Multiple EG.5* Lineages with S:A475V

[NkRMnZr]

### Multiple `EG.5.1*` Lineages with `S:A475V` or `S:A475S`
- [x] [Branch 1](#branch_1) Designated as **HK.3.14** after transferred to cov-lineages/pango-designation#2389, phylogenetic order follows: **HK.3** > C22986T(**S:A475V**) > T20600C(ORF1b:I2378T) [Query: `T20600C, G22927T, C22986T`]
- [ ] [Branch 2](#branch_2) Transferred to cov-lineages/pango-designation#2398 **EG.5.1.1** > C5812T > G22927T(**S:L455F**) > A26565C(**M:K15Q**), C28770G(**N:T166R**) > A10323G(ORF1a:K3353R), C22986T(**S:A475V**)
- [ ] [Branch 3](#branch_3) Transferred to cov-lineages/pango-designation#2456 **KB.2** > C25916T(ORF3a:T175I) > T10795A, C22986T(**S:A475V**) [Query: `C12100G, C14676A, C22986T`, 48 seqs, 01/12]
- [ ] [Branch 4](#branch_4) **JG.3** > G16975T(ORF1b:V1170F) > C4551T(ORF1a:T1429I), A17853G, C22986T(**S:A475V**) [Query: `C7086T, G16975T, C22986T`, 28 seqs, 02/10] many with `S:F157L`dead
- [ ] [Branch 5](#branch_5) **JG.3** > C22986T(**S:A475V**), A25756G(ORF3a:R122G) [Query: `C7086T, C22986T, A25756G`, 23 seqs, 02/10]quasi-dead
- [ ] [Branch 6](#branch_6) **HK.3** > C14889T > G10364A(ORF1a:V3367I), A23971G(S:S803S), A26392G(**E:S50G**) > C6026T(ORF1a:P1921S) > C18162T > G1265T(ORF1a:G334C), C5832T(ORF1a:S1856F), C22986T(**S:A475V**) [Query: `C6026T, C18162T, C22986T`, 12 seqs, 01/22] dead
- [ ] [Branch 7](#branch_7) **HK.3.2.2** > G8561A(ORF1a:V2766I), C29085T(**N:T271I**) > C22986T(**S:A475V**) [Query: `C4543T, G8561A, C22986T`, 13 seqs, 01/22] with credit to @aviczhl2 dead
- [ ] [Branch 8](#branch_8) **HK.3** > C14889T > C22986T(**S:A475V**) [Query: `G13627A, C14889T, C22986T, -G10364A`, 26 seqs, 01/22] ⚠ Please check if Branch 6 is part of this
- [ ] [Branch 9](#branch_9) **HK.3** > C7504T > C21370A(ORF1b:Q2635K) > C3876T(ORF1a:A1204V) > C4084T > C5167T, G8612A(ORF1a:V2783I), C22986T(**S:A475V**), C26885T [Query: `C3876T, C4084T, C22986T`, 52 seqs, 02/10]
- [ ] [Branch 10](#branch_10) **HK.3** > C8320T > C13019T > A25492G(ORF3a:T34A) > G29204A(**N:A311T**) > G6532T(ORF1a:E2089D), C22986T(**S:A475V**) [Query: `C13019T, C22986T, A25492G`, 6 seq, 01/22] dead
- [ ] #965 proposed by @aviczhl2 **HK.3.4 (EG.5.1.1.3.4)** > T20322C, T27451C(ORF7a:Y20H) > T28088C > ORF1a:Δ141-143(Δ686-694), C22986T(**S:A475V**) [Query: `C1284T, T13324C, C22986T`, 8 seqs, 10/27]dead
- [x] Designated **HK.26.1** from cov-lineages/pango-designation#2343 proposed by @krosa1910 , **HK.3 (EG.5.1.1.3)** > C25546A(ORF3a:L52I) > T14988C > C22986T(**S:A475V**) [Query: `T14988C, C22986T, C25546A, -G26199T`]
- [ ] proposed #1071 from former doublet: HK.27.1> G22985T(**S:A475S**) [Query: `C5031T, G22927T, G22985T`, 6, 11/08] dead

• Singlets, Doublets, Triplets, Quadruplets and Quintuplets; Query for all EG.5* with S:A475X minus designated ones: spike_A475, C9693T, T22930A, -T4427C, -C17747A, -T20600C, 353 seqs, 01/12]

Clusters

Branch 1:

Designated as HK.3.14

Designates as **HK.3.14** via cov-lineages/pango-designation@28b294f , after Transferred to cov-lineages/pango-designation#2389 **Defining Mutations:** `HK.3` > `C22986T(S:A475V)` > `T20600C(ORF1b:I2378T)` **Query:** `T20600C, G22927T, C22986T` **Earliest seq:** 2023-10-27 (`EPI_ISL_18473305`, Singapore, travel history: Australia; _OR_ `EPI_ISL_18466748`, England, UK) **Latest seq:** 2023-11-17 (`EPI_ISL_18542832`, Trieste, Italy) **Sampled Countries:** UK (8: EN), Australia (3: NSW; QLD; VIC), Italy (1), Singapore (1: ex. Australia)

Genomes:

`EPI_ISL_18466748, EPI_ISL_18473305, EPI_ISL_18497108, EPI_ISL_18497147, EPI_ISL_18499663, EPI_ISL_18499738, EPI_ISL_18499758, EPI_ISL_18513959, EPI_ISL_18521358, EPI_ISL_18524613, EPI_ISL_18525460, EPI_ISL_18542832`

**UShER:** https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2fdff_3f2eb0.json?label=id:node_3538721 

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Branch 2: Sub-lineage to Branch 28 of #537

Transferred to main repo

_Transferred to cov-lineages/pango-designation#2398_ **Defining Mutations:** `EG.5.1.1` > `C5812T` > `G22927T(S:L455F)` > `A26565C(M:K15Q), C28770G(N:T166R)` > `A10323G(ORF1a:K3353R), C22986T(S:A475V)` **Query:** `C5812T, C22986T, A26565C` **Earliest seq:** 2023-09-20 (`EPI_ISL_18382304`, South Korea) **Latest seq:** 2023-10-11 (`EPI_ISL_18503952`, South Korea) **Sampled Countries:** South Korea (5), USA (2: ex. South Korea)

Genomes:

`EPI_ISL_18368528, EPI_ISL_18382304, EPI_ISL_18386641, EPI_ISL_18438964, EPI_ISL_18501908, EPI_ISL_18503952, EPI_ISL_18503974`

**UShER:** https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b1c8_bb3ee0.json?f_userOrOld=uploaded%20sample&label=id:node_3497629 

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Branch 3:

Transferred to main repo

_Transferred to cov-lineages/pango-designation#2456_ **Defining Mutations:** `KB.2 (EG.5.1.8.2)` > `C25916T(ORF3a:T175I)` > `T10795A, C22986T(S:A475V)` **Query:** `C12100G, C14676A, C22986T` **Earliest seq:** 2023-09-29 (`EPI_ISL_18488866`, South Korea) **Latest seq:** 2023-12-25 (`EPI_ISL_18705835`, South Australia, Australia) **Sampled Countries:** **South Korea** (36), **Australia** (6: NSW/5; SA), **Japan** (4), **USA** (2: AZ; IL)

Genomes:

`EPI_ISL_18430654, EPI_ISL_18439024, EPI_ISL_18488866, EPI_ISL_18503877, EPI_ISL_18503932, EPI_ISL_18513973, EPI_ISL_18539777, EPI_ISL_18566615, EPI_ISL_18577217, EPI_ISL_18597062, EPI_ISL_18597066, EPI_ISL_18597121, EPI_ISL_18597285, EPI_ISL_18597370, EPI_ISL_18633505, EPI_ISL_18639272, EPI_ISL_18639338, EPI_ISL_18639341-18639342, EPI_ISL_18683380, EPI_ISL_18686668, EPI_ISL_18686673, EPI_ISL_18686675, EPI_ISL_18686687, EPI_ISL_18686694, EPI_ISL_18686702, EPI_ISL_18686706-18686708, EPI_ISL_18686712, EPI_ISL_18686736, EPI_ISL_18686739, EPI_ISL_18686754, EPI_ISL_18705835, EPI_ISL_18709158, EPI_ISL_18712264, EPI_ISL_18712277, EPI_ISL_18712287, EPI_ISL_18712294, EPI_ISL_18712303, EPI_ISL_18712315, EPI_ISL_18725256, EPI_ISL_18725258, EPI_ISL_18732906, EPI_ISL_18740673, EPI_ISL_18740700, EPI_ISL_18751891, EPI_ISL_18751911`

**UShER:** https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1a7e2_3af540.json?f_userOrOld=uploaded%20sample&label=id:node_3446691 

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Branch 4: many with S:F157L

Defining Mutations: JG.3 > G16975T(ORF1b:V1170F) > C4551T(ORF1a:T1429I), A17853G, C22986T(S:A475V) Query: C7086T, G16975T, C22986T Earliest seq: 2023-10-09 (EPI_ISL_18423301, Auvergne-Rhône-Alpes) Latest seq: 2023-11-19 (EPI_ISL_18536520, Auvergne-Rhône-Alpes) Sampled Countries: France (6: ARA)

Genomes:

`EPI_ISL_18423301, EPI_ISL_18468951, EPI_ISL_18536505, EPI_ISL_18536519-18536520, EPI_ISL_18537708`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice3_genome_8473_3e8220.json?label=id:node_3554460

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Branch 5

Defining Mutations: JG.3 > C22986T(S:A475V), A25756G(ORF3a:R122G) Query: C7086T, C22986T, A25756G Earliest seq: 2023-11-06 (EPI_ISL_18522345, Saint-Dizier, France) Latest seq: 2023-11-21 (EPI_ISL_18572408, Dublin, Ireland) Sampled Countries: France (6), Ireland (1)

Genomes:

`EPI_ISL_18522345-18522346, EPI_ISL_18545041, EPI_ISL_18553418, EPI_ISL_18553594-18553595, EPI_ISL_18572408`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_410f2_c68190.json?label=id:node_3574549

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Branch 6

Defining Mutations: HK.3 > C14889T > G10364A(ORF1a:V3367I), A23971G(S:S803S), A26392G(E:S50G) > C6026T(ORF1a:P1921S) > C18162T > G1265T(ORF1a:G334C), C5832T(ORF1a:S1856F), C22986T(S:A475V) Query: C6026T, C18162T, C22986T Earliest seq: 2023-11-04 (EPI_ISL_18529679, New York) Latest seq: 2023-12-08 (EPI_ISL_18643089, New York) Sampled Countries: USA (8: NY)

Genomes:

`EPI_ISL_18529679, EPI_ISL_18575335, EPI_ISL_18575363, EPI_ISL_18602259, EPI_ISL_18643066, EPI_ISL_18643089, EPI_ISL_18643128, EPI_ISL_18644936`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_13cb9_3e6520.json?label=id:node_3492568

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Branch 7

with credit to @aviczhl2

Defining Mutations: HK.3.2.2 > G8561A(ORF1a:V2766I), C29085T(N:T271I) > C22986T(S:A475V) Query: C4543T, G8561A, C22986T Earliest seq: 2023-11-08 (EPI_ISL_18593060, Honolulu, USA) Latest seq: 2023-12-02 (EPI_ISL_18654623, British Columbia, Canada) Sampled Countries: USA (3: UT/2; HI), Japan (2), Canada (1: BC)

Genomes:

`EPI_ISL_18588818, EPI_ISL_18593060, EPI_ISL_18622632, EPI_ISL_18642509, EPI_ISL_18646853, EPI_ISL_18654623`

UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3a01a_3ea1c0.json?label=id:node_3490386

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Branch 8

⚠ Please check if Branch 6 is part of this

Defining Mutations: HK.3 > C14889T > C22986T(S:A475V) Query: G13627A, C14889T, C22986T, -G10364A Earliest seq: 2023-10-25 (EPI_ISL_18495954, Tokyo, Japan) Latest seq: 2023-12-27 (EPI_ISL_18737413, Cork, Ireland) Sampled Countries: Japan (7), Denmark (3), Germany (2), Austria (1), Ireland (1), Netherlands (1), USA (1)

Genomes:

`EPI_ISL_18495954, EPI_ISL_18588819, EPI_ISL_18617736, EPI_ISL_18651478, EPI_ISL_18687819, EPI_ISL_18693369, EPI_ISL_18695263, EPI_ISL_18695284, EPI_ISL_18701998, EPI_ISL_18704077, EPI_ISL_18704634, EPI_ISL_18720939, EPI_ISL_18728552, EPI_ISL_18737413, EPI_ISL_18740808, EPI_ISL_18740824`

UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_41a04_3b43d0.json?label=id:node_3530757

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Branch 9

Defining Mutations: HK.3 > C7504T > C21370A(ORF1b:Q2635K) > C3876T(ORF1a:A1204V) > C4084T > C5167T, G8612A(ORF1a:V2783I), C22986T(S:A475V), C26885T Query: C3876T, C4084T, C22986T Earliest seq: 2023-10-16 (EPI_ISL_18511454, South Korea) Latest seq: 2023-12-30 (EPI_ISL_18751690, S. Korea) Sampled Countries: South Korea (32)

Genomes:

`EPI_ISL_18511454, EPI_ISL_18539467, EPI_ISL_18564762-18564763, EPI_ISL_18597351, EPI_ISL_18686801, EPI_ISL_18686803-18686804, EPI_ISL_18686806, EPI_ISL_18687490, EPI_ISL_18687534, EPI_ISL_18687585, EPI_ISL_18706584, EPI_ISL_18711542-18711549, EPI_ISL_18711565, EPI_ISL_18711873-18711874, EPI_ISL_18712013, EPI_ISL_18732965, EPI_ISL_18733695, EPI_ISL_18751678, EPI_ISL_18751680, EPI_ISL_18751685, EPI_ISL_18751690, EPI_ISL_18752148`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_31ff0_3b7830.json?label=id:node_3522273

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Branch 10

Defining Mutations: HK.3 > C8320T > C13019T > A25492G(ORF3a:T34A) > G29204A(N:A311T) > G6532T(ORF1a:E2089D), C22986T(S:A475V) Query: C13019T, C22986T, A25492G Earliest seq: 2023-11-09 (EPI_ISL_18703071, California) Latest seq: 2023-11-29 (EPI_ISL_18739525, California) Sampled Countries: USA (6: CA)

Genomes:

`EPI_ISL_18670399, EPI_ISL_18703071, EPI_ISL_18703283, EPI_ISL_18703314, EPI_ISL_18703523, EPI_ISL_18739525`

UShER: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice6_genome_test_597bc_3a8020.json?label=id:node_3526232

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Incidents

Singlets

• USA/OH-ODH-SC3033244/2023|EPI_ISL_18507063|2023-10-30 (Sub-lineage to Branch 20 of #537) EG.5.1.1 > C2644T > G22927T(S:L455F) > T7957C, G29348T(N:A359S) > C3244T > G12131A(ORF1a:A3956T) > C16376T(ORF1b:P970L), A28295G(N:N8D) > C22986T(S:A475V) [Query: T7957C, C16376T, C22986T, 11/15]

• Yunnan/YNCDC-3127/2023|EPI_ISL_18454383|2023-10-08 (Sub-lineage to Branch 79 of #537) EG.5.1.1 > T6736C > T23287C(S:A575A) > C22075T(S:V171V) > C8389T, A16668G, C17474T(ORF1b:T1336I), G22927T(S:L455F), G26416T(E:V58F) > G21255C, G21604C(S:Q14H) > C22986T(S:A475V), G28655T(N:D128Y) [Query: T6736C, A16668G, C22986T, 10/31]

• Japan/PG-575437/2023|EPI_ISL_18377931|2023-09-22 (Sub-lineage to Branch 17 of #537) EG.5.1.1 > C9118T > G16813T(ORF1b:V1116L), G22927T(S:L455F) > C100T, C2855T(ORF1a:L864F), C22986T(S:A475V), C23709T(S:T716I) [Query: C9118T, G16813T, C22986T, 10/12]

• Canada/ON-PHL-23-48290/2023|EPI_ISL_18697280|2023-12-13 (Sub-lineage to Branch 2 of #537) EG.5.1.1 > C12053T(ORF1a:L3930F) > C503T(ORF1a:P80S), A8116G > C18175T(ORF1b:P1570S), G22927T(S:L455F) > C7732T > G6337A > T6580C, T7192C, G11335T, G13897T(ORF1b:D144Y), C18912T, C22986T(S:A475V), C29466T(N:A398V) [Query: G6337A, C7732T, C22986T, 12/27]

• USA/WA-S24198/2023|EPI_ISL_18615733|2023-10-17 (Sub-lineage to Branch 2 of #537) EG.5.1.1 > C12053T(ORF1a:L3930F) > C503T(ORF1a:P80S), A8116G > C18175T(ORF1b:P1570S), G22927T(S:L455F) > C7732T > G27962A > T26310C > T27713C(ORF7a:I107T) > A24742G(S:V1060V) > C17339T(ORF1b:A1291V) > G4205A(ORF1a:A1314T), T17424C, T18689C(ORF1b:F1741S), C22986T(S:A475V) [Query: C7732T, C17339T, C22986T, 12/12]

• Japan/PG-556842/2023|EPI_ISL_18434659|2023-08-07 potentially Molnupiravir/Favipiravir driven saltation EG.5.1.1 > A21137G(ORF1b:K2557R) > A5269G, T5393C(ORF1a:F1710L), A9121G, A23416T(S:T618T) > C20016T > C11750T(ORF1a:L3829F) > C629T(ORF1a:L122F), G1156A(ORF1a:M297I), T1602C(ORF1a:L446P), A2285G(ORF1a:S674G), G2424A(ORF1a:C720Y), A3082G, C3874T, G7553A(ORF1a:V2430I), G7925A(ORF1a:A2554T), G8612A(ORF1a:V2783I), C9223T, C9510T(ORF1a:T3082I), C12120T(ORF1a:P3952L), G12163A, G13471A(ORF1b:V2I), T18168C, T19278C, C20077T(ORF1b:P2204S), A20093G(ORF1b:K2209R), G20477A(ORF1b:G2337D), G20626A(ORF1b:G2387S), C22986T(S:A475V), C24771T(S:A1070V), G25217A(S:G1219S), G26505A, T27266C(ORF6:F22S), C27513T, G29692A [Query: T5393C, C11750T, C22986T, 10/25]

• Italy/LOM_ASSTMonza_6000305097_20231027112700/2023|EPI_ISL_18506678|2023-10-27 EG.5.1.1 > T26609C > T20407C(ORF1b:F2314L) > T27401C(ORF7a:I3T) > A349C, T18947C(ORF1b:L1827P), C20719T, C22986T(S:A475V) [Query: T20407C, C22986T, T27401C, 11/15]

• Shanghai/SCDC-XG10-14336/2023|EPI_ISL_18438504|2023-09-26 HK.3 (EG.5.1.1.3) > T4888C > C2434T > G1820A(ORF1a:G519S), C2485T, T15030C, C22986T(S:A475V), C27213T [Query: C2434T, T4888C, C22986T, 10/26]

• Finland/THL-07356/2023|EPI_ISL_18347834|2023-09-24 HK.3 > T4888C > T15176C(ORF1b:I570T) > C22986T(S:A475V) [Query: T4888C, T15176C, C22986T, 10/05]

• Xinjiang/XJCDCTC-217/2023|EPI_ISL_18659017|2023-11-12 HK.3 > C8320T > C21602A(S:Q14K) > C9598T, G22985T(S:A475S), C29095T [Query: C8320T, G13627A, G22985T, 12/19]

• Spain/MD-HRYC-12935260/2023|EPI_ISL_18489776|2023-10-23 HK.3 > C10369T > C25728T > C10615T > G3562A, C3653T(ORF1a:L1130F), C22986T(S:A475V) [Query: C10615T, C22986T, C25728T, 11/10]

• USA/CA-HLX-STM-TZHZAXZNB/2023|EPI_ISL_18394572|2023-09-22 HK.3 > C10834T > G23624A(S:A688T) > C3510T(ORF1a:A1082V), C12318T(ORF1a:S4018F), C18929T(ORF1b:P1821L), C22986T(S:A475V), T28245G(ORF8:L118V), G29781T [Query: C10834T, C22986T, G23624A, 10/16]

• Anhui/BZCDC-167/2023|EPI_ISL_18409200|2023-09-01 HK.3 > C11775T(ORF1a:A3837V), T20061C > C3130T, C9051T(ORF1a:P2929L), C11195T(ORF1a:L3644F), T11677C, T12436G, C22986T(S:A475V), G29465T(N:A398S) [Query: C11775T, T20061C, C22986T, 10/19]

• Gansu/GSCDC-0796/2023|EPI_ISL_18683160|2023-11-14 HK.3 > C13944T > C12781T > C6388T, C22986T(S:A475V) [Query: C12781T, C13944T, C22986T, 12/24]

• New_Zealand/23YA6751/2023|EPI_ISL_18561642|2023-11-15 HK.3 > T14832C > C884G(ORF1a:R207G), A5971G, G18318T > C3165T(ORF1a:A967V), C18570T > C4084T, C22986T(S:A475V) [Query: A5971G, C18570T, C22986T, 11/30]

• USA/CA-HLX-STM-Z77AK2MSK/2023|EPI_ISL_18446601|2023-10-18 HK.3 > C25546A(ORF3a:L52I) > T14988C > G26199T > G25217T(S:G1219C) > C2397T(ORF1a:T711M) > C22986T(S:A475V) [Query: C2397T, T14988C, C22986T, 10/30]

• South_Korea/KDCA272649/2023|EPI_ISL_18535555|2023-10-15 HK.3 > C27889T > C11008T > C22986T(S:A475V) [Query: C11008T, C22986T, C27889T, 11/23]

• USA/NJ-CDC-QDX90145450/2023|EPI_ISL_18692005|2023-12-11 HK.3.1 > C19017T > C20133T > C26681T > T1683C(ORF1a:I473T) > G9190T > T24490C(S:V976V) > T17343C, C22986T(S:A475V) [Query: T1683C, G9190T, C22986T, 12/26]

• Australia/NSW-ICPMR-50115/2023|EPI_ISL_18461744|2023-10-09 HK.3.1 > A29700G > C10776T(ORF1a:P3504L), C13384T > T20046C > C2902T, C22986T(S:A475V) [Query: C10776T, T20046C, C22986T, 11/03]

• Liaoning/LNCDC-419-2/2023|EPI_ISL_18518307|2023-10-24 HK.3.2 > C10039T > C29555T > C23638T(S:I692I) > T1270C, A4233C(ORF1a:D1323A), C5512T, T5752C, C7267T, A20400G, C22986T(S:A475V), C23589T(S:T676I), G26167T(ORF3a:V259L), C28818A(N:A182D), A29316C(N:D348A) [Query: C10039T, C22986T, C23638T, 11/17]

• Shanghai/SCDC-XG10-14704/2023|EPI_ISL_18475155|2023-10-11 HK.3.2 > T16038C > C100T, A4547G(ORF1a:K1428E), C8499T(ORF1a:A2745V), C21742G(S:S60), C22986T(S:A475V), G24603C(S:R1014), C28531T(ORF9b:T83I) [Query: C853T, T16038C, C22986T, 11/07]

• Yunnan/YNCDC-3516/2023|EPI_ISL_18672370|2023-11-30 HK.3.2 > C22591T(S:N343N) > G22113C(S:G184A) > C25047T(S:P1162L) > C18946T, G21422A(ORF1b:R2652K) > G2588A(ORF1a:E775K), G5230T(ORF1a:K1655N), A12820G, C16830T, C18508T(ORF1b:L1681F) > C22986T(S:A475V) [Query: G5230T, C18946T, C22986T, 12/21]

• Heilongjiang/HLJCDC-2447/2023|EPI_ISL_18465057|2023-10-04 HK.12 > C15656T(ORF1b:T730I) > G7223T(ORF1a:A2320S) > C15960T, C22986T(S:A475V), C25810T(ORF3a:L140F) [Query: G7223T, C15656T, C22986T, 11/03]

• Liaoning/LNCDC-373-1/2023|EPI_ISL_18388957|2023-09-21 HK.13 > C3096T(ORF1a:S944L) > C13620T, C23248T(S:F562) > C22986T(S:A475V) [Query: C3096T, C13620T, C22986T, 10/13]

• Singapore/R77MR192/2023|EPI_ISL_18444965|2023-10-21 HK.13.1 > G17079A > C28948T > G2468T(ORF1a:A735S) > C22986T(S:A475V) [Query: G2468T, G17079A, C22986T, 10/30], thanks to @FedeGueli

• New_Zealand/23ZA6517/2023|EPI_ISL_18671577|2023-11-23 JG.3 > C186T > C21812A(S:L84I) > A1807C, T6637G, A10042G, C22986T(S:A475V) [Query: C186T, C21812A, C22986T, 12/22]

• Colombia/DC-INS-VG-31192/2023|EPI_ISL_18721228|2023-11-21 JG.3 > T1579A > A23919G(S:K786R) > T2587C, T14191C > C2023T, A26086T(ORF3a:I232F) > C723T(ORF1a:P153L), C22986T(S:A475V) [Query: C2023T, T14191C, C22986T, 01/04]

• USA/IA-SHL-2376797/2023|EPI_ISL_18683008|2023-12-10 JG.3 > C5365T > C15720T > C22995G(S:T478R), G26350A(E:A36T), G28044T(ORF8:A51S) > _G670T_rev(ORF1a:R135Srev), C22986T(S:A475V) [Query: C5365T, C15720T, C22986T, 12/24]

• Japan/PG-587118/2023|EPI_ISL_18740639|2023-12-13 JG.3 > G6671A(ORF1a:D2136N) > C2878T, C28310T(N:P13F) > C27970T(ORF8:T26I) > T19584C > G10517A(ORF1a:D3418N), C22986T(S:A475V), C25499A(ORF3a:P36Q), C27630T, G29100A(N:R276K) [Query: C2878T, T19584C, C22986T, 01/10]

• USA/FL-CDC-QDX84838519/2023|EPI_ISL_18307973|2023-09-06 JG.3 > T8826C(ORF1a:I2854T) > G1820A(ORF1a:G519S) > C22986T(S:A475V), A23899C(S:Q779H), C27371T(ORF6:P57L) [Query: G1820A, T8826C, C22986T, 09/26]

• USA/MN-MDH-37954/2023|EPI_ISL_18609676|2023-11-17 JG.3 > G16975T(ORF1b:V1170F) > C17802T > T20331C > G23222C(S:E554Q) > C6286A, C24865T, T25754C(ORF3a:V121A), C29095T > C22986T(S:A475V) [Query: C6286A, C17802T, C22986T, 12/11]

• France/ARA-HCL023191380602/2023|EPI_ISL_18675985|2023-12-04 JG.3 > G23593T(S:Q677H) > A19815G > A16180C, C22986T(S:A475V) [Query: A16180C, A19815G, G23593T, 12/22]

• Canada/ON-PHL-23-45499/2023|EPI_ISL_18610683|2023-11-27 JG.3 > C26256T > C12115T, A22910G(S:N450D) [potentially a JG.3.2 dropout/misplaced branch] > C22986T(S:A475V), C25714T(ORF3a:L108F) [Query: C7086T, C12115T, C22986T, 12/11]

• USA/MN-CDC-VSX-A17688/2023|EPI_ISL_18713964|2023-12-10 JG.3.2 > G10334A(ORF1a:A3357T), C10894T > C22986T(S:A475V) [Query: G10334A, C10894T, C22986T, 01/03]

• Canada/AB-ABPHL-108267/2023|EPI_ISL_18538862|2023-11-12 (Sub-lineage to Branch 35 of #537) EG.5.1.4 > C26111T(ORF3:P240L) > C18555T > T17268C > G22927T(S:L455F) > C3096T(ORF1a:S944L) > T25711C(ORF3a:Y107H) > A18579T(ORF1b:R1704S), C22986T(S:A475V) [Query: T17268C, C3096T, C22986T, 11/23]

• USA/CA-HLX-STM-X9JSAT994/2023|EPI_ISL_18407938|2023-10-02 HV.1 (EG.5.1.6.1) > C12513T(ORF1a:T4083M) > T2058C(ORF1a:M598T) > G11966A, G22985T(S:A475S), C28435T(ORF9b:P51L) [Query: T2058C, C12513T, G22985T, 10/19]

• Denmark/DCGC-669423/2023|EPI_ISL_18741120|2023-12-04 EG.5.1.8 > C12100G > C29347T > A12091G > C2306T(ORF1a:L681F) > T23308A(S:L582L) > A11167G > C4456T, C5140T, C22986T(S:A475V) [Query: C2306T, A11167G, C22986T, 01/10]

• England/CLIMB-CM7YR5A8/2023|EPI_ISL_18717869|2023-12-23 KB.1 (EG.5.1.8.1) > A26945G > A25439G(ORF3a:K16R) > A6442G > C7267T > C22564T(S:N334N) > C2485T, A4091G(ORF1a:I1276V), C5849T(ORF1a:P1862S), C18814T, C22986T(S:A475V) [Query: A6442G, C7267T, C22986T, 01/04]

• Spain/CT-HUB08881/2023|EPI_ISL_18653994|2023-11-18 EG.5.1.19 > C745T, C18981T > C22594T(S:A344A) > T7106C(ORF1a:Y2281H) > C20132T(ORF1b:A2222V), G22985A(S:A475T) [Query: T7106C, G22985A, 12/19]

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Doublets

• Italy/VEN-ULSS3GEN-7002638749_VE/2023|EPI_ISL_18449360|2023-10-16 and Denmark/DCGC-666338/2023|EPI_ISL_18634682|2023-12-04, the latter with extra S:L455F EG.5.1.1 > C1875T(ORF1a:A537V), T11186C > C22986T(S:A475V) [Query: C1875T, T11186C, C22986T, 2 seqs, 12/15]

• Sichuan/NCCDC-NC89/2023|EPI_ISL_18246339|2023-08-23 and Sichuan/LZCDC-XG151/2023|EPI_ISL_18261473|2023-08-25 HK.3 (EG.5.1.1.3) > G2971A(ORF1a:M902I) > A22069T(S:E169D) > C22986T(S:A475V) [Query: G2971A, G13627A, A22069T, C22986T, 2 seqs, 09/14] dead

• Italy/VEN-AOUIVR-7341832501_VR/2023|EPI_ISL_18675267|2023-12-11 and Italy/VEN-AOUIVR-7342782201_VR/2023|EPI_ISL_18722075|2023-12-22 HK.3 > T5653C > C17274T, C26807T > G6816A(ORF1a:R2184K), C22986T(S:A475V), C28377A(N:A35E) [Query: T5653C, C17274T, C22986T, 2 seqs, 01/05]

• Sichuan/ZGCDC-zgxg378/2023|EPI_ISL_18246376|2023-08-28 and Taiwan/CDC-F89511/2023|EPI_ISL_18520827|2023-11-02 HK.3 > C12415T > C17397A > C22986T(S:A475V), C23802T(S:T747I) [Query: C12415T, C17397A, C22986T, 3 seqs, 02/10] dead

• USA/CA-HLX-STM-HXJ2W6UKA/2023|EPI_ISL_18497875|2023-10-25 and USA/NY-CDC-QDX87285009/2023|EPI_ISL_18528703|2023-11-02 HK.3 > C25924T(ORF3a:P178S) > T568C, T9982C > C18032T > G21853T(S:K97N), C22986T(S:A475V), G23345A(S:V595I) [Query: T568C, C18032T, C22986T, 2 seqs, 11/21]

• Singapore/R85MR8/2023|EPI_ISL_18544526|2023-11-15 and Singapore/R85MR135/2023|EPI_ISL_18544497|2023-11-16 HK.3.2 > C10039T > C29555T > T13890C > C22986T(S:A475V) [Query: C10039T, T13890C, C22986T, 3 seqs, 02/10]

• Netherlands/NB-MVD-2300610/2023|EPI_ISL_18520180|2023-11-08 and Netherlands/NB-MVD-2300665/2023|EPI_ISL_18544331|2023-11-19 HK.8 > C337T, T838C, C3117T(ORF1a:T951I), C22986T(S:A475V), C23679T(S:A706V), G26257A(E:V5I), C29200T [Query: C6541T, C11779T, C22986T, 2 seqs, 11/27]dead

• Italy/LOM_Unimi-4521-23/2023|EPI_ISL_18622371|2023-11-26 and Italy/UMB-LAOP-146-2-22/2023|EPI_ISL_18702730|2023-12-23 HK.26 > G27798T(ORF7a:A15S) > C10369T > C2143T > C10252T > C22986T(S:A475V) [Query: C2143T, C10252T, C22986T, 2 seqs, 12/29] dead

• Finland/THL-10280/2023|EPI_ISL_18713151|2023-12-05 and Finland/THL-10368/2023|EPI_ISL_18713229|2023-12-12 EG.5.1.8 > C12100G > T27322C(ORF6:S41P), T28177G(ORF8:L95W) > A22453T(S:S297S) > C2788T, A6438G(ORF1a:Q2058R), T6673C, C22986T(S:A475V) [Query: C12100G, C22986T, T27322C, 2 seqs, 01/03] dead

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Triplets

• New_Zealand/23YA6445/2023|EPI_ISL_18562037|2023-11-10; New_Zealand/23YA6442/2023|EPI_ISL_18562034|2023-11-12 and New_Zealand/23ZA6129/2023|EPI_ISL_18561887|2023-11-16 HK.1.2 > C11704T > C26192T(ORF3a:P267L) > C22986T(S:A475V) [Query: C11704T, C22986T, C26192T, 3 seqs, 11/30]dead

• France/CVL-ChuTo-9800121129/2023|EPI_ISL_18536835|2023-10-19; France/BRE-IPP28732/2023|EPI_ISL_18598709|2023-11-15 and Ireland/D-NVRL-GIRL00109770/2023|EPI_ISL_18755907|2023-12-14 JG.1 (EG.5.1.3.1) > A5538G(ORF1a:Q1758R), C6558T(ORF1a:A2098V) > G23915A(S:V785I), C25976A(ORF3a:S195Y) > A7580G(ORF1a:N2439D), T10423A, C22986T(S:A475V) [Query: A5538G, C6558T, C22986T, 3 seqs, 02/10]dead

• USA/NE-NM_L371122742/2023|EPI_ISL_18553710|2023-11-13; USA/IA-SHL-2368041/2023|EPI_ISL_18592009|2023-11-24 and USA/NE-NM_L372005469/2023|EPI_ISL_18642576|2023-12-01 JG.3.1 > T14418C > A19403G(ORF1b:H1979R) > C22986T(S:A475V) [Query: T14418C, A19403G, C22986T, 5 seqs, 02/10]dead

• 928 proposed by @aviczhl2 , JJ.1 (EG.5.1.4.1) > C25624T(ORF3a:H78Y) > A4079C(ORF1a:S1272R) > C5031T(ORF1a:T1589I), G21019A(ORF1b:A2518T) > C22986T(S:A475V) [Query: A4079C, C5031T, C22986T, 3 seqs, 10/13] dead

• CA-HLX-STM-55KMU22WT/2023|EPI_ISL_18614714|2023-11-19; USA/CA-HLX-STM-ZRYFRVWTW/2023|EPI_ISL_18663259|2023-11-19 and USA/CA-HLX-STM-W6SJ6RJUV/2023|EPI_ISL_18663290|2023-11-20 HV.1 > A23539T(S:S659S) > C5407T, C27707T(ORF7a:A105V) > C22986T(S:A475V) [Query: C5407T, C22986T, C27707T, 3 seqs, 12/20] dead

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Quadruplets

• South_Korea/KDCA273263/2023|EPI_ISL_18539819|2023-10-30; South_Korea/KDCA276600/2023|EPI_ISL_18639734|2023-11-15; South_Korea/KDCA277289/2023|EPI_ISL_18686776|2023-11-20 and South_Korea/KDCA277309/2023|EPI_ISL_18686794|2023-11-21 HK.33 > C27208T(ORF6:H3Y) > C20178T > T3741C(ORF1a:I1159T), C9565T, T20426C(ORF1b:I2320T), C22986T(S:A475V) [Query: C2644T, C20178T, C22986T, 4 seqs, 12/26] dead

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Quintuplets

• France/IDF-IPP27265/2023|EPI_ISL_18541069|2023-11-13; France/GES-IPP29084/2023|EPI_ISL_18618080|2023-11-27; France/GES-IPP29128/2023|EPI_ISL_18618122|2023-11-27; France/GES-IPP30006/2023|EPI_ISL_18653323|2023-12-04 and France/GES-IPP30007/2023|EPI_ISL_18653324|2023-12-04 (Sub-lineage to Branch 10 of #537) EG.5.1.1 > C11173T > G22927T(S:L455F) > C24418T(S:V952V) > G6482A(ORF1a:G2073R), A15936G, C22986T(S:A475V) [Query: C11173T, C22986T, C24418T, 6 seqs, 10/02] dead

• USA/AZ-CDC-QDX88030478/2023|EPI_ISL_18602209|2023-11-19; USA/AZ-CDC-LC1077822/2023|EPI_ISL_18715681|2023-12-12; USA/AZ-CDC-LC1077849/2023|EPI_ISL_18715816|2023-12-16; USA/AZ-CDC-LC1077852/2023|EPI_ISL_18715881|2023-12-18 and USA/AZ-ASPHL-00012/2023|EPI_ISL_18742606|2023-12-21 HK.3 (EG.5.1.1.3) > G2971A(ORF1a:M902I) > T25467A > T22196C(S:L212L), C22986T(S:A475V) [Query: G2971A, C22986T, T25467A, 5 seqs, 01/10]dead

• USA/CA-HLX-STM-E4NNM2W74/2023|EPI_ISL_18614863|2023-11-07; USA/CA-SBCPHL-GS00058/2023|EPI_ISL_18611843|2023-11-16; USA/CA-HLX-STM-BFZKE82FR/2023|EPI_ISL_18614904|2023-11-16; USA/CA-SBCPHL-GS00059/2023|EPI_ISL_18611844|2023-11-19 and USA/CA-SBCPHL-GS00079/2023|EPI_ISL_18611854|2023-11-30 HK.3 > C26781T(M:L87F) > A27947G > T14910C, C25047T(S:P1162L) > C22986T(S:A475V) > G9601A [Query: G9601A, T14910C, C22986T, 24 seqs, 02/10] Dead

• Australia/TAS006371/2023|EPI_ISL_18651574|2023-11-28; Australia/VIC-VIDRL-00012672/2023|EPI_ISL_18667300|2023-11-30; Australia/TAS006369/2023|EPI_ISL_18651559|2023-12-01; Australia/VIC-VIDRL-00012755/2023|EPI_ISL_18667227|2023-12-08 and Australia/VIC-VIDRL-00012758/2023|EPI_ISL_18667230|2023-12-08 HK.3.2 >A27669G > T8623C > C25339T(S:D1259D) > C29153A(N:Q294K) > A5599G, C6606T(ORF1a:S2114F), A19815G, G25599T(ORF3a:W69C), C28087T(ORF8:A65V) > C22986T(S:A475V) [Query: A5599G, A19815G, C22986T, 6 seqs, 02/10] dead

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---

Recombinant

• Spain/PV-HUD-70493145/2023|EPI_ISL_18419828|2023-10-16 EG.5.1.3 and JD.1.1 with S:G446T/G22899C recombinant that swapped EG.5's T22930A to JD.1's T22928C, query: C1889T, G22899C

---

Trivia:

• Thanks to @oobb45729 for great work tracking FLip + A475V (that should also get a pun, right?) this is mostly just taken from that issue.
• As of now A475V seems way less homoplastic than T470I or K356T on EG.5* backbone, but many seqs are recent, maybe worth tracking for a while.

[xz-keg]

Haha, you love challenging collections that have potential to become very very big.

The EG.5+475V is sure to be scales larger than GK+475V series.

[FedeGueli]

• SouthKorea/KDCA267387/2023|EPI_ISL_18382304|2023-09-20; USA/CA-GBW-H10-016-7718/2023|EPI_ISL_18368528|2023-10-01 and USA/CA-GBW-H20-333-8745/2023|EPI_ISL_18386641|2023-10-01 EG.5.1.1 > C5812T > G22927T(S:L455F) [Branch 28 of Multiple EG.5.1* Lineages with S:L455F #537] > A26565C(M:K15Q), C28770G(N:T166R) > A10323G(ORF1a:K3353R), C22986T(S:A475V) [Query: C5812T, C22986T, A26565C, 3, 10/13] This grew today to 4 again from S.Korea

[FedeGueli]

• USA/AZ-CDC-LC1065287/2023|EPI_ISL_18430654|2023-10-09 EG.5.1.8 > C12100G > C14676A > G22203A(S:R214H) > T10795A, C15952T, C22986T(S:A475V), C25916T(ORF3a:T175I), C29762T [Query: C12100G, C14676A, C22986T, 10/24]

this grew to 2 today from SK

[FedeGueli]

HK.13.1 Singlet from Singapore with 475V :

EPI_ISL_18444965 Query (putative):C22986T,G2468T,G17079A https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_34830_c5240.json

[FedeGueli]

Branch 1 went to 8, last one from Australia, (there is one more Australian sample but unsure if belongs to this one lacking the 20600 mutation) https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1b8f7_76cb40.json?label=id:node_3523234

[FedeGueli]

QUADRUPLET WENT TO 7 AND A TRIPLET WENT TO 6

[NkRMnZr]

Tracking updates

11-20, Adding branch 2 & 3 from former triplet or quadruplet 11-26, Branch 2, +5 (S. Korea) 12-02, Branch 4, +4; Adding Branch 5 12-15, Branch 3, +7 12-20, Adding Branch 6 and 7

[FedeGueli]

Branch 1 now went to 10 it seems fast.

[FedeGueli]

Please propose Branch 1 now it is likely very fast: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=JN.1*&nucMutations1=T20600C%2CG22927T%2CC22986T&analysisMode=CompareToBaseline&

[xz-keg]

Branch 5 designated HK.3.11

[xz-keg]

JG.3 > G16975T(ORF1b:V1170F) > C4551T(ORF1a:T1429I), A17853G, C22986T(S:A475V) [Query: C7086T, G16975T, C22986T, 2 seqs, 11/06]

This branch is 6 now and adds S:F157L

[NkRMnZr]

Branch 1 transferred to cov-lineages/pango-designation#2389 Branch 2, +5 (S. Korea) EPI_ISL_18535616, EPI_ISL_18535618, EPI_ISL_18535641, EPI_ISL_18535683, EPI_ISL_18539641

[FedeGueli]

Thank you great work as usual

[FedeGueli]

parental linegae of Branch 3 now designated KB.2 via https://github.com/cov-lineages/pango-designation/commit/682de0ec3675554f54a6aecad02d76b7b4edfa75

[NkRMnZr]

Branch 4, +4 (FR, IT, JP) EPI_ISL_18544031, EPI_ISL_18547106, EPI_ISL_18568612, EPI_ISL_18568625 Adding Branch 5 from former doublet

[FedeGueli]

please propose branch 4

[NkRMnZr]

12-15, Branch 3, +7 (Australia, Japan, South Korea) EPI_ISL_18577217, EPI_ISL_18597062, EPI_ISL_18597066, EPI_ISL_18597121, EPI_ISL_18597285, EPI_ISL_18597370, EPI_ISL_18633505

[xz-keg]

Japan/TKYnat15813/2023|EPI_ISL_18495954|2023-10-25; USA/NY-SUNYQB-X7119/2023|EPI_ISL_18529679|2023-11-04; USA/NY-SUNYQB-X7263/2023|EPI_ISL_18575363|2023-11-15 and USA/NY-SUNYQB-X7330/2023|EPI_ISL_18575335|2023-11-17 HK.3 > C14889T > C2106T(ORF1a:T614I), C2973T(ORF1a:A903V), C22986T(S:A475V) [Query: G13627A, C14889T, G22927T, C22986T, 4 seqs, 12/02]

This one is splitted into two separate branches. One USA branch with 8 seqs and a Japanese branch of 3.

[xz-keg]

There seems to be a new one under HK.3.2.2

[NkRMnZr]

12-20 Adding Branch 6 and 7 with credit to @aviczhl2

[FedeGueli]

Branch 3 reached 33 all from South Korea please propose it if it reaches 50 sequences in a short time.

[FedeGueli]

Branch 3 further up to 41 , please propose it.

[FedeGueli]

Branch 1 designated HK.3.14

[FedeGueli]

Branch 4 went to 27

[FedeGueli]

Branch 8 to 26, it should be checked if real or being part of B6

[xz-keg]

Branch 9 is 52 now

[FedeGueli]

@NkRMnZr pleae propose branch 9 that is circulating in Japan. i m closing this issue after updating, most of the lineages seem dead. there was a quintuplet now 24 but all from December.