL_18349877, EPI_ISL_18354962, EPI_ISL_18363349, EPI_ISL_18376465, EPI_ISL_18376494, EPI_ISL_18384477, EPI_ISL_18384508, EPI_ISL_18388887, EPI_ISL_18388889, EPI_ISL_18388891, EPI_ISL_18438085, EPI_ISL_18438311, EPI_ISL_18438356, EPI_ISL_18438359, EPI_ISL_18438427, EPI_ISL_18441693, EPI_ISL_18442727, EPI_ISL_18442730, EPI_ISL_18447747, EPI_ISL_18457659, EPI_ISL_18461703, EPI_ISL_18461971, EPI_ISL_18463327, EPI_ISL_18463426, EPI_ISL_18464919, EPI_ISL_18464984, EPI_ISL_18465193, EPI_ISL_18465381, EPI_ISL_18465391, EPI_ISL_18466345, EPI_ISL_18473414, EPI_ISL_18473645, EPI_ISL_18475163, EPI_ISL_18475178`Back to Tasklist
Branch 14
Defining Mutations:
EG.5.1.1>A8443G>G22927T(S:L455F)Query:C6541T, A8443G, G22927TEarliest seq: 2023-07-22 (EPI_ISL_18060879Ziyang, Sichuan) Latest seq: 2023-08-09 (EPI_ISL_18146071, Xiaogan, Hubei) Sampled Countries: China (3: Sichuan/2; Hubei/1)Genomes:
`EPI_ISL_18060879, EPI_ISL_18146071, EPI_ISL_18166195`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_140e3_db750.json?f_userOrOld=uploaded%20sample
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Branch 15
Designated with levels: HK.23, HK.23.1 and HK.23.1.1
Designated as three levels: [HK.23](https://github.com/cov-lineages/pango-designation/commit/12691b30210c9ab9b68ebfe04bda957d9a09b806), [HK.23.1](https://github.com/cov-lineages/pango-designation/commit/b83d9aa28a32b8a70a6e049b29986577cf07f23a) and [HK.23.1.1](https://github.com/cov-lineages/pango-designation/commit/b47c3ca2d6369c236951efde3b954e9ac022e5b7) _Transferred to cov-lineages/pango-designation#2340_ **Defining Mutations:** `EG.5.1.1` > `C28087T(ORF8:A65V)` > `G22927T(S:L455F)` **Query:** `C6541T, G22927T, C28087T, -A4306G, -G4444A, -A6889G, -G8171A, -T8305C, -C10039T, -C19185T, -C25207T` **Earliest seq:** 2023-08-10 (`EPI_ISL_18138246`, Shanghai) **Latest seq:** 2023-08-14 (`EPI_ISL_18208534`, Shanghai) **Sampled Countries:** China (3: Shanghai)Genomes:
`EPI_ISL_18138040, EPI_ISL_18138246, EPI_ISL_18208534`Back to Tasklist
Branch 16
Defining Mutations:
EG.5.1.1>C8074T > T17811C>C7604T, C10789T, C10834T, C12815T, G20348T(ORF1b:S2294I), G22927C(S:L455F), A25998GQuery:C6541T, C8074T, G22927CEarliest seq: 2023-08-22 (EPI_ISL_18217203, Hubei, China) Latest seq: 2023-08-22 (EPI_ISL_18217204, Hubei, China) Sampled Countries: China (3)Genomes:
`EPI_ISL_18217202-18217204`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c2cf_6feba0.json?c=gt-S_455&gmax=25384&gmin=21563&label=id:node_6949824
Back to Tasklist
Branch 17
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2341_ **Defining Mutations:** `EG.5.1.1` > `C9118T` > `G22927T(S:L455F)` **Query:** `C6541T, C9118T, G22927T, -C25546A` **Earliest seq:** 2023-08-14 (`EPI_ISL_18214798`, Osaka, Japan) **Latest seq:** 2023-10-02 (`EPI_ISL_18373543`, England, UK) **Sampled Countries:** Japan (37), USA (4: TX/2; NJ; SC), South Korea (2), UK (2: EN), Australia (1: WA), Canada (1: ON), France (1)Genomes:
`EPI_ISL_18162837, EPI_ISL_18166739, EPI_ISL_18214798, EPI_ISL_18214838, EPI_ISL_18226559, EPI_ISL_18235760, EPI_ISL_18236014, EPI_ISL_18242568, EPI_ISL_18243896, EPI_ISL_18247826-18247827, EPI_ISL_18253490, EPI_ISL_18261506, EPI_ISL_18271898, EPI_ISL_18279175, EPI_ISL_18279234, EPI_ISL_18285272, EPI_ISL_18285440, EPI_ISL_18294200, EPI_ISL_18300272, EPI_ISL_18338985, EPI_ISL_18342460, EPI_ISL_18354762, EPI_ISL_18354776, EPI_ISL_18362312, EPI_ISL_18370698, EPI_ISL_18370761, EPI_ISL_18371874, EPI_ISL_18372806, EPI_ISL_18373146, EPI_ISL_18373543, EPI_ISL_18376280, EPI_ISL_18376286, EPI_ISL_18377931, EPI_ISL_18382356, EPI_ISL_18382437, EPI_ISL_18382737, EPI_ISL_18385259, EPI_ISL_18387636, EPI_ISL_18390707, EPI_ISL_18390782, EPI_ISL_18390836, EPI_ISL_18397002, EPI_ISL_18402105, EPI_ISL_18402112, EPI_ISL_18411313, EPI_ISL_18413797, EPI_ISL_18413896`Back to Tasklist
Branch 18
Merged into HK.3
**Defining Mutations:** `EG.5.1.1` > `C22264T` > `G22927T(S:L455F)` **Query:** `G13627A, C22264T, G22927T` **Earliest seq:** 2023-07-30 (`EPI_ISL_18129236`, British Columbia, Canada) **Latest seq:** 2023-08-28 (`EPI_ISL_18213253`, Fujian, China) **Sampled Countries:** Canada (1, BC), China (1, Fujian), UK (1, England)Genomes:
`EPI_ISL_18129236, EPI_ISL_18142517, EPI_ISL_18213253`Back to Tasklist
Branch 19
Merged under HK.13, no longer tracking
**Defining Mutations:** `EG.5.1.1` > `C29167T` > `G1186A, T4871C(ORF1a:Y1536H), C7011T(ORF1a:A2249V), G17741A(ORF1b:R1425H), G22927C(S:L455F)` **Query:** `T4871C, G17741A` **Earliest seq:** 2023-08-09 (`EPI_ISL_18160385`, New York, USA) **Latest seq:** 2023-08-19 (`EPI_ISL_18214905`, Ibaraki, Japan) **Sampled Countries:** China (1, Shanghai), Japan (1), USA (1, NY)Genomes:
`EPI_ISL_18160385, EPI_ISL_18208589, EPI_ISL_18214905`Back to Tasklist
Branch 20
Designated as HK.33
_Designated as HK.33 via cov-lineages/pango-designation@7ad122e_ **Defining Mutations:** `EG.5.1.1` > `C2644T` > `T7957C, G22927T(S:L455F), G29348T(N:A359S)` **Query:** `C2644T, G13627A, G22927T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18222131`, `SEA` airport, Washington, USA, travel history: UK) **Latest seq:** 2023-08-25 (`EPI_ISL_18208454`, Shanghai, China) **Sampled Countries:** USA (2, ex. UK), China (1, Shanghai)Genomes:
`EPI_ISL_18147035, EPI_ISL_18208454, EPI_ISL_18222131`Back to Tasklist
Branch 21, now pulled under HK.3.8
Pulled under HK.3.8
**Defining Mutations:** `EG.5.1.1` > `C18747T` > `C643T, T13060C, G19723T(ORF1b:V2086F), G22927T(S:L455F)` **Query:** `C643T, C18747T, G22927T` **Earliest seq:** 2023-08-11 (`EPI_ISL_18208543`, Shanghai) **Latest seq:** 2023-08-28 (`EPI_ISL_18232547`, Shanghai Customs, travel history to Japan **Sampled Countries:** China (3, SH)Genomes:
`EPI_ISL_18208543, EPI_ISL_18208548, EPI_ISL_18232547`Back to Tasklist
Branch 22, Now pulled under
HK.3.2>A708C(ORF1a:E148A)>C10969T, G23593T(S:Q677H), G28056A(ORF8:A55T), no longer tracking.Pulled under HK.3.2
**Defining Mutations:** `HK.5` > `G22927T(S:L455F)` **Query:** `spike_Q52H, spike_L455F, spike_Q677H` **Earliest seq:** 2023-08-13 (`EPI_ISL_18146068`, Hubei) **Latest seq:** 2023-08-24 (`EPI_ISL_18226161`, Virginia) **Sampled Countries:** USA (2, VA), China (1, HB)Genomes:
`EPI_ISL_18146068, EPI_ISL_18226161-18226162`Back to Tasklist
Branch 23
Transferred to main repo:
_Transferred to main repo cov-lineages/pango-designation#2319_ **Defining Mutations:** `HK.2` > `G22927T(S:L455F)` **Query:** `C6541T, G21604T, G22927T, -A518G, -C934T, -C1426T, -G3663A, -C5031T, -C7712T, -A7849G, -C8320T, -T16545G` **Earliest seq:** 2023-08-21 (`EPI_ISL_18141161`, Singapore) **Latest seq:** 2023-08-23 (`EPI_ISL_18232599`, Shanghai) **Sampled Countries:** Singapore (1), China (2, SH)Genomes:
`EPI_ISL_18141161, EPI_ISL_18232598-18232599`Back to Tasklist
Branch 24, Designated as
HK.20via cov-lineages/pango-designation@71cf97b ; follow-upS:G482R/G23006Cdesignated asHK.20.1Designated as HK.20 and HK.20.1
_Transferred to cov-lineages/pango-designation#2353_ **Defining Mutations:** `EG.5.1.1` > `C6695T(ORF1a:P2144S)` > `C9448A` > `C5575T, G22927T(S:L455F)` **Query:** `C6695T, C9448A, G22927T` **Earliest seq:** 2023-08-13 (`EPI_ISL_18114870`, Shanghai Customs, travel history to Japan) **Latest seq:** 2023-10-20 (`EPI_ISL_18448529`, Ontario, Canada) **Sampled Countries:** China (13, SH/6; SC/4; FJ/1; ex. Japan/1; ex. S. Korea/1), USA (12: CA/8; AZ/1; OH/1; TX/1; ex. Nepal/1), Singapore (6: Local/5; ex. China/1), Italy (5), UK (3: EN), Australia (2: NSW; QLD), Canada (2: ON), Japan (2), South Korea (2), Switzerland (2), Denmark (1), France (1), Spain (1)Genomes:
`EPI_ISL_18114870, EPI_ISL_18208555, EPI_ISL_18208592, EPI_ISL_18208601, EPI_ISL_18232643, EPI_ISL_18246292, EPI_ISL_18284706, EPI_ISL_18285031, EPI_ISL_18285192, EPI_ISL_18306956, EPI_ISL_18307066, EPI_ISL_18320793, EPI_ISL_18328004, EPI_ISL_18352555, EPI_ISL_18354001, EPI_ISL_18355023, EPI_ISL_18360344, EPI_ISL_18360616, EPI_ISL_18361723, EPI_ISL_18366403, EPI_ISL_18370066, EPI_ISL_18370200, EPI_ISL_18371411, EPI_ISL_18376528, EPI_ISL_18385607, EPI_ISL_18386446, EPI_ISL_18386489, EPI_ISL_18387133, EPI_ISL_18397207, EPI_ISL_18403093, EPI_ISL_18407761, EPI_ISL_18409112, EPI_ISL_18411495, EPI_ISL_18415804, EPI_ISL_18421982, EPI_ISL_18423702, EPI_ISL_18425050, EPI_ISL_18428715, EPI_ISL_18429030, EPI_ISL_18430106, EPI_ISL_18433978, EPI_ISL_18435244, EPI_ISL_18442967, EPI_ISL_18443714, EPI_ISL_18443742-18443744, EPI_ISL_18443746, EPI_ISL_18444154, EPI_ISL_18446641, EPI_ISL_18448416, EPI_ISL_18448529`Back to Tasklist
Branch 25: Mostly with
S:A684VDefining Mutations: EG.5.1.1 >
C29296T>G22927T(S:L455F)Query:C6541T, G22927T, C29296TEarliest seq: 2023-08-06 (EPI_ISL_18133933, Qinghai) Latest seq: 2023-08-30 (EPI_ISL_18245873, Gansu) Sampled Countries: China (4: SC/2; GS; QH)Genomes:
`EPI_ISL_18133933, EPI_ISL_18245873, EPI_ISL_18246316, EPI_ISL_18246328`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_fec3_1b4b0.json?label=id:node_10825408
Back to Tasklist
Branch 26
Transferred to main repo
_Transferred to main repo cov-lineages/pango-designation#2320_ **Defining Mutations:** `HK.11` > `T13228C` > `T4789A` > `G22927T(S:L455F)` **Query:** `T4789A, T13228C, G22927T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18221467`, Halland, Sweden) **Latest seq:** 2023-08-21 (`EPI_ISL_18244247`, Denmark) **Sampled Countries:** Denmark (2), Sweden (1)Genomes:
`EPI_ISL_18221467, EPI_ISL_18244233, EPI_ISL_18244247`Back to Tasklist
Branch 27
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2342_ **Defining Mutations:** `EG.5.1.1` > `C25493A(ORF3a:T34K)` > `G28884C(N:G204P)` > `G22927T(S:L455F)` **Query:** `C6541T, G22927T, C25493A` **Earliest seq:** 2023-07-18 (`EPI_ISL_18245992`, Heilongjiang) **Latest seq:** 2023-10-10 (`EPI_ISL_18397223`, Singapore) **Sampled Countries:** China (18: HL/10; LN/2; SH/2; HB; SC; SX; YN), Singapore (14), Denmark (4), Italy (3), USA (3: CA/2; NY), France (2), Australia (1: NSW), Germany (1), South Korea (1), Sweden (1)Genomes:
`EPI_ISL_18138073, EPI_ISL_18232576, EPI_ISL_18244264, EPI_ISL_18245964, EPI_ISL_18245971, EPI_ISL_18245992, EPI_ISL_18246139, EPI_ISL_18246193, EPI_ISL_18282065, EPI_ISL_18300796, EPI_ISL_18306948, EPI_ISL_18306976, EPI_ISL_18306993, EPI_ISL_18307005-18307006, EPI_ISL_18307019, EPI_ISL_18307026, EPI_ISL_18313136, EPI_ISL_18320696, EPI_ISL_18324230, EPI_ISL_18329168, EPI_ISL_18330265, EPI_ISL_18339790, EPI_ISL_18352920, EPI_ISL_18356975, EPI_ISL_18361976, EPI_ISL_18362045, EPI_ISL_18376532, EPI_ISL_18376955, EPI_ISL_18377536, EPI_ISL_18377636, EPI_ISL_18382895, EPI_ISL_18384393, EPI_ISL_18384413, EPI_ISL_18384418, EPI_ISL_18384426, EPI_ISL_18384448, EPI_ISL_18384625, EPI_ISL_18384643, EPI_ISL_18391206-18391207, EPI_ISL_18397223, EPI_ISL_18397241, EPI_ISL_18397267, EPI_ISL_18397584, EPI_ISL_18401938, EPI_ISL_18405209, EPI_ISL_18406218`Back to Tasklist
Branch 28
Transferred to main repo:
_Transferred to cov-lineages/pango-designation#2398_ **Defining Mutations:** **EG.5.1.1** > `C5812T` > `G22927T(S:L455F)`, mostly with >> `A26565C(M:K15Q), C28770G(N:T166R)` **Query:** `C5812T, G22927T, C28770G` (for major `A26565C(M:K15Q), C28770G(N:T166R)` sub-branch only) **Earliest seq:** 2023-08-09 (`EPI_ISL_18214077`, South Korea) **Latest seq:** 2023-11-09 (`EPI_ISL_18547984`, Nevada, USA) **Sampled Countries:** South Korea (68), USA (5: NV/2; NC/1; ex. S. Korea/2), Australia (2: NSW; QLD), China (2: SC/1; ex. S. Korea/1), Denmark (2), Hungary (2), Finland (1), Japan (1)Genomes:
`EPI_ISL_18214077, EPI_ISL_18236938, EPI_ISL_18293068, EPI_ISL_18293497, EPI_ISL_18347905, EPI_ISL_18353940, EPI_ISL_18354370, EPI_ISL_18354403, EPI_ISL_18355265, EPI_ISL_18355547, EPI_ISL_18368528, EPI_ISL_18382157, EPI_ISL_18382304, EPI_ISL_18382505, EPI_ISL_18382615, EPI_ISL_18386641, EPI_ISL_18408701-18408702, EPI_ISL_18408814, EPI_ISL_18408878, EPI_ISL_18411301, EPI_ISL_18415920, EPI_ISL_18435710, EPI_ISL_18438964, EPI_ISL_18439203, EPI_ISL_18439262-18439263, EPI_ISL_18439368, EPI_ISL_18439436, EPI_ISL_18460639, EPI_ISL_18460726, EPI_ISL_18460826, EPI_ISL_18461023, EPI_ISL_18461030, EPI_ISL_18461109, EPI_ISL_18461117, EPI_ISL_18461139, EPI_ISL_18488790, EPI_ISL_18488878, EPI_ISL_18488904, EPI_ISL_18489119, EPI_ISL_18501908, EPI_ISL_18502007, EPI_ISL_18503617, EPI_ISL_18503624, EPI_ISL_18503755, EPI_ISL_18503952, EPI_ISL_18503974, EPI_ISL_18511170, EPI_ISL_18511222, EPI_ISL_18511248, EPI_ISL_18511257, EPI_ISL_18511484, EPI_ISL_18513699, EPI_ISL_18518361, EPI_ISL_18535616, EPI_ISL_18535618, EPI_ISL_18535641, EPI_ISL_18535643-18535644, EPI_ISL_18535683, EPI_ISL_18539076, EPI_ISL_18539319, EPI_ISL_18539641, EPI_ISL_18539827, EPI_ISL_18540358, EPI_ISL_18544082, EPI_ISL_18547609, EPI_ISL_18547984, EPI_ISL_18550336, EPI_ISL_18552522, EPI_ISL_18559930, EPI_ISL_18564453, EPI_ISL_18564477, EPI_ISL_18564533, EPI_ISL_18564565, EPI_ISL_18564603, EPI_ISL_18564701, EPI_ISL_18564813, EPI_ISL_18564892, EPI_ISL_18564897, EPI_ISL_18565136`Back to Tasklist
Branch 29
Now pulled under HK.3
**Defining Mutations:** **EG.5.1.1** > `C16726T(ORF1b:H1087Y)` > `G9424T, A12472G, G22927T(S:L455F), T23030C(**S:F490P**), G27621T(ORF7a:Q76H)` **Query:** `A12472G, G22927T, G27621T` **Earliest seq:** 2023-08-25 (`EPI_ISL_18245860`, Fujian, China) **Latest seq:** 2023-09-06 (`EPI_ISL_18243501`, Singapore) **Sampled Countries:** Singapore (2), China (1, FJ)Genomes:
`EPI_ISL_18243491, EPI_ISL_18243501, EPI_ISL_18245860`Back to Tasklist
Branch 30
Now pulled under HK.3
**Defining Mutations:** **EG.5.1.1** > `C4423T` > `G22927T(S:L455F)` **Query:** `C4423T, G13627A, G22927T` **Earliest seq:** 2023-08-12 (`EPI_ISL_18246284`, Sichuan, China) **Latest seq:** 2023-08-25 (`EPI_ISL_18235973`, Chiba, Japan) **Sampled Countries:** China (2, SC), Japan (1)Genomes:
`EPI_ISL_18232772, EPI_ISL_18235973, EPI_ISL_18246284`Back to Tasklist
Branch 31
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2321_ **Defining Mutations:** **EG.5.1.1** > `C12020T(ORF1a:L3919F), T24496C` > `C2232T(ORF1a:A656V), C21516T, G22927T(S:L455F)` **Query:** `C6541T, C12020T, G22927T, -G6337T, -C8982A, -G18445A, -C28087T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18216560`, Galway, Ireland) **Latest seq:** 2023-09-04 (`EPI_ISL_18254216`, Hubei) **Sampled Countries:** China (1), Ireland (1), UK (1)Genomes:
`EPI_ISL_18216560, EPI_ISL_18244531, EPI_ISL_18254216`Back to Tasklist
Branch 32
Defining Mutations: EG.5.1.1 >
T4579A>G2329A, A8443G>G22927T(S:L455F)Query:T4579A, A8443G, G22927TEarliest seq: 2023-08-08 (EPI_ISL_18166186, Sichuan) Latest seq: 2023-08-26 (EPI_ISL_18254268, Hubei) Sampled Countries: China (5)Genomes:
`EPI_ISL_18166186, EPI_ISL_18232746, EPI_ISL_18245861, EPI_ISL_18246325, EPI_ISL_18254268`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_647e_1a2900.json?label=id:node_6956460
Back to Tasklist
Branch 33
Designated as EG.5.1.19
_Designated as **EG.5.1.19** via cov-lineages/pango-designation@0807c23 , after transferred to cov-lineages/pango-designation#2322_ **Defining Mutations:** **EG.5.1** > `T26171A(ORF3a:M260K)` > `A17615G(ORF1b:K1383R), G22927T(S:L455F)` **Query:** `G21718T, G22927T, T26171A` **Earliest seq:** 2023-08-09 (`EPI_ISL_18134871`, Daknam, Belgium) **Latest seq:** 2023-09-03 (`EPI_ISL_18252041`, `SEA` airport, Washington, with travel hisotry: Netherlands) **Sampled Countries:** Belgium (1), France (1), Romania (1), USA (1, ex. Netherlands)Genomes:
`EPI_ISL_18134871, EPI_ISL_18229094, EPI_ISL_18252041, EPI_ISL_18254718`Back to Tasklist
Branch 34, NOT FLip but with
S:L455SDefining Mutations: EG.5.1.3 >
G2946A(ORF1a:G894D), T15264C, T22926C(S:L455S)Query:C1889T, C2334T, T22926C, -A4340G, -A10703CEarliest seq: 2023-07-27 (EPI_ISL_18248425, Zagreb, Croatia) Latest seq: 2023-07-31 (EPI_ISL_18248430, Zagreb, Croatia) Sampled Countries: Croatia (4)Genomes:
`EPI_ISL_18248425, EPI_ISL_18248427, EPI_ISL_18248429-18248430`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1ed45_24dab0.json?f_userOrOld=uploaded%20sample&label=id:node_10831638
Back to Tasklist
Branch 35, side-branch to JJ.1
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2354_ **Defining Mutations:** **EG.5.1.4** > `C26111T(ORF3:P240L)` > `C18555T` > `T17268C` > `G22927T(S:L455F)` **Query:** `T17268C, G22927T, C26111T` **Earliest seq:** 2023-08-08 (`EPI_ISL_18132133`, Newfoundland and Labrador) **Latest seq:** 2023-10-23 (`EPI_ISL_18448815`, Ontario, Canada) **Sampled Countries:** Canada (49: ON/22; NL/15; AB/10; BC/1; NS/1), US (7: CA/2; NY/2; AZ/1; UT/1; VA/1), France (1)Genomes:
`EPI_ISL_18132133, EPI_ISL_18256806, EPI_ISL_18258767, EPI_ISL_18258769-18258770, EPI_ISL_18258773, EPI_ISL_18258778, EPI_ISL_18291996, EPI_ISL_18291998, EPI_ISL_18292017, EPI_ISL_18292020-18292022, EPI_ISL_18292026-18292028, EPI_ISL_18333999, EPI_ISL_18344763, EPI_ISL_18357035, EPI_ISL_18372328, EPI_ISL_18372367, EPI_ISL_18383112, EPI_ISL_18383123-18383124, EPI_ISL_18383697, EPI_ISL_18388693, EPI_ISL_18395288, EPI_ISL_18395414, EPI_ISL_18395581, EPI_ISL_18404467, EPI_ISL_18425010, EPI_ISL_18425420, EPI_ISL_18425431, EPI_ISL_18425847, EPI_ISL_18425967, EPI_ISL_18426727, EPI_ISL_18427300, EPI_ISL_18427492, EPI_ISL_18427494, EPI_ISL_18427496, EPI_ISL_18427507, EPI_ISL_18427602, EPI_ISL_18431345, EPI_ISL_18436820, EPI_ISL_18437028, EPI_ISL_18437176, EPI_ISL_18438632, EPI_ISL_18438777, EPI_ISL_18448237, EPI_ISL_18448584-18448585, EPI_ISL_18448588, EPI_ISL_18448699-18448700, EPI_ISL_18448702, EPI_ISL_18448740, EPI_ISL_18448815`Back to Tasklist
Branch 36
Transferred to main repo:
_Transferred to cov-lineages/pango-designation#2399_ **Defining Mutations:** **EG.5.1.1** > `C22388T(S:L276L)` > `G22927T(S:L455F)`, mostly with >> `C1853T` sub-branch **Query:** `C1853T, G13627A, G22927T, -C4780T, -C5031T, -C6627T, -C8982A` (for major `C1853T` sub-branch only) **Earliest seq:** 2023-08-14 (`EPI_ISL_18224087`, Colorado, USA) **Latest seq:** 2023-11-20 (`EPI_ISL_18568071`, `SEA` airport, travel history: France) **Sampled Countries:** France (20), Norway (12), Germany (11), Switzerland (8), USA (6: CO/2; ex. France/2; ex.Germany/2), UK (4: EN), China (3: XJ/2; FJ/1), Denmark (3), Ukraine (3), Canada (2: NB; ON), Finland (2), Spain (2), Belgium (1), Italy (1), Japan (1), Singapore (1)Genomes:
`EPI_ISL_18224087, EPI_ISL_18224096, EPI_ISL_18233134, EPI_ISL_18239749, EPI_ISL_18263561, EPI_ISL_18263571, EPI_ISL_18263574, EPI_ISL_18263576, EPI_ISL_18272601-18272602, EPI_ISL_18280654, EPI_ISL_18280813, EPI_ISL_18290994, EPI_ISL_18291008, EPI_ISL_18291011, EPI_ISL_18308259, EPI_ISL_18313749, EPI_ISL_18326424, EPI_ISL_18326608, EPI_ISL_18327645, EPI_ISL_18337648, EPI_ISL_18337651, EPI_ISL_18338378, EPI_ISL_18373487, EPI_ISL_18373856, EPI_ISL_18380089, EPI_ISL_18380091, EPI_ISL_18388662, EPI_ISL_18388711, EPI_ISL_18411952, EPI_ISL_18412072, EPI_ISL_18421745, EPI_ISL_18421949, EPI_ISL_18428144, EPI_ISL_18428460, EPI_ISL_18428992, EPI_ISL_18433011, EPI_ISL_18441991, EPI_ISL_18451507, EPI_ISL_18464584, EPI_ISL_18464947, EPI_ISL_18468968, EPI_ISL_18476770, EPI_ISL_18485554, EPI_ISL_18486361, EPI_ISL_18486756, EPI_ISL_18493947, EPI_ISL_18494748, EPI_ISL_18495920, EPI_ISL_18496297, EPI_ISL_18496628, EPI_ISL_18496636, EPI_ISL_18496703, EPI_ISL_18499460, EPI_ISL_18505686, EPI_ISL_18505750, EPI_ISL_18519177-18519178, EPI_ISL_18525816, EPI_ISL_18530654, EPI_ISL_18530657-18530658, EPI_ISL_18530757, EPI_ISL_18530938, EPI_ISL_18530967, EPI_ISL_18538000, EPI_ISL_18540615, EPI_ISL_18540768, EPI_ISL_18540871, EPI_ISL_18540915, EPI_ISL_18544152, EPI_ISL_18552615, EPI_ISL_18553571, EPI_ISL_18556840, EPI_ISL_18568060, EPI_ISL_18568071, EPI_ISL_18568733-18568735, EPI_ISL_18570228`Back to Tasklist
Branch 37
⚠
C29095Tbecame homoplastic across the EG.5.1+L455F tree, no longer tracking.No longer tracking
**Defining Mutations:** **EG.5.1.1** > `C29095T` > `G22927T(S:L455F)` **Query:** `G13627A, G22927T, C29095T` **Earliest seq:** 2023-08-28 (`EPI_ISL_18246374`, Sichuan, China) **Latest seq:** 2023-08-31 (`EPI_ISL_18264700`, Texas, USA) **Sampled Countries:** USA (2: TX), China (1: SC)Genomes:
`EPI_ISL_18246374, EPI_ISL_18264482, EPI_ISL_18264700`Back to Tasklist
Branch 38
Defining Mutations: EG.5.1.1 >
T24583C>G22927T(S:L455F)Query:C6541T, G22927T, T24583CEarliest seq: 2023-08-03 (EPI_ISL_18166149, Sichuan) Latest seq: 2023-08-26 (EPI_ISL_18268462Shanghai) Sampled Countries: China (3: SC/2; SH/1)Genomes:
`EPI_ISL_18166149, EPI_ISL_18232692, EPI_ISL_18268462`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_f9a8_5a58c0.json?f_userOrOld=uploaded%20sample&label=id:node_10885352
Back to Tasklist
Branch 39
Defining Mutations: HK.1 (EG.5.1.1.1) >
G22927T(S:L455F)Query:C6541T, G13627A, G22332T, G22927T+C6541T, G13627A, G22332A, G22927TEarliest seq: 2023-08-09 (EPI_ISL_18146086, Hubei) Latest seq: 2023-08-28 (EPI_ISL_18254226, Hubei) Sampled Countries: China (7)Genomes:
`EPI_ISL_18146086, EPI_ISL_18146100, EPI_ISL_18254226-18254227, EPI_ISL_18268425, EPI_ISL_18138066, EPI_ISL_18254258`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1cca6_5afd40.json?f_userOrOld=uploaded%20sample&label=id:node_6971951
Back to Tasklist
Branch 40
Defining Mutations: EG.5.1.1 >
C10615T>G22927T(S:L455F)>C1426T, G25691T(ORF3a:G100V)Query:C1426T, C10615T, G22927TEarliest seq: 2023-08-08 (EPI_ISL_18138249, Shanghai) Latest seq: 2023-08-25 (EPI_ISL_18268441, Shanghai) Sampled Countries: China (4: SH)Genomes:
`EPI_ISL_18138249, EPI_ISL_18208636, EPI_ISL_18268441, EPI_ISL_18268482`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20010_5b23f0.json?f_userOrOld=uploaded%20sample&label=id:node_6983332
Back to Tasklist
Branch 41
Defining Mutations: EG.5.1.1 >
C24023T>C2485T, G15025A(ORF1b:A520T), G22927C(S:L455F)Query:C6541T, G22927C, C24023TEarliest seq: 2023-08-14 (EPI_ISL_18239206, South Korea) Latest seq: 2023-08-24 (EPI_ISL_18254859, South Korea) Sampled Countries: South Korea (3)Genomes:
`EPI_ISL_18239206, EPI_ISL_18254859, EPI_ISL_18271926`UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_26c10_8252f0.json?f_userOrOld=uploaded%20sample&label=id:node_10885690
Back to Tasklist
Branch 42
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2355_ **Defining Mutations:** **EG.5.1.1** > `C22687T` > `G22927T(S:L455F)` **Query:** `C6541T, C22687T, G22927T, -T2145C, -A16482C, -C21191T` **Earliest seq:** 2023-08-14 (`EPI_ISL_18279039`, Singapore, travel history: China) **Latest seq:** 2023-09-01 (`EPI_ISL_18278560`, Alberta, Canada) **Sampled Countries:** China (21: GS/4; HB/3; XJ/3; AH/2; SC/2; SX/2; FJ/1; HK/1; QH/1; SH/1; YN/1), Australia (12: NSW/5; SA/4; QLD/1; TA/1; VIC/1), South Korea (8), Canada (6: AB), USA (3: AZ/1; ex. Australia/2), Singapore (2: Local/1; ex. China/1), Japan (1)Genomes:
`EPI_ISL_18146046, EPI_ISL_18213336, EPI_ISL_18217223, EPI_ISL_18278558, EPI_ISL_18278560, EPI_ISL_18279039, EPI_ISL_18289881, EPI_ISL_18293677, EPI_ISL_18293698, EPI_ISL_18311984, EPI_ISL_18312274, EPI_ISL_18312380, EPI_ISL_18313209, EPI_ISL_18327623, EPI_ISL_18327666, EPI_ISL_18346251, EPI_ISL_18346325, EPI_ISL_18347707, EPI_ISL_18350428, EPI_ISL_18360224, EPI_ISL_18361336, EPI_ISL_18361999, EPI_ISL_18365676, EPI_ISL_18365684, EPI_ISL_18365890, EPI_ISL_18366374, EPI_ISL_18382081, EPI_ISL_18382589, EPI_ISL_18382710, EPI_ISL_18384562, EPI_ISL_18388967, EPI_ISL_18389014, EPI_ISL_18389016, EPI_ISL_18390872, EPI_ISL_18396110, EPI_ISL_18401894, EPI_ISL_18401903, EPI_ISL_18401983, EPI_ISL_18404054, EPI_ISL_18408752, EPI_ISL_18411422, EPI_ISL_18411665, EPI_ISL_18411717, EPI_ISL_18411753, EPI_ISL_18425089, EPI_ISL_18427884, EPI_ISL_18435235, EPI_ISL_18438336, EPI_ISL_18438338, EPI_ISL_18438347, EPI_ISL_18439100, EPI_ISL_18447517, EPI_ISL_18447771`Back to Tasklist
Branch 43
now seems to be pulled under HK.3, no longer tracking
Pulled under HK.3
**Defining Mutations:** **EG.5.1.1** > `C19524T` > `G22927T(S:L455F), A28254Δ` **Query:** `G13627A, C19524T, G22927T, -C5031T` **Earliest seq:** 2023-08-19 (`EPI_ISL_18246322`, Sichuan) **Latest seq:** 2023-09-07 (`EPI_ISL_18277156`, Fujian) **Sampled Countries:** China (3: FJ; HL; SC)Genomes:
`EPI_ISL_18246049, EPI_ISL_18246322, EPI_ISL_18277156`Back to Tasklist
Branch 44, "FLippeR"
Transferred to main Repo
_Transferred to cov-lineages/pango-designation#2296_ **Defining Mutations:** **EG.5.1** > `A22106C(S:K182Q)` > `C22995G(S:T478R), A25664G(ORF3a:Y91C)` > `C1613T(ORF1a:L450F), G20995T(ORF1b:G2510C), G22927C(S:L455F), C25803T, A27388C` **Query:** `A22106C, G22927C, C22995G` **Earliest seq:** 2023-08-14 (`EPI_ISL_18160020`, Denmark, or, `EPI_ISL_18278998`, Singapore) **Latest seq:** 2023-09-04 (`EPI_ISL_18243476`, Singapore) **Sampled Countries:** Singapore (2), Denmark (1)Genomes:
`EPI_ISL_18160020, EPI_ISL_18243476, EPI_ISL_18278998`Back to Tasklist
Branch 45
Transferred to main Repo
_Transferred to cov-lineages/pango-designation#2308_ **Defining Mutations:** `EG.5.1.1` > `C13968A, A15885G` > `T11449C` > `C10369T, G22927T(S:L455F), C29077T, G29140T(N:Q289H)` **Query:** `T11449C, C13968A, G22927T` **Earliest seq:** 2023-09-06 (`EPI_ISL_18273676`, England) **Latest seq:** 2023-09-07 (`EPI_ISL_18284457`, `IAD` Airport, DC, travel history: Italy) **Sampled Countries:** UK (2: EN) USA (2, ex. Italy)Genomes:
`EPI_ISL_18273676, EPI_ISL_18281373, EPI_ISL_18284072, EPI_ISL_18284457`Back to Tasklist
Branch 46 with a sub-lineage of
S:L452Q, designated as HK.22parental lineage of HK.22
_Branch 46 + S:L452Q designated as HK.22 via cov-lineages/pango-designation@2d3115a_ **Defining Mutations:** `EG.5.1.1` > `G25407T(ORF3a:M5I)` > `C2662T` > `G22927T(S:L455F)` **Query:** `C2662T, G22927T, G25407T` **Earliest seq:** 2023-08-06 (`EPI_ISL_18114750`, Shanghai) **Latest seq:** 2023-09-06 (`EPI_ISL_18284970`, Shanghai) **Sampled Countries:** China (4: SH)Genomes:
`EPI_ISL_18114750, EPI_ISL_18232688, EPI_ISL_18284888, EPI_ISL_18284970`Back to Tasklist
Branch 47
Defining Mutations:
EG.5.1.1>C7600T>G22927T(S:L455F)>T10216CQuery:C7600T, T10216C, G22927TEarliest seq: 2023-08-22 (EPI_ISL_18246331, Sichuan) Latest seq: 2023-09-04 (EPI_ISL_18284731, Hubei) Sampled Countries: China (5)Genomes:
`EPI_ISL_18246331, EPI_ISL_18284731, EPI_ISL_18284776, EPI_ISL_18284783, EPI_ISL_18284960`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3ad47_b108e0.json?f_userOrOld=uploaded%20sample&label=id:node_10899080
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Branch 48
Transferred to main repo
Transferred to cov-lineages/pango-designation#2360 ⚠️ Please check potential misplacement. **Defining Mutations:** `EG.5.1.1` > `A23539T(S:S659S)` > `G22927T(S:L455F)` **Query:** `G13627A, G22927T, A23539T, -T899C, -C2662T, -C10015T, -T12865C, -G22332A` **Earliest seq:** 2023-08-16 (`EPI_ISL_18141107`, Singapore) **Latest seq:** 2023-10-22 (`EPI_ISL_18440472`, Netherlands) **Sampled Countries:** Australia (32: NSW/14; SA/8; QLD/4; VIC/3; TAS/1; WA/1), China (10: SC/4; HB/2; SH/2; FJ/1; XJ/1), New Zealand (9), Singapore (4), Netherlands (3), USA (2), France (1)Genomes:
`EPI_ISL_18141107, EPI_ISL_18246326, EPI_ISL_18278997, EPI_ISL_18279955, EPI_ISL_18292475, EPI_ISL_18300669, EPI_ISL_18307132, EPI_ISL_18320781, EPI_ISL_18324527, EPI_ISL_18324537, EPI_ISL_18324951, EPI_ISL_18346779, EPI_ISL_18346805, EPI_ISL_18346818, EPI_ISL_18347516, EPI_ISL_18347639, EPI_ISL_18347703-18347704, EPI_ISL_18347710, EPI_ISL_18352381, EPI_ISL_18355046, EPI_ISL_18360352, EPI_ISL_18365605, EPI_ISL_18365672, EPI_ISL_18365874, EPI_ISL_18376439, EPI_ISL_18388898, EPI_ISL_18396188, EPI_ISL_18411419, EPI_ISL_18411467, EPI_ISL_18411551, EPI_ISL_18411564, EPI_ISL_18411674, EPI_ISL_18411695, EPI_ISL_18423924, EPI_ISL_18427871, EPI_ISL_18428112, EPI_ISL_18435043, EPI_ISL_18438373, EPI_ISL_18440466, EPI_ISL_18440472, EPI_ISL_18440476, EPI_ISL_18442757, EPI_ISL_18442774, EPI_ISL_18447732, EPI_ISL_18454463, EPI_ISL_18454489, EPI_ISL_18457508, EPI_ISL_18459380, EPI_ISL_18459604, EPI_ISL_18459721, EPI_ISL_18459855, EPI_ISL_18459912, EPI_ISL_18459940, EPI_ISL_18461585, EPI_ISL_18461782, EPI_ISL_18461792, EPI_ISL_18461895, EPI_ISL_18461916, EPI_ISL_18461956, EPI_ISL_18464115`Back to Tasklist
Branch 49
Now at least 3 smaller clusters seems pulled together a
S:L455Fbranch right under EG.5.1.4 polytomy, hard to catch by proper query now.Query failed
**Defining Mutations:** `EG.5.1.4` > `C8407T, C11008A(ORF1a:H3581Q), G22927T(S:L455F), G25538T(ORF3a:G49V), C25572T` **Query:** `A18492G, A21137G, G22927T, -C6120T, -G13627A, -C26111T` **Earliest seq:** 2023-08-21 (`EPI_ISL_18284756`, Hubei) **Latest seq:** 2023-09-03 (`EPI_ISL_18284729`, Hubei) **Sampled Countries:** China (3)Genomes:
`EPI_ISL_18284721, EPI_ISL_18284729, EPI_ISL_18284756`Back to Tasklist
Branch 50
Defining Mutations:
EG.5.1.1>G28904T(N:A211S)>G22927T(S:L455F), G27261T, C28744TQuery:C6541T, G22927T, G28904TEarliest seq: 2023-08-30 (EPI_ISL_18268410, Shanghai) Latest seq: 2023-09-03 (EPI_ISL_18254255, Hubei) Sampled Countries: China (5)Genomes:
`EPI_ISL_18254255, EPI_ISL_18268410, EPI_ISL_18289864, EPI_ISL_18289874, EPI_ISL_18289889`UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_523af_c118f0.json?f_userOrOld=uploaded%20sample&label=id:node_6955662
Back to Tasklist
Branch 51
Transferred to main repo
_transferred to cov-lineages/pango-designation#2365_ **Defining Mutations:** EG.5.1.1 > `C10015T` > `G22927T(S:L455F)` **Query:** `C6541T, C10015T, G22927T, -C4586T` **Earliest seq:** 2023-07-31 (`EPI_ISL_18246153`, Heilongjiang) **Latest seq:** 2023-10-31 (`EPI_ISL_18473950`, Spain) **Sampled Countries:** China (20: SH/6; HL/5; LN/3; AH/1; BJ/1; GS/1; HB/1; SC/1; SX/1; XJ/1), Canada (10: ON/9; NS/1), Australia (5: NSW/4; QLD/1), Singapore (5), Spain (5), Croatia (4), USA (3: NY/2; HI/1), Denmark (2), Japan (2), Belgium (1), France (1), Italy (1), Switzerland (1)Genomes:
`EPI_ISL_18246153, EPI_ISL_18268220, EPI_ISL_18284760, EPI_ISL_18289806, EPI_ISL_18304238, EPI_ISL_18307185, EPI_ISL_18309728, EPI_ISL_18320892, EPI_ISL_18333882, EPI_ISL_18354453, EPI_ISL_18356455, EPI_ISL_18362071, EPI_ISL_18382338, EPI_ISL_18384364, EPI_ISL_18388937, EPI_ISL_18388943, EPI_ISL_18392626, EPI_ISL_18392641, EPI_ISL_18395616, EPI_ISL_18398918, EPI_ISL_18401900, EPI_ISL_18422863, EPI_ISL_18425076, EPI_ISL_18433557, EPI_ISL_18438020, EPI_ISL_18438314, EPI_ISL_18438838, EPI_ISL_18445101, EPI_ISL_18445501, EPI_ISL_18446144, EPI_ISL_18448315, EPI_ISL_18448907-18448908, EPI_ISL_18448913-18448914, EPI_ISL_18461557, EPI_ISL_18461608, EPI_ISL_18461684, EPI_ISL_18461722, EPI_ISL_18464481, EPI_ISL_18464633, EPI_ISL_18465094, EPI_ISL_18465113, EPI_ISL_18465171, EPI_ISL_18465395, EPI_ISL_18465403, EPI_ISL_18466062, EPI_ISL_18466326-18466327, EPI_ISL_18466420, EPI_ISL_18466590, EPI_ISL_18470572, EPI_ISL_18471609, EPI_ISL_18471611, EPI_ISL_18473319, EPI_ISL_18473421, EPI_ISL_18473950, EPI_ISL_18475156, EPI_ISL_18475172, EPI_ISL_18475181, EPI_ISL_18475190, EPI_ISL_18475453`Back to Tasklist
Branch 52, now pulled under HK.3.2
Now part of HK.3.2
**Defining Mutations:** `EG.5.1.1` > `C26029A(ORF3a:Q213K)` > `G22927T(S:L455F)` **Query:** `C6541T, G22927T, C26029A, -G24944T, -A26901G` **Earliest seq:** 2023-08-16 (`EPI_ISL_18146001`, Hubei, China) **Latest seq:** 2023-09-20 (`EPI_ISL_18340137`, Illinois, USA) **Sampled Countries:** China (5: HB/3; SC; YN) USA (3: IL; NY; WA), Oman (1)Genomes:
`EPI_ISL_18146001, EPI_ISL_18246341, EPI_ISL_18290983, EPI_ISL_18292780, EPI_ISL_18313122, EPI_ISL_18322921, EPI_ISL_18330205, EPI_ISL_18333620, EPI_ISL_18340137`Back to Tasklist
Branch 53
Transferred to main repo
_transferred to cov-lineages/pango-designation#2366_ **Defining Mutations:** `EG.5.1.1` > `C27741T` > `C1912T, C1968T(ORF1a:T568I), T7111C, A20010T(ORF1b:Q2181H), T20592C, G22927C(S:L455F), C28093T(ORF8:S67F)` **Query:** `C6541T, G22927C, C27741T` **Earliest seq:** 2023-08-28 (`EPI_ISL_18345224`, Cork, Ireland) **Latest seq:** 2023-10-23 (`EPI_ISL_18471085`, Connecticut, USA) **Sampled Countries:** UK (17: EN/16; WS/1), USA (14: NY/3; NJ/2; TX/2; UT/2; AZ/1; CA/1; CT/1; MN/1; OH/1), Ireland (9), Canada (4: ON/3; BC/1), Denmark (2), France (2), China (2: SC/1; ex. Spain/1), Belgium (1), South Korea (1), Netherlands (1)Genomes:
`EPI_ISL_18250090, EPI_ISL_18284832, EPI_ISL_18290882, EPI_ISL_18290915, EPI_ISL_18308328, EPI_ISL_18308339, EPI_ISL_18315360, EPI_ISL_18321565, EPI_ISL_18332107, EPI_ISL_18332505, EPI_ISL_18345224, EPI_ISL_18354139, EPI_ISL_18362839, EPI_ISL_18362880-18362881, EPI_ISL_18362951, EPI_ISL_18375850, EPI_ISL_18377642, EPI_ISL_18385706, EPI_ISL_18385720, EPI_ISL_18385728, EPI_ISL_18385734, EPI_ISL_18388184, EPI_ISL_18388760-18388761, EPI_ISL_18389241, EPI_ISL_18398829, EPI_ISL_18399988, EPI_ISL_18400877, EPI_ISL_18403587, EPI_ISL_18403998, EPI_ISL_18407932, EPI_ISL_18416430, EPI_ISL_18416450, EPI_ISL_18420893, EPI_ISL_18420911, EPI_ISL_18422267, EPI_ISL_18427521, EPI_ISL_18429173, EPI_ISL_18429518, EPI_ISL_18430506, EPI_ISL_18433870, EPI_ISL_18438642, EPI_ISL_18442008, EPI_ISL_18443922, EPI_ISL_18448322, EPI_ISL_18452961, EPI_ISL_18456955, EPI_ISL_18467439, EPI_ISL_18467445, EPI_ISL_18467479, EPI_ISL_18471085, EPI_ISL_18475314`Back to Tasklist
Branch 54:
Defining Mutations:
EG.5.1.1>G24368T(S:D936Y)>G22927T(S:L455F)Query:G13627A, G22927T, G24368T, -G3567A, -C4012T, -C5031T, -T13234C, -C17976TEarliest seq: 2023-09-11 (EPI_ISL_18312655, South Korea) Latest seq: 2023-11-24 (EPI_ISL_18567787, Veneto, Italy) Sampled Countries: Finland (15), South Korea (15), USA (9: NY/7; UT/2), Italy (2), Singapore (2), Australia (1: QLD), Germany (1)Genomes:
`EPI_ISL_18312655, EPI_ISL_18343453, EPI_ISL_18347772, EPI_ISL_18347778, EPI_ISL_18347783, EPI_ISL_18347794, EPI_ISL_18347862, EPI_ISL_18354114, EPI_ISL_18394470, EPI_ISL_18408694, EPI_ISL_18411981, EPI_ISL_18411986, EPI_ISL_18412002, EPI_ISL_18412024, EPI_ISL_18412052, EPI_ISL_18412131, EPI_ISL_18439287, EPI_ISL_18439475, EPI_ISL_18445086, EPI_ISL_18445161, EPI_ISL_18449963, EPI_ISL_18458264, EPI_ISL_18458329, EPI_ISL_18460569, EPI_ISL_18502041, EPI_ISL_18503589, EPI_ISL_18511443, EPI_ISL_18533418, EPI_ISL_18533465, EPI_ISL_18533560, EPI_ISL_18533727, EPI_ISL_18534149, EPI_ISL_18539237, EPI_ISL_18539435, EPI_ISL_18539679, EPI_ISL_18539701, EPI_ISL_18539776, EPI_ISL_18541395, EPI_ISL_18541532, EPI_ISL_18544389, EPI_ISL_18547900, EPI_ISL_18554927, EPI_ISL_18555070, EPI_ISL_18564736, EPI_ISL_18567787`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_28b3b_c482d0.json?label=id:node_3526683
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Branch 55
Designated with 2 levesl: HK.24 and HK.24.1
Designated as [HK.24](https://github.com/cov-lineages/pango-designation/commit/211018361b201eda9d492fdb25dc7fbcad217804) and [HK.24.1](https://github.com/cov-lineages/pango-designation/commit/77596389b8d6291450be40a5b8a7c1701c9e5309) **Defining Mutations:** `EG.5.1.1` > `G23522A(S:E654K)` > `G22927T(S:L455F)` **Query:** `C6541T, G22927T, G23522A` **Earliest seq:** 2023-08-26 (`EPI_ISL_18284795`, Shanghai, China) **Latest seq:** 2023-09-24 (`EPI_ISL_18346833`, South Australia, Australia) **Sampled Countries:** Australia (6: QLD/2; WA/2; NSW; SA), China (3: SH), New Zealand (1)Genomes:
`EPI_ISL_18284795, EPI_ISL_18284982, EPI_ISL_18324864, EPI_ISL_18346833, EPI_ISL_18347678, EPI_ISL_18352382, EPI_ISL_18352389, EPI_ISL_18352581, EPI_ISL_18354460, EPI_ISL_18360253`Back to Tasklist
Branch 56
Defining Mutations:
EG.5.1.1>A22582G(S:E340)>G22927T(S:L455F)Query:G13627A, A22582G, G22927T, -G3153AEarliest seq: 2023-08-30 (EPI_ISL_18303241, Portugal) Latest seq: 2023-09-25 (EPI_ISL_18355054, Singapore) Sampled Countries: Portugal (2), Singapore (2), China (1: QH), UK (1: EN)Genomes:
`EPI_ISL_18268272, EPI_ISL_18274005, EPI_ISL_18303241, EPI_ISL_18303432, EPI_ISL_18307200, EPI_ISL_18355054`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_61cc_2ffcf0.json?label=id:node_3450332
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Branch 57
Defining Mutations:
EG.5.1.1>A22582G(S:E340)>G3153A(ORF1a:G963D)>G22927T(S:L455F)Query:G3153A, A22582G, G22927TEarliest seq: 2023-08-14 (EPI_ISL_18146012, Hubei, China) Latest seq: 2023-09-26 (EPI_ISL_18350530, Basque, Spain) Sampled Countries: China (4: FJ; HB; HK; SH), Japan (2), South Korea (2), USA (2: ex. Greece), Spain (1)Genomes:
`EPI_ISL_18146012, EPI_ISL_18277143, EPI_ISL_18293356, EPI_ISL_18306220, EPI_ISL_18306632, EPI_ISL_18306769, EPI_ISL_18309318, EPI_ISL_18309324, EPI_ISL_18350530, EPI_ISL_18354289, EPI_ISL_18360277`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_61cc_2ffcf0.json?label=id:node_3450116
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Branch 58, formerly singlet, thanks to @aviczhl2 for updated info
Defining Mutations:
EG.5.1>T26972C>C28909T>C2106A(ORF1a:T614N), G28423T(ORF9b:R47L)>A21759G(S:H66R), G22927T(S:L455F), G24004A(S:K814), C25572TQuery:A18492G, G22927T, C28909TEarliest seq: 2023-08-21 (EPI_ISL_18271704, S. Korea) Latest seq: 2023-09-19 (EPI_ISL_18355498, S. Korea) Sampled Countries: South Korea (6)Genomes:
`EPI_ISL_18271704, EPI_ISL_18354058, EPI_ISL_18354072, EPI_ISL_18354264, EPI_ISL_18355236, EPI_ISL_18355498`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_26418_30eca0.json?label=id:node_3429102
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Branch 59: ⚠️ careful with potential dropout/misplacement.
Defining Mutations:
EG.5.1.1>G20134T(ORF1b:V2223L)>G22927T(S:L455F)Query:G13627A, G20134T, G22927TEarliest seq: 2023-09-04 (EPI_ISL_18300595, New South Wales) Latest seq: 2023-10-03 (EPI_ISL_18361370, NSW) Sampled Countries: Australia (17: NSW/16; QLD)Genomes:
`EPI_ISL_18300595, EPI_ISL_18300598, EPI_ISL_18300624, EPI_ISL_18300634, EPI_ISL_18300676-18300679, EPI_ISL_18300732, EPI_ISL_18300745-18300746, EPI_ISL_18300790, EPI_ISL_18324806, EPI_ISL_18352578, EPI_ISL_18361360-18361361, EPI_ISL_18361370`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_4fa9_6ad320.json?label=id:node_3451611
Trivia:
Heilongjiang/HLJCDC-2004/2023|EPI_ISL_18245889|2023-07-25, please check potential HK.3-dropout/misplacement.Back to Tasklist
Branch 60: Formerly
Y144Fartifact branch now maskedDefining Mutations:
EG.5.1.1>T16545G>C1471T, G22927T(S:L455F)Query:G13627A, T16545G, G22927TEarliest seq: 2023-08-25 (EPI_ISL_18228384, Finland) Latest seq: 2023-10-04 (EPI_ISL_18362018, Singapore) Sampled Countries: Singapore (7), China (3: SH/2; HB), Finland (1)Genomes:
`EPI_ISL_18228384, EPI_ISL_18243407, EPI_ISL_18254180, EPI_ISL_18306951, EPI_ISL_18320869, EPI_ISL_18360325, EPI_ISL_18361717, EPI_ISL_18361964, EPI_ISL_18362005, EPI_ISL_18362018, EPI_ISL_18362077`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_108b5_6b1720.json?f_userOrOld=uploaded%20sample&label=id:node_3457632
Trivia:
Y144Fartifact sub-branch now seems masked, thanks to @FedeGueli for the quick analysis and query.Back to Tasklist
Branch 61
⚠️ Please check potential reversion/artifact/misplacement,
C26681Tis quite homoplastic in HK.3*, no longer trackingpotential HK.3 dropout
**Defining Mutations:** `EG.5.1.1` > `C26681T` > `T5327C, C5986T, T22032C(S:F157S), G22927T(S:L455F)` **Query:** `T22032C, G22927T, C26681T` **Earliest seq:** 2023-09-03 (`EPI_ISL_18376557`, Sichuan) **Latest seq:** 2023-09-11 (`EPI_ISL_18376558`, Sichuan, _OR_ `EPI_ISL_18277141`, Fujian) **Sampled Countries:** China (5: SC/4; FJ)Genomes:
`EPI_ISL_18277141, EPI_ISL_18376556-18376559`Back to Tasklist
Branch 62: With a sub-branch of FLippeR
Defining Mutations:
EG.5.1.1>C18559T(ORF1b:L1698F)>T15927C, G22927T(S:L455F)Query:C6541T, C18559T, G22927TEarliest seq: 2023-08-31 (EPI_ISL_18285056, Sichuan, China) Latest seq: 2023-09-20 (EPI_ISL_18382134, South Korea) Sampled Countries: China (4: SC/2; SH/2), South Korea (1)Genomes:
`EPI_ISL_18285056-18285057, EPI_ISL_18320863, EPI_ISL_18360320, EPI_ISL_18382134`UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_24de1_9159b0.json?label=id:node_3445922
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Branch 63
⚠️ Please check potential misplacement
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2400_ **Defining Mutations:** `EG.5.1.1` > `T14034C` > `T6556C` > `G22927T(S:L455F)` **Query:** `T6556C, T14034C, G22927T` **Earliest seq:** 2023-08-28 (`EPI_ISL_18236022`, Chiba, Japan) **Latest seq:** 2023-11-16 (`EPI_ISL_18568493`, Ardèche, France) **Sampled Countries:** South Korea (66), Japan (11), France (7), China (2: Taiwan), Singapore (2), Germany (1), Ireland (1), UK (1: England)Genomes:
`EPI_ISL_18236022, EPI_ISL_18307101, EPI_ISL_18307183, EPI_ISL_18312967, EPI_ISL_18354179, EPI_ISL_18354386, EPI_ISL_18371409, EPI_ISL_18371437, EPI_ISL_18376385, EPI_ISL_18381917, EPI_ISL_18382077, EPI_ISL_18382170, EPI_ISL_18382306, EPI_ISL_18382313, EPI_ISL_18384744, EPI_ISL_18390972, EPI_ISL_18408733, EPI_ISL_18408999, EPI_ISL_18409046, EPI_ISL_18409110, EPI_ISL_18418096, EPI_ISL_18418099, EPI_ISL_18420466, EPI_ISL_18423347, EPI_ISL_18438958, EPI_ISL_18439063, EPI_ISL_18439157, EPI_ISL_18439221, EPI_ISL_18439371, EPI_ISL_18460530, EPI_ISL_18460541, EPI_ISL_18460589, EPI_ISL_18460966, EPI_ISL_18460978, EPI_ISL_18461033, EPI_ISL_18461094, EPI_ISL_18461485, EPI_ISL_18465933, EPI_ISL_18468665, EPI_ISL_18486472, EPI_ISL_18491815, EPI_ISL_18496187, EPI_ISL_18501996, EPI_ISL_18502046, EPI_ISL_18502053, EPI_ISL_18502059, EPI_ISL_18503696, EPI_ISL_18503846, EPI_ISL_18510036, EPI_ISL_18510038, EPI_ISL_18511034, EPI_ISL_18511095, EPI_ISL_18511104, EPI_ISL_18511108, EPI_ISL_18511172, EPI_ISL_18511241, EPI_ISL_18511380, EPI_ISL_18511416, EPI_ISL_18511461, EPI_ISL_18511469, EPI_ISL_18511480, EPI_ISL_18511508, EPI_ISL_18511521, EPI_ISL_18511532, EPI_ISL_18511557, EPI_ISL_18511580, EPI_ISL_18511661, EPI_ISL_18511670, EPI_ISL_18535606, EPI_ISL_18535663, EPI_ISL_18535697, EPI_ISL_18539307, EPI_ISL_18539369, EPI_ISL_18539422, EPI_ISL_18539428, EPI_ISL_18539447, EPI_ISL_18539483, EPI_ISL_18539547, EPI_ISL_18545014, EPI_ISL_18564392, EPI_ISL_18564436, EPI_ISL_18564462-18564463, EPI_ISL_18564564, EPI_ISL_18564669, EPI_ISL_18564752, EPI_ISL_18564926, EPI_ISL_18565014, EPI_ISL_18565195, EPI_ISL_18568493, EPI_ISL_18570360`Back to Tasklist
Branch 64
Defining Mutations:
EG.5.1.6>C28236T(ORF8:R115C)>C16092T>C10969T>G526T(ORF1a:E87D)>C23380T(S:N606)>A12485G(ORF1a:I4074V)>T877C, A15270T(ORF1b:E601D), G22927T(S:L455F)Query:G526T, A15270T, G22927TEarliest seq: 2023-10-08 (EPI_ISL_18404805, New Brunswick, Canada) Latest seq: 2023-10-15 (EPI_ISL_18427247, Ontario, Canada) Sampled Countries: Canada (4: ON/3; NB)Genomes:
`EPI_ISL_18404805, EPI_ISL_18426514, EPI_ISL_18426586, EPI_ISL_18427247`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_21e1_9e19a0.json?label=id:node_3437762
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Branch 65
Defining Mutations:
EG.5.1>A3210G(ORF1a:D982G)>G26888A>G26227T(_TRS of Envelope_), C28720T(_TRS of ORF9c_)>T8909C>G22927T(S:L455F)Query:A3210G, T8909C, G22927TEarliest seq: 2023-09-07 (EPI_ISL_18419405, Sicily, Italy) Latest seq: 2023-09-18 (EPI_ISL_18329969, Denmark) Sampled Countries: Italy (13), Denmark (1)Genomes:
`EPI_ISL_18258788-18258789, EPI_ISL_18329969, EPI_ISL_18419405, EPI_ISL_18419417, EPI_ISL_18419442, EPI_ISL_18419446, EPI_ISL_18419449, EPI_ISL_18419451, EPI_ISL_18419459, EPI_ISL_18419472, EPI_ISL_18419474, EPI_ISL_18419478, EPI_ISL_18419484`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b9a_9e23b0.json?label=id:node_3428133
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Branch 66
Defining Mutations:
EG.5.1.1>C11779T>C12525T(ORF1a:T4087I)>G22927T(S:L455F)Query:C11779T, C12525T, G22927TEarliest seq: 2023-08-27 (EPI_ISL_18360191, England) Latest seq: 2023-10-09 (EPI_ISL_18421921, Belgium) Sampled Countries: South Korea (4), Canada (3: BC), Belgium (1), China (1: SH), New Zealand (1), Singapore (1), UK (1: EN)Genomes:
`EPI_ISL_18227053, EPI_ISL_18292157, EPI_ISL_18355538, EPI_ISL_18360191, EPI_ISL_18381927, EPI_ISL_18382266, EPI_ISL_18397328, EPI_ISL_18408737, EPI_ISL_18421921, EPI_ISL_18430928, EPI_ISL_18431490, EPI_ISL_18431860`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_34aaf_9ea630.json?label=id:node_3493682
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Branch 67
Defining Mutations:
EG.5.1.1>C25613T(ORF3a:S74F)>G22927C(S:L455F)Query:C6541T, G22927C, C25613T, -C26681T, -G26840AEarliest seq: 2023-10-12 (EPI_ISL_18428810, Singapore) Latest seq: 2023-10-16 (EPI_ISL_18428772, Singapore) Sampled Countries: Singapore (5)Genomes:
`EPI_ISL_18428766, EPI_ISL_18428769, EPI_ISL_18428771-18428772, EPI_ISL_18428810`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_41fd2_a0fe0.json?label=id:node_3487648
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Branch 68
Defining Mutations:
EG.5.1.1>G16710A>G22927T(S:L455F)Query:G16710A, G13627A, G22927T, -G28904TEarliest seq: 2023-09-25 (EPI_ISL_18355035, Singapore) Latest seq: 2023-10-18 (EPI_ISL_18428623, Singapore) Sampled Countries: Singapore (11)Genomes:
`EPI_ISL_18355035, EPI_ISL_18361806, EPI_ISL_18361914, EPI_ISL_18361935, EPI_ISL_18362103, EPI_ISL_18397258, EPI_ISL_18397453, EPI_ISL_18428554, EPI_ISL_18428623, EPI_ISL_18428638, EPI_ISL_18428659`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_c933_9f2590.json?label=id:node_3474466
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Branch 69
Defining Mutations:
EG.5.1.1>G1085T(ORF1a:V274L)>G1535A(ORF1a:V424I), G22927T(S:L455F)Query:G1085T, G13627A, G22927T, -A11000G, -C29375T, Earliest seq: 2023-10-02 (EPI_ISL_18361916, Singapore) Latest seq: 2023-10-16 (EPI_ISL_18428661, Singapore) Sampled Countries: Singapore (5)Genomes:
`EPI_ISL_18361916, EPI_ISL_18397376, EPI_ISL_18397599, EPI_ISL_18428562, EPI_ISL_18428661`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_18f8d_9f5e00.json?label=id:node_3486178
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Branch 70
Defining Mutations:
EG.5.1.1>T21748C(S:V62)>A16225G(ORF1b:T920A), T25036C>G22927C(S:L455F)Query:A16225G, T21748C, G22927CEarliest seq: 2023-08-10 (EPI_ISL_18438105, Beijing, China) Latest seq: 2023-10-09 (EPI_ISL_18426675, Montana, USA) Sampled Countries: China (13: BJ/11; HB/1; HL/1), Netherlands (2), Singapore (1), USA (1: MT)Genomes:
`EPI_ISL_18254239, EPI_ISL_18331365, EPI_ISL_18362093, EPI_ISL_18384410, EPI_ISL_18386767, EPI_ISL_18426675, EPI_ISL_18438074-18438075, EPI_ISL_18438082, EPI_ISL_18438103, EPI_ISL_18438105, EPI_ISL_18438108, EPI_ISL_18438114, EPI_ISL_18438136, EPI_ISL_18438177-18438178, EPI_ISL_18438235`UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4eb1c_b77620.json?label=id:node_3464035
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Branch 71
Defining Mutations:
EG.5.1.1>C6638T(ORF1a:H2125Y)>G22927T(S:L455F)Query:C6638T, G13627A, G22927T, -C14889TEarliest seq: 2023-09-11 (EPI_ISL_18313157, Hubei, China) Latest seq: 2023-10-09 (EPI_ISL_18438431, Hubei, China) Sampled Countries: China (5: HB), South Korea (1)Genomes:
`EPI_ISL_18313157-18313158, EPI_ISL_18382135, EPI_ISL_18438389, EPI_ISL_18438415, EPI_ISL_18438431`UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_b5b8_b7aee0.json?f_userOrOld=uploaded%20sample&label=id:node_3482675
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Branch 72
Defining Mutations:
EG.5.1.1>C11779T>G10261A>C9611T(ORF1a:L3116F), C18348T>G22927T(S:L455F)Query:C9611T, C11779T, G22927TEarliest seq: 2023-09-06 (EPI_ISL_18313115, Hubei, China) Latest seq: 2023-10-09 (EPI_ISL_18406324, Vienna, Austria) Sampled Countries: South Korea (6), Singapore (2), Austria (1), China (1: HB)Genomes:
`EPI_ISL_18313115, EPI_ISL_18355007, EPI_ISL_18355538, EPI_ISL_18376812, EPI_ISL_18381927, EPI_ISL_18382266, EPI_ISL_18406324, EPI_ISL_18408737, EPI_ISL_18435658, EPI_ISL_18439298`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b3db_cbcfb0.json?label=id:node_3497922
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Branch 73
Defining Mutations:
EG.5.1.1>C19170T>G22927T(S:L455F)Query:G13627A, C19170T, G22927T, -C1909T, -C3736T, -C5031T, -C7504T, -A18153GEarliest seq: 2023-08-31 (EPI_ISL_18438072, Beijing) Latest seq: 2023-10-14 (EPI_ISL_18442753, Sichuan) Sampled Countries: China (6: SC/3; BJ/1; HB/1; SC/1), South Korea (1)Genomes:
`EPI_ISL_18320875, EPI_ISL_18360251, EPI_ISL_18360272, EPI_ISL_18438072, EPI_ISL_18438352, EPI_ISL_18439041, EPI_ISL_18442753`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_26c5d_cced10.json?label=id:node_3466266
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Branch 74
Defining Mutations:
EG.5.1.3>A28032G(ORF8:I47V)>A1047C(ORF1a:K261T)>C3608A(ORF1a:L1115I), C18261T, G22927T(S:L455F)Query:A1047C, C1889T, G22927TEarliest seq: 2023-09-11 (EPI_ISL_18314192, France) Latest seq: 2023-10-12 (EPI_ISL_18441710, Netherlands) Sampled Countries: Belgium (2), France (2), Netherlands (1)Genomes:
`EPI_ISL_18314192, EPI_ISL_18337916, EPI_ISL_18338399, EPI_ISL_18399343, EPI_ISL_18441710`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_38cb6_cd6010.json?f_userOrOld=uploaded%20sample&label=id:node_3458506
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Branch 75
Defining Mutations:
EG.5.1.1>C29253T(N:S327L)>G22927T(S:L455F)Query:G13627A, G22927T, C29253T, -G1067T, -C2110T, -A2730CEarliest seq: 2023-08-17 (EPI_ISL_18389043, Xinjiang, China) Latest seq: 2023-10-24 (EPI_ISL_18445150, Singapore, travel history: Malaysia) Sampled Countries: Denmark (3), China (2: XJ), Singapore (2)Genomes:
`EPI_ISL_18320957, EPI_ISL_18377581, EPI_ISL_18377610, EPI_ISL_18389043, EPI_ISL_18397195, EPI_ISL_18442952, EPI_ISL_18445150`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c2e8_a8650.json?label=id:node_3492354
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Branch 76
Defining Mutations:
EG.5.1.1>T26609C>C5907T(ORF1a:T1881I), T17454A>G22927T(S:L455F)Query:G13627A, T17454A, G22927TEarliest seq: 2023-09-20 (EPI_ISL_18445852, Castilla y León, Spain) Latest seq: 2023-10-13 (EPI_ISL_18402965, Donostia-San Sebastián, Spain) Sampled Countries: Spain (9)Genomes:
`EPI_ISL_18402961, EPI_ISL_18402965, EPI_ISL_18419672, EPI_ISL_18421286, EPI_ISL_18445852, EPI_ISL_18445906, EPI_ISL_18445934, EPI_ISL_18446071-18446072`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b023_af570.json?label=id:node_3474073
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Branch 77
Transferred to main repo
_Transferred to cov-lineages/pango-designation#2401_ **Defining Mutations:** `EG.5.1.6` > `C925T, C27161T` > `C14919A` > `G14559A` > `G22927T(S:L455F)` **Query:** `C5835T, G14559A, G22927T` **Earliest seq:** 2023-09-11 (`EPI_ISL_18381025`, British Columbia, Canada) **Latest seq:** 2023-11-21 (`EPI_ISL_18572342`, Israel) **Sampled Countries:** Canada (59: AB/25; BC/25; SK/7; ON/1; QC/1), Israel (5), USA (3: NY/2; CA), Finland (2), Sweden (2), Austria (1), Ireland (1), UK (1: EN)Genomes:
`EPI_ISL_18313726, EPI_ISL_18374552, EPI_ISL_18381025, EPI_ISL_18381642, EPI_ISL_18399548, EPI_ISL_18405416, EPI_ISL_18429724, EPI_ISL_18431316, EPI_ISL_18431484, EPI_ISL_18431577, EPI_ISL_18448820, EPI_ISL_18449315, EPI_ISL_18451058, EPI_ISL_18452675, EPI_ISL_18453011, EPI_ISL_18453157, EPI_ISL_18456002, EPI_ISL_18456201, EPI_ISL_18493062, EPI_ISL_18499142, EPI_ISL_18501414, EPI_ISL_18501469, EPI_ISL_18501539, EPI_ISL_18501675, EPI_ISL_18512520, EPI_ISL_18512575, EPI_ISL_18512726, EPI_ISL_18512904, EPI_ISL_18512975, EPI_ISL_18513012, EPI_ISL_18516832, EPI_ISL_18516837, EPI_ISL_18517029, EPI_ISL_18517372, EPI_ISL_18517374-18517375, EPI_ISL_18517477, EPI_ISL_18517505, EPI_ISL_18526773, EPI_ISL_18526937-18526938, EPI_ISL_18526942, EPI_ISL_18526999, EPI_ISL_18527195, EPI_ISL_18532450-18532451, EPI_ISL_18533407, EPI_ISL_18538515, EPI_ISL_18538528, EPI_ISL_18538535, EPI_ISL_18538740, EPI_ISL_18538774, EPI_ISL_18538986, EPI_ISL_18541507-18541508, EPI_ISL_18547665, EPI_ISL_18552699, EPI_ISL_18553923, EPI_ISL_18553948, EPI_ISL_18558921, EPI_ISL_18560813, EPI_ISL_18563933, EPI_ISL_18563975, EPI_ISL_18563992, EPI_ISL_18564064, EPI_ISL_18564086, EPI_ISL_18564088, EPI_ISL_18564119, EPI_ISL_18564154, EPI_ISL_18564182, EPI_ISL_18564194, EPI_ISL_18572342, EPI_ISL_18572380, EPI_ISL_18572384`Back to Tasklist
Branch 78
Defining Mutations:
EG.5.1.1>C18395T(ORF1b:A1643V)>G22927T(S:L455F)Query:C6541T, C18395T, G22927TEarliest seq: 2023-08-16 (EPI_ISL_18146006, Hubei, China) Latest seq: 2023-10-15 (EPI_ISL_18453170, British Columbia, Canada) Sampled Countries: Canada (7: BC), China (6: FJ/3; HB/2; GS/1), Japan (2)Genomes:
`EPI_ISL_18146006, EPI_ISL_18330196, EPI_ISL_18330296, EPI_ISL_18330311, EPI_ISL_18376315, EPI_ISL_18405472, EPI_ISL_18409239, EPI_ISL_18425055, EPI_ISL_18452695, EPI_ISL_18452923, EPI_ISL_18452979, EPI_ISL_18453059, EPI_ISL_18453168, EPI_ISL_18453170, EPI_ISL_18454186`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3e744_1f9880.json?label=id:node_3476703
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Branch 79
Defining Mutations:
EG.5.1.1>T6736C>T23287C(S:A575)>C22075T(S:V171)>C8389T, A16668G, C17474T(ORF1b:T1336I), G22927T(S:L455F), G26416T(E:V58F)Query:T6736C, G13627A, G22927TEarliest seq: 2023-08-17 (EPI_ISL_18241549, Yunnan) Latest seq: 2023-10-14 (EPI_ISL_18454380, Yunnan) Sampled Countries: China (12: YN)Genomes:
`EPI_ISL_18241549, EPI_ISL_18384462, EPI_ISL_18384468, EPI_ISL_18384485, EPI_ISL_18384488, EPI_ISL_18384501, EPI_ISL_18384510, EPI_ISL_18384514, EPI_ISL_18384522, EPI_ISL_18454363, EPI_ISL_18454380, EPI_ISL_18454383`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6626_1fc330.json?label=id:node_3476751
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Branch 80
Defining Mutations:
EG.5.1.1>C8146T>G2035A, G6373T(ORF1a:M2036I), G22927T(S:L455F)Query:C8146T, G13627A, G22927T, -C27557TEarliest seq: 2023-08-28 (EPI_ISL_18289791, Anhui, China) Latest seq: 2023-10-07 (EPI_ISL_18454332, Yunnan, China) Sampled Countries: South Korea (6), China (3: AH, HB, YN)Genomes:
`EPI_ISL_18289791, EPI_ISL_18376503, EPI_ISL_18382123, EPI_ISL_18454332, EPI_ISL_18460781, EPI_ISL_18460783, EPI_ISL_18460821-18460822, EPI_ISL_18460834`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1d9d0_762270.json?label=id:node_3494057
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Branch 81
Defining Mutations:
EG.5.1.1>C2857T>G22927T(S:L455F)Query:C2857T, G13627A, G22927T, -C5031T, -T17475CEarliest seq: 2023-09-14 (EPI_ISL_18388886, Hubei, China) Latest seq: 2023-10-13 (EPI_ISL_18461038, South Korea) Sampled Countries: China (7: TW/5; HB; SC), Belgium (1), Japan (1), South Korea (1)Genomes:
`EPI_ISL_18388886, EPI_ISL_18399792, EPI_ISL_18427833, EPI_ISL_18432501, EPI_ISL_18438519, EPI_ISL_18440359, EPI_ISL_18440668, EPI_ISL_18461038, EPI_ISL_18461507, EPI_ISL_18461514`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5f66_766bb0.json?label=id:node_3485431
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Branch 82
Defining Mutations:
EG.5.1.1>T16494C, T22307C>G22927C(S:L455F)Query:G13627A, T16494C, G22927CEarliest seq: 2023-09-12 (EPI_ISL_18376962, Singapore, Travel History: Malaysia) Latest seq: 2023-10-09 (EPI_ISL_18461687, New South Wales, Australia) Sampled Countries: Singapore (7), China (2: HL), Australia (1: NSW)Genomes:
`EPI_ISL_18355070, EPI_ISL_18355078, EPI_ISL_18355084, EPI_ISL_18355119, EPI_ISL_18376962, EPI_ISL_18397262, EPI_ISL_18397335, EPI_ISL_18461687, EPI_ISL_18465032, EPI_ISL_18465036`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice14_genome_1351a_73edc0.json?label=id:node_3508527
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Branch 83
Defining Mutations:
EG.5.1.1>C29358T(N:T362I)>T23803C(S:T747T)>C842T(ORF1a:P193S), C15141T, T16743C, C22450T(S:L296L), G22927T(S:L455F), C24442T(S:N960N), C25916T(ORF3a:T175I), C28232TQuery:G22927T, T23803C, C29358TEarliest seq: 2023-09-11 (EPI_ISL_18384535, Yunnan, China) Latest seq: 2023-10-31 (EPI_ISL_18473684, Singapore) Sampled Countries: Singapore (11), France (2), Australia (1: NSW), Canada (1: ON), China (1: YN), Germany (1)Genomes:
`EPI_ISL_18327437, EPI_ISL_18384535, EPI_ISL_18423274, EPI_ISL_18428663, EPI_ISL_18455125, EPI_ISL_18461961, EPI_ISL_18472175, EPI_ISL_18473491, EPI_ISL_18473552, EPI_ISL_18473557, EPI_ISL_18473565, EPI_ISL_18473584, EPI_ISL_18473600, EPI_ISL_18473608, EPI_ISL_18473617, EPI_ISL_18473635, EPI_ISL_18473684`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_33d1_b55240.json?label=id:node_3483621
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Branch 84
Defining Mutations:
HK.19>C2455T>G22927T(S:L455F), C23533T(S:N657)Query:C2455T, C22033A, G22927T, -G25606AEarliest seq: 2023-09-20 (EPI_ISL_18327665,SEAairport, travel history: China) Latest seq: 2023-10-06 (EPI_ISL_18454355, Yunnan China) Sampled Countries: China (7)Genomes:
`EPI_ISL_18327626, EPI_ISL_18327665, EPI_ISL_18454355, EPI_ISL_18475173-18475174, EPI_ISL_18481030, EPI_ISL_18481032`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_14b93_98620.json?label=id:node_3515333
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Branch 85: Mostly with
ORF6:N34K/C27303ADefining Mutations:
EG.5.1.1>C7390T>G22927T(S:L455F)Query:C7390T, G13627A, G22927TEarliest seq: 2023-08-31 (EPI_ISL_18312335, South Korea) Latest seq: 2023-10-30 (EPI_ISL_18494555, Denmark) Sampled Countries: China (7: SC/3; HB/2; XJ/2), South Korea (4), Australia (2), Denmark (1), Spain (1)Genomes:
`EPI_ISL_18284798, EPI_ISL_18312335, EPI_ISL_18312767, EPI_ISL_18313150, EPI_ISL_18330217, EPI_ISL_18355417, EPI_ISL_18361365, EPI_ISL_18376681, EPI_ISL_18402975, EPI_ISL_18447796, EPI_ISL_18461975, EPI_ISL_18475119, EPI_ISL_18481228, EPI_ISL_18494555, EPI_ISL_18495106`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_25e0e_b6750.json?label=id:node_3492892
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Branch 86: many with
S:N17T/A21612CDefining Mutations:
EG.5.1.1>G25855T(ORF3a:D155Y)>G22927T(S:L455F)Query:A21612C, G22927T, G25855TEarliest seq: 2023-08-31 (EPI_ISL_18284769, Sichuan, China) Latest seq: 2023-10-24 (EPI_ISL_18458002, Kuala Lumpur, Malaysia) Sampled Countries: China (9: YN/6; SC/3), Malaysia (3), Japan (1)Genomes:
`EPI_ISL_18284769, EPI_ISL_18324153, EPI_ISL_18324208, EPI_ISL_18324235, EPI_ISL_18384546, EPI_ISL_18419659, EPI_ISL_18419662, EPI_ISL_18454181, EPI_ISL_18458002, EPI_ISL_18475350, EPI_ISL_18481259, EPI_ISL_18488097, EPI_ISL_18488110`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_372c6_bbb70.json?label=id:node_3488769
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Branch 87
Defining Mutations:
EG.5.1>C15960T>C16260T>G22927T(S:L455F), C24771T(S:A1070V), C25658T(ORF3a:T89I)Query:C15960T, C16260T, A18492G, G22927TEarliest seq: 2023-09-01 (EPI_ISL_18384575, Yunnan, China) Latest seq: 2023-10-27 (EPI_ISL_18493260, Alberta, Canada) Sampled Countries: China (5: SH/3; SX; YN), Canada (3: AB), South Korea (2)Genomes:
`EPI_ISL_18384575, EPI_ISL_18426071, EPI_ISL_18436785, EPI_ISL_18460945-18460946, EPI_ISL_18475132, EPI_ISL_18481223, EPI_ISL_18493260, EPI_ISL_18495087, EPI_ISL_18495466`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice95_genome_43bfd_a83e0.json?label=id:node_3517572
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Branch 88
⚠️ sibling to Branch 32 please check potential misplacement
Defining Mutations:
EG.5.1.1>T4579A>A4576T>G22927T(S:L455F)Query:A4576T, G13627A, G22927TEarliest seq: 2023-08-18 (EPI_ISL_18239385, South Korea) Latest seq: 2023-10-30 (EPI_ISL_18520721, Saitama, Japan) Sampled Countries: South Korea (39), Japan (2), USA (2, ex. Japan), China (1, ex. S. Korea)Genomes:
`EPI_ISL_18239385, EPI_ISL_18313064, EPI_ISL_18320761, EPI_ISL_18354110, EPI_ISL_18355244, EPI_ISL_18355256, EPI_ISL_18355270, EPI_ISL_18355539, EPI_ISL_18368435, EPI_ISL_18368571, EPI_ISL_18382929, EPI_ISL_18408987, EPI_ISL_18411143, EPI_ISL_18432570, EPI_ISL_18439431, EPI_ISL_18460891, EPI_ISL_18460981, EPI_ISL_18461196, EPI_ISL_18503870, EPI_ISL_18510989, EPI_ISL_18511173, EPI_ISL_18511218, EPI_ISL_18511236, EPI_ISL_18511259, EPI_ISL_18511379, EPI_ISL_18511388, EPI_ISL_18511531, EPI_ISL_18511534, EPI_ISL_18511636, EPI_ISL_18511644, EPI_ISL_18511659, EPI_ISL_18511666, EPI_ISL_18511675, EPI_ISL_18511683, EPI_ISL_18520721, EPI_ISL_18535535, EPI_ISL_18539100, EPI_ISL_18539189, EPI_ISL_18539430, EPI_ISL_18539531, EPI_ISL_18539554, EPI_ISL_18539681, EPI_ISL_18539751, EPI_ISL_18539824`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2459b_3b16b0.json?f_userOrOld=uploaded%20sample&label=id:node_3488766
view from
EG.5.1.1>T4579Abranch, sibling to Branch 32?details
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Branch 89
Defining Mutations:
EG.5.1.1>C27406T(ORF7a:L5F)>G22927T(S:L455F)Query:C6541T, G13627A , G22927T, C27406TEarliest seq:2023-08-11(EPI_ISL_18145981, Hubei, China) Latest seq: 2023-10-18 (EPI_ISL_18487967, Henan, China) Sampled Countries: China (6: HA/2; HB/2; SC/2; BJ), South Korea (1)Genomes:
`EPI_ISL_18145981, EPI_ISL_18320871, EPI_ISL_18360327, EPI_ISL_18382216, EPI_ISL_18438321, EPI_ISL_18485262, EPI_ISL_18487967`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice16_genome_15d09_3ad150.json?label=id:node_3506957
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Branch 90
Defining Mutations:
EG.5.1.1>C13724T(ORF1a:A4487V), A25636T(ORF3a:N82Y)>T10750C, G22927T(S:L455F)Query:G13627A, C13724T, G22927T, -C5031TEarliest seq: 2023-08-22 (EPI_ISL_18272130, South Korea) Latest seq: 2023-10-19 (EPI_ISL_18451971,SEAairport, travel history: South Korea) Sampled Countries: South Korea (6), USA (2: ex. South Korea)Genomes:
`EPI_ISL_18272130, EPI_ISL_18376686, EPI_ISL_18376765, EPI_ISL_18451971, EPI_ISL_18460748, EPI_ISL_18488908-18488909, EPI_ISL_18492194`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_42b73_3bb260.json?label=id:node_3520099
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Branch 91
Defining Mutations:
EG.5.1.1>C22987T(S:A475A)>G22927T(S:L455F)>G19419A, G21974C(S:D138H)Query:G13627A, G19419A, G21974CEarliest seq: 2023-08-24 (EPI_ISL_18284675, Beijing, China) Latest seq: 2023-11-04 (EPI_ISL_18486471, Dublin, Ireland) Sampled Countries: China (6: SC/4; BJ; YN), Ireland (2), Greece (1)Genomes:
`EPI_ISL_18284675, EPI_ISL_18409255, EPI_ISL_18409302, EPI_ISL_18429520, EPI_ISL_18438109, EPI_ISL_18442759, EPI_ISL_18454352, EPI_ISL_18486471, EPI_ISL_18490986`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_6555_3bdc60.json?label=id:node_3502929
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Branch 92
Defining Mutations:
EG.5.1.1>C629T(ORF1a:L122F)>A1168G>C22987T(S:A475A)>T595C, C20148T, G22927T(S:L455F)Query:A1168G, G22927T, C22987TEarliest seq: 2023-09-08 (EPI_ISL_18330247, Hubei, China) Latest seq: 2023-10-30 (EPI_ISL_18539359, South Korea) Sampled Countries: South Korea (5), Japan (2), China (1, HB), USA (1: CA)Genomes:
`EPI_ISL_18330247, EPI_ISL_18435755, EPI_ISL_18443954, EPI_ISL_18446528, EPI_ISL_18502023, EPI_ISL_18503555, EPI_ISL_18511230, EPI_ISL_18520709, EPI_ISL_18539359`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6555_3bdc50.json?label=id:node_3498262
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Branch 93
Defining Mutations:
EG.5.1>G26051T(ORF3a:S220I)>G9269A(ORF1a:G3002S)>T1216C, A9034G, A12121T, A12519G(ORF1a:D4085G), G22927T(S:L455F)Query:G9269A, G22927T, G26051TEarliest seq: 2023-10-21 (EPI_ISL_18453659, South Australia) Latest seq: 2023-11-05 (EPI_ISL_18524643, Queensland) Sampled Countries: Australia (7: QLD/6; SA)Genomes:
`EPI_ISL_18453659, EPI_ISL_18489126, EPI_ISL_18501702, EPI_ISL_18501758, EPI_ISL_18524643, EPI_ISL_18524655, EPI_ISL_18524668`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice52_genome_199a5_39a640.json?label=id:node_3459700
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Branch 94
a sub-branch of #1074 proposed by @aviczhl2
Defining Mutations:
EG.5.1.13> _G670T_rev(ORF1a:R135S_rev)_ >T28861C>G8889A(ORF1a:R2875H)>C13381T>G22424T(S:A288S)>C25047T(S:P1162L)>G25855T(ORF3a:D155Y)>G22927T(S:L455F)Query:G8889A, C13381T, G22927TEarliest seq: 2023-10-10 (EPI_ISL_18486858, Temuco, Chile) Latest seq: 2023-11-26 (EPI_ISL_18582164, Ontario, Canada) Sampled Countries: Canada (14: ON/13; NS), Chile (3), USA (3: NY/2; PA)Genomes:
`EPI_ISL_18483588, EPI_ISL_18483657, EPI_ISL_18486858, EPI_ISL_18523437, EPI_ISL_18534577, EPI_ISL_18548162, EPI_ISL_18581551-18581554, EPI_ISL_18581688, EPI_ISL_18581705, EPI_ISL_18582159, EPI_ISL_18582162, EPI_ISL_18582164, EPI_ISL_18582914, EPI_ISL_18582921-18582922, EPI_ISL_18582983, EPI_ISL_18602138`UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_7d45_55cdd0.json?label=id:node_3474267
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Singlets
Guangdong/GDCDC_GZ_0568/2023|EPI_ISL_18033894|2023-06-28EG.5.1 > G1069A > C12005T > C9803T, A13707G, C14809T(ORF1b:R448C), C18348T, G22927C(S:L455F) [Query:C14809T, C18348T, G22927C, 07/24]Japan/PG-568093/2023|EPI_ISL_18279075|2023-09-05EG.5.1 > T15198A > C1191A(ORF1a:P309Q), A24999C(S:D1146A), A27642G > A21137G(ORF1a:K2557R) > T25851C > C6120T(ORF1a:S1952L), T13030C, G22927T(S:L455F) [Query:C1191A, T15198A, G22927T, 09/19]Canada/QC-L00671579001/2023|EPI_ISL_18478213|2023-10-30EG.5.1 > T15198A > G22317C(S:G252A) > C3267T(ORF1a:T1001I), T8421C(ORF1a:M2719T), G22927T(S:L455F), C22949T(S:P463S) [Query:T15198A, G22317C, G22927T, 11/08]Sichuan/NJCDC-0906-7/2023|EPI_ISL_18261486|2023-08-30EG.5.1.1 > A3069G(ORF1a:D935G) > C367T, A1197C(ORF1a:E311A), A6925G, G22927T(S:L455F), T27212C(ORF6:L4P) [Query:A3069G, C6541T, G22927T, 09/14]Shanghai/SCDC-HP-XG-0731-1/2023|EPI_ISL_18138078|2023-07-31EG.5.1.1 > G3242A(ORF1a:G993S) > G1595A(ORF1a:E444K), C6628T, G22927T(S:L455F), A27721G(ORF7a:I110V) [Query:G3242A, C6541T, G22927T, 08/25]Shanghai/SCDC-XG09-13670/2023|EPI_ISL_18285000|2023-09-07EG.5.1.1 > C3653T(ORF1a:L1130F) > G410T(ORF1a:G49C), C1498T, C2227A, C6395T, C11563T, G22927C(S:L455F), G27604T(ORF7a:V71L) [Query:C3653T, C6541T, G22927C, 09/19]South_Korea/KDCA262399/2023|EPI_ISL_18271956|2023-08-22EG.5.1.1 > C7764T(ORF1a:S2500F) > T5448C(ORF1a:V1728A), G22927T(S:L455F), C25539T [Query:C7764T, G13627A, G22927T, 09/18]Japan/TKYnat15208/2023|EPI_ISL_18285185|2023-09-01EG.5.1.1 > C13730T(ORF1b:A88V) > T12727C, G22927T(S:L455F) [Query:C6541T, C13730T, G22927T, -C11779T, 09/20]Australia/QLD0x01374B/2023|EPI_ISL_18122559|2023-08-09FLIP+346I+478R EG.5.1.1 > C16830T, C18348T, G22599T(S:R346I), G22927T(S:L455F), C22995G(S:T478R), T23176C [Query:C18348T, G22599T, G22927T, 08/22]South_Korea/KDCA262306/2023|EPI_ISL_18271874|2023-08-15EG.5.1.1 > C21588T(S:P9L) > G22927T(S:L455F), C28770T(N:T166I) [Query:G13627A, C21588T, G22927T, 09/18]Anhui/HCDC-176/2023|EPI_ISL_18289771|2023-09-04EG.5.1.1 > C24130T > G9177T(ORF1a:G2971V), T28705C > A10863C(ORF1a:E3533A), G22927T(S:L455F), G25522A(ORF3a:G44R), G27933A(ORF8:A14T) [Query:G9177T, G22927T, C24130T, 09/20]GZSCDC-GY07-14/2023|EPI_ISL_18074217|2023-07-18EG.5.1.1 > G24926T(S:V1122L) > C1960T, C12076T, T22926C(S:L455S), T27428A(ORF7a:L12H) [Query:G13627A, T22926C, G24926T, 08/07]England/CLIMB-CM7YRMOM/2023|EPI_ISL_18227115|2023-08-22EG.5.1.3 > A4340G(ORF1a:I1359V) > A2163G(ORF1a:E633G) > C23185T > T11932G, T14022C, T22926C(S:L455S) [Query:A2163G, A4340G, T22926C, 09/06]Sweden/W-49492298L6/2023|EPI_ISL_18249322|2023-08-23EG.5.1.3 > A10703C > C1314T(ORF1a:T350I), C9118T > G4907A(ORF1a:G1548S) > C6936G(ORF1a:S2224C), C18959T(ORF1b:A1831V), G22094T(S:D178Y), T22926C(S:L455S), G27160A(M:S213N) [Query:G4907A, C9118T, T22926C, 09/12]Spain/CT-HUGTiP-B1R154/2023|EPI_ISL_18281164|2023-09-13EG.5.1.3 > T14568C > T7651C, G27962T(ORF8:Q23H) > T4579A, C19017T, G22927T(S:L455F) [Query:C1889T, T7651C, G22927T, 09/19]Canada/ON-PHL-23-30576/2023|EPI_ISL_18277805|2023-09-11EG.5.1.4 > C26111T(ORF3a:P240L) > C21622A > C9430T > C20133T > G22927T(S:L455F) [Query:C9430T, C20133T, G22927T, 09/18]USA/NY-URMC-N6S1J239-1/2023|EPI_ISL_18247548|2023-08-27EG.5.1.4 > C26111T(ORF3:P240L) > G25563T(ORF3a:Q57H) > C1427T(ORF1a:H388Y) > G25494A > A21759G(S:H66R), G22927T(S:L455F) [Query:G22927T, G25494A, G25563T, 09/11]USA/MD-HP49490-PIDPVKAURD/2023|EPI_ISL_18432449|2023HV.1 (EG.5.1.6.1) > C2695T > C26964T(M:H148Y) > C27600T > C14376T > A5424G(ORF1a:K1720R) > C4752T(ORF1a:T1496I), G22927T(S:L455F) [Query:A5424G, C14376T, G22927T, 10/24]USA/OH-ODH-SC3032871/2023|EPI_ISL_18422243|2023-09-29HV.1 > A5021G(ORF1a:M1586V) > C6117T(ORF1a:A1951V), G22927T(S:L455F), C29028T(N:A252V) [Query:A5021G, C5835T, G22927T, 10/23]Back to Tasklist
Doublets
USA/NY-NYULH-16857/2023|EPI_ISL_18440726|2023-10-19andUSA/NY-CDC-VSX-A357619/2023|EPI_ISL_18534359|2023-10-26EG.5.1 > C2147T(ORF1a:L628F), T6115C > G18498T(ORF1b:M1677I) > C21811T, A22911T(S:N450I), G22927T(S:L455F) [Query:C2147T, G18498T, G22927T, 2 seqs, 11/22] (Another 3 seqs not on GISAID yetShanghai/SCDC-MH200506/2023|EPI_ISL_18114819|2023-07-30andLiaoning/LNCDC-360-1/2023|EPI_ISL_18330279|2023-09-12EG.5.1 > C6706T > C7482T(ORF1a:S2406L) > C2507T(ORF1a:P748S), C4543T, C8251T, G22927T(S:L455F) [Query:C6706T, C7482T, G22927T, 2 seqs, 09/30]Shanghai/SCDC-804/2023|EPI_ISL_18268355|2023-09-02andShanghai/SCDC-831/2023|EPI_ISL_18284896|2023-09-09EG.5.1.1 > A3021G(ORF1a:H919R), A21493C > C1913T(ORF1a:R550C), C4965T(ORF1a:T1567I), C17977T(ORF1b:L1504F), A19237C, G22927T(S:L455F), C27393T, C28791T(N:A173V) [Query:A3021G, A21493C, G22927T, 2 seqs, 09/19]Taiwan/CDC-W30906/2023|EPI_ISL_18164789|2023-07-29andUSA/HI-H2324424/2023|EPI_ISL_18283168|2023-08-29EG.5.1.1 > C6317T(ORF1a:P2018S) > C1567T, C8152T, C16192T(ORF1b:P909S), G22927C(S:L455F), G25606A(ORF3a:A72T) [Query:C6317T, C6541T, G22927C, 2 seqs, 09/19]Sichuan/YACDC-XGcx133/2023|EPI_ISL_18232742|2023-08-14andSichuan/YACDC-XGCX151/2023|EPI_ISL_18304270|2023-09-18EG.5.1.1 > C6327T(ORF1a:T2021I) > C1684A, A17008G(ORF1b:I1181V), G22927C(S:L455F), G27217T(ORF6:D6Y) [Query:C6327T, C6541T, G22927C, 2 seqs, 09/25]Hubei/HCDC-ES2799/2023|EPI_ISL_18254184|2023-08-30andEngland/CLIMB-CM7YEDUX/2023|EPI_ISL_18274069|2023-09-08EG.5.1.1 > C9142T > G22927T(S:L455F) [Query:C9142T, G13627A, G22927T, 2 seqs, 09/18]Shanghai/SCDC-XG08-12942/2023|EPI_ISL_18268428|2023-08-27andShanghai/SCDC-836/2023|EPI_ISL_18284901|2023-09-10EG.5.1.1 > C9996T(ORF1a:S3244L) > G22927T(S:L455F) [Query:C6541T, C9996T, G22927T, 2 seqs, 09/19]Sichuan/CDCDC-3-LZJ/2023|EPI_ISL_18166147|2023-07-29andSichuan/CDCDC-19-CX2806/2023|EPI_ISL_18246264|2023-08-20EG.5.1.1 > C11779T > C7420T > A12644G(ORF1a:I4127V), G16662A, G22927T(S:L455F), A27736T(ORF7a:T115S), C28585T [Query:C7420T, C11779T, G22927T, 2 seqs, 09/11]USA/OR-OSPHL08951/2023|EPI_ISL_18285283|2023-09-07andUSA/OR-OSPHL08953/2023|EPI_ISL_18285285|2023-09-10EG.5.1.1 > C11956T > C17746T(ORF1b:P1427S), T20252C(ORF1b:I2262T), G22927T(S:L455F) [Query:C11956T, G13627A, G22927T, 2 seqs, 09/20]Shanghai/SCDC-XG09-13443/2023|EPI_ISL_18284954|2023-08-30andSichuan/MYCDC-XGCX312/2023|EPI_ISL_18284766|2023-09-03EG.5.1.1 > C14571T > T16340C(ORF1b:I958T), T17736C, G22927T(S:L455F) [Query:C6541T, C14571T, G22927T, -A1051G, 2 seqs, 09/19]Germany/NW-RKI-I-1137155/2023|EPI_ISL_18131003|2023-08-02andUkraine/81521/2023|EPI_ISL_18539909|2023-10-12EG.5.1.3 > C1059T(ORF1a:T265I) > G22927C(S:L455F) [Query:C1059T, C1889T, G22927C, 2 seqs, 11/23]Canada/QC-L00650653001/2023|EPI_ISL_18252385|2023-08-28andCanada/QC-L00650647001/2023|EPI_ISL_18252388|2023-08-29EG.5.1.3 > C17718T > A17066G(ORF1b:Y1200C), A17622G, G22927T(S:L455F) [Query:C1889T, C17718T, G22927T, 2 seqs, 09/12]Canada/ON-PHL-23-36533/2023|EPI_ISL_18448204|2023-10-18andCanada/ON-PHL-23-36753/2023|EPI_ISL_18448385|2023-10-20HV.1 (EG.5.1.6.1) > C12513T(ORF1a:T4083M) > T17343C > G22918T(S:R452) > T22926C(S:L455S), C29784T [Query:C12513T, T17343C, T22926C, 2 seqs, 10/30]USA/HI-H2325918/2023|EPI_ISL_18487957|2023-10-26andUSA/HI-H2325960/2023|EPI_ISL_18535129|2023-11-03HV.1 > T23198C(S:L546L) > C29466T > T28417C(ORF9b:I45T) > C875T(ORF1a:L204F), G22927T(S:L455F) [Query:G22927T, T23198C, T28417C, 2 seqs, 11/22]Back to Tasklist
Triplets
Shanghai/SCDC-770/2023|EPI_ISL_18232641|2023-08-20;Shanghai/SCDC-802/2023|EPI_ISL_18268353|2023-08-31andGermany/NW-RKI-I-1138223/2023|EPI_ISL_18343384|2023-09-19EG.5.1.1 > G347A(ORF1a:V28I) > T27956C > G3091A > C13959T, T22020G(S:M153R), G22927T(S:L455F) [Query:G347A, G3091A, G22927T, 3 seqs, 10/04]Shanghai/SCDC-0823-3241/2023|EPI_ISL_18208400|2023-08-21;France/BRE-IPP21293/2023|EPI_ISL_18350826|2023-09-18andUSA/CA-GBW-H20-334-1265/2023|EPI_ISL_18357649|2023-09-26EG.5.1.1 > G347A(ORF1a:V28I) > T27956C > G22927T(S:L455F), A26117G(ORF3a:E242G) [Query:G347A, G22927T, T27956C, -G3091A, 3 seqs, 10/06]Yunnan/YNCDC-2364/2023|EPI_ISL_18166234|2023-08-02;Yunnan/YNCDC-2493/2023|EPI_ISL_18241493|2023-08-28andYunnan/YNCDC-2972/2023|EPI_ISL_18384579|2023-09-22EG.5.1.1 > C629T(ORF1a:L122F) > A1168G > T6640C > C18864T, G22927T(S:L455F), A25506G [Query:C629T, T6640C, G22927T, 3 seqs, 10/12]Xinjiang/XJCDCWLMQ-412/2023|EPI_ISL_18161044|2023-07-29;South_Korea/KDCA271622/2023|EPI_ISL_18511017|2023-10-20;Shanghai/SCDC-JD1024_1/2023|EPI_ISL_18495067|2023-10-21andDenmark/DCGC-663353/2023|EPI_ISL_18518786|2023-11-06EG.5.1.1 > C4832T > G22927T(S:L455F) [Query:C4832T, G13627A, G22927T, C27874T, 3 seqs, 11/18]Shanghai/SCDC-FX0906-018/2023|EPI_ISL_18284805|2023-09-03;Hubei/HCDC-JZ3118/2023|EPI_ISL_18376469|2023-09-25andHubei/HCDC-YC3307/2023|EPI_ISL_18438465|2023-09-27EG.5.1.1 > C26151T > C19524G, C20235T, G22927T(S:L455F), G29044A [Query:C19524G, G22927T, C26151T, 3 seqs, 10/26]Australia/SA708969/2023|EPI_ISL_18453685|2023-10-23;Australia/SA832208/2023|EPI_ISL_18536619|2023-11-14andAustralia/SA832209/2023|EPI_ISL_18536620|2023-11-14EG.5.1.3 > C1057T > G18462A > C6578T(ORF1a:L2105F) > G22927T(S:L455F), C26058T, T27210C [Query:C1057T, C6578T, G22927T, 3 seqs, 11/23] thanks to @FedeGueliSpain/CU-19903/2023|EPI_ISL_18294739|2023-08-22;Denmark/DCGC-661638/2023|EPI_ISL_18442881|2023-10-16andItaly/LOM_Unimi-3611-23/2023|EPI_ISL_18443629|2023-10-19EG.5.1.6 > C12513T(ORF1a:T4083M) > G22927T(S:L455F) [Query:C5835T, C12513T, G22927T, 3 seqs, 10/28]Back to Tasklist
Quadruplets
Shanghai/SCDC-826/2023|EPI_ISL_18284891|2023-09-07;Yunnan/YNCDC-3103/2023|EPI_ISL_18454372|2023-10-13;Sichuan/CDCDC-19-CX3446/2023|EPI_ISL_18457460|2023-10-22andHubei/HCDC-WH3507/2023|EPI_ISL_18485337|2023-10-25EG.5.1.1 > A2483G(ORF1a:I740V) > T15996C, G22927C(S:L455F) [Query:A2483G, G13627A, G22927C, 4, 11/08], many withS:R158K/G22035AandS:E554K/G23222ASouth_Korea/KDCA267746/2023|EPI_ISL_18408949|2023-09-18;South_Korea/KDCA268248/2023|EPI_ISL_18411258|2023-09-19;South_Korea/KDCA269573/2023|EPI_ISL_18460793|2023-10-04; andSouth_Korea/KDCA269703/2023|EPI_ISL_18460915|2023-10-09EG.5.1.1 > C3695T > G22927T(S:L455F) [Query:C3695T, G13627A, G22927T, -T2959C, 4 seq, 11/03]France/COR-HCL-723001296701/2023|EPI_ISL_18387770|2023-09-25;France/NAQ-HCL723001378601/2023|EPI_ISL_18423405|2023-10-09;Austria/AGES-1141981/2023|EPI_ISL_18485506|2023-10-18andGermany/BY-MVP-000022265/2023|EPI_ISL_18525885|2023-10-30EG.5.1.3 > C6151T > G2468A(ORF1a:A735T), T22926G(S:L455W) [Query:C6151T, T22926G, 4 seqs, 11/21]Back to Tasklist
Quintuplets
Fujian/FCDC-QZ08S024/2023|EPI_ISL_18145964|2023-08-18;England/CLIMB-CM7YJZ4C/2023|EPI_ISL_18392773|2023-10-05;Yunnan/YNCDC-3090/2023|EPI_ISL_18454344|2023-10-12;Yunnan/YNCDC-3139/2023|EPI_ISL_18488099|2023-10-12;Singapore/R78MR69/2023|EPI_ISL_18444918|2023-10-25;South_Korea/KDCA273761/2023|EPI_ISL_18535687|2023-10-31andUSA/MN-MDH-37408/2023|EPI_ISL_18510684|2023-11-01EG.5.1.1 > C25578T > G22927T(S:L455F) [Query:C8320T, G22927T, C25578T, 5 seqs, 11/23]Back to Tasklist