Multiple BA.2.86* Lineages with S:A475X (5 branches)

[NkRMnZr]

### Multiple `BA.2.86*` Lineages with `S:A475V` or `S:A475S`
- [x] [Branch 1](#branch_1) Designated as **JN.10** via [cov-lineages/pango-designation@`0a75629`](https://github.com/cov-lineages/pango-designation/commit/0a75629f83ff54c756aa129e1aa74f18e01803d3) , phylogenetic order follows: **BA.2.86.1** > C12815T > T3565C > C22986T(**S:A475V**) [Query: `T3565C, C12815T, C22986T`]
- [x] [Branch 2](#branch_2) Designated as **JN.5.1** via [cov-lineages/pango-designation@`5186c33`](https://github.com/cov-lineages/pango-designation/commit/5186c33727df8117d3f3d75501bc0be4d348b0ea) , phylogenetic order follows: **JN.5 (N:T135I)** > C5806T > G4720A, G16416T > T2950A, G22985T(**S:A475S**), A28052G, C29541T [Query: `G4720A, G16416T, G22985T`] many with `S:S680F/C23601T`
- [ ] [Branch 3](#branch_3) **BA.2.86.1** [with C12815T] > A14397G > C22986T(**S:A475V**) [Query: A6183G, A14397G, C22986T, 46 seqs, 03/03] proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1386
- [ ] [Branch 4](#branch_4) **JN.2** > G22985T(**S:A475S**) [Query: `A2127G, C12815T, G22985T, -G16221T, -A27107T`, 17 seqs, 03/03]
- [x] Designated **JN.4** via [cov-lineages/pango-designation@`8c291c7`](https://github.com/cov-lineages/pango-designation/commit/8c291c77c2451fdbd2c0e9a3ff6ce38ea734c66c) , proposed as #1009 by @HynnSpylor , phylogenetic order follows: `BA.2.86.1 (pre-C12815T)` > `C22986T(S:A475V)` , query: `A6183G, C22986T, -C12815T`

• Singlets, Doublets, Triplets, Quadruplets and Quintuplets ; Query for all BA.2.86* with S:A475X minus most of already designated ones: spike_A475, A7842, C8293T, G8393A, -T2950A, -T3565C, -T3745C, -C5170T, -C6541T, -T10033C, -T10372C, -C13366T, 293 seqs, 01/12]

Branch 1

Designated as JN.10

Designated as **JN.10** via cov-lineages/pango-designation@0a75629 **Defining Mutations:** `BA.2.86.1` > `C12815T` > `T3565C` > `C22986T(S:A475V)` **Query:** `T3565C, C12815T, C22986T` **Earliest seq:** 2023-09-17 (`EPI_ISL_18311030`, `SEA` airport, with travel history to: Spain) **Latest seq:** 2023-09-30 (`EPI_ISL_18361497`, Galicia, Spain) **Sampled Countries:** Spain (3), USA (2: ex. Spain)

Genomes:

`EPI_ISL_18311029-18311030, EPI_ISL_18361497, EPI_ISL_18388492, EPI_ISL_18388567`

**UShER:** https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice111_genome_bf96_a5c5f0.json?label=id:node_4338909 

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---

Branch 2: Three sub-lineages follows S:S221L/C22224T , S:S680F/C23601T and S:E780Q/G23900C respectively

Designated as JN.5.1

Designated as **JN.5.1** via cov-lineages/pango-designation@5186c33 **Defining Mutations:** `JN.5` > `C5806T` > `G4720A, G16416T` > `T2950A, G22985T(S:A475S), A28052G, C29541T` **Query:** `G4720A, G16416T, G22985T` **Earliest seq:** 2023-10-19 (`EPI_ISL_18466912`, England, UK) **Latest seq:** 2023-11-06 (`EPI_ISL_18499740`, England, UK) **Sampled Countries:** UK (7: EN), Belgium (1)

Genomes:

`EPI_ISL_18450459, EPI_ISL_18466912, EPI_ISL_18492464, EPI_ISL_18499728, EPI_ISL_18499734, EPI_ISL_18499736, EPI_ISL_18499740, EPI_ISL_18499746`

**UShER:** https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2a3c6_379270.json?label=id:node_4432643 

---

Branch 3:

Defining Mutations: BA.2.86.1 [with C12815T] > A14397G > C22986T(S:A475V) Query: A6183G, A14397G, C22986T Earliest seq: 2023-10-28 (EPI_ISL_18473823, England, UK) **Latest seq:** 2023-12-19 ( EPI_ISL_18700444,Indonesia) Sampled Countries: UK (3: EN), USA (3: IL/2; DE), Malaysia (2), China (1: ex. Malaysia) Indonesia (1)

Genomes:

`EPI_ISL_18473823, EPI_ISL_18525476, EPI_ISL_18566205-18566206, EPI_ISL_18601884, EPI_ISL_18641580, EPI_ISL_18698127, EPI_ISL_18698131, EPI_ISL_18700444, EPI_ISL_18703833`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_189ee_4a0320.json?label=id:node_6827454

Branch 4:

Defining Mutations: JN.2 > G22985T(S:A475S) Query: A2127G, C12815T, G22985T, -G16221T, -A27107T Earliest seq: 2023-11-19 (EPI_ISL_18547191, Stockholm, Sweden) Latest seq: 2023-12-30 (EPI_ISL_18738130, Ontario, Canada) Sampled Countries: Sweden (5) Canada (3: ON/2; QC), China (1: ex. Canada)

Genomes:

`EPI_ISL_18547191, EPI_ISL_18582068, EPI_ISL_18642928, EPI_ISL_18642942, EPI_ISL_18703807, EPI_ISL_18738130, EPI_ISL_18741962, EPI_ISL_18754391, EPI_ISL_18754404`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_31dc6_4aafe0.json?label=id:node_6870660

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---

Singlets

• Sweden/M-SUS0022883/2023|EPI_ISL_18718382|2023-12-19 BA.2.86.1 [with C12815T] > C364T > C22993T(S:N477N) > C486T(ORF1a:S74L), A4372C, C9541T, C13536T, C21654T(S:S31F), C28102A(ORF8:P70H) > G20487T(ORF1b:K2340N), G22985T(S:A475S), C27476T(ORF7a:T28I) [Query: A4372C, C9541T, G22985T, 01/04] dead

• Netherlands/LI-RIVM-133791/2023|EPI_ISL_18612450|2023-11-20 BA.2.86.1 [with C12815T] > C1326T(ORF1a:A354V) > G22985T(S:A475S) [Query: C1326T, C12815T, G22985T, 12/12] dead

• Austria/AGES-1144169/2023|EPI_ISL_18704149|2023-12-13 BA.2.86.1 [with C12815T] > A3864C(ORF1a:E1200A), C5986T > T5614A, T14386G(ORF1b:L307V), C19983T, G22985T(S:A475S) [Query: A3864C, C5986T, G22985T, 12/30] dead

• Denmark/DCGC-669708/2023|EPI_ISL_18744560|2023-12-11 BA.2.86.1 [with C12815T] > C7528T > G24872T(S:V1104L) > A8456G(ORF1a:S2731G), G24193T(S:L877L) > G3471A(ORF1a:G1069E), C18109T(ORF1b:P1548S), A26019G, T27645C > G22985T(S:A475S) [Query: G3471A, C18109T, G22985T, 01/11] dead

• Ireland/KE-NVRL-GIRL00102673/2023|EPI_ISL_18635963|2023-11-22 BA.2.86.1 [with C12815T] > T11614C > C7086T(ORF1a:T2274I) > A9328G, C22986T(S:A475V), G25459T(ORF3a:A23S), G29513T(N:A414S) [Query: C7086T, T11614C, C22986T, 12/15] dead

• Canary_Islands/CHUIMI-021437123508/2023|EPI_ISL_18546329|2023-11-10 BA.2.86.1 [with C12815T] > T11614C > G29449T > A6521C(ORF1a:I2086L) > C22986T(S:A475V) [Query: A6521C, T11614C, C22986T, 3seqs 02/10] dead

• Austria/AGES-AZ-1670440/2023|EPI_ISL_18638439|2023-11-29 XBB.2.86.1 [with C12815T] > C15613T(ORF1b:H716Y) > C832T, G22985T(S:A475S) [Query: C12815T, C15613T, G22985T, 2seqs 02/10] dead

• Germany/MV-RKI-I-1141703/2023|EPI_ISL_18661607|2023-12-05 BA.2.86.1 [with C12815T] > T19260C, G22985T(S:A475S), G28116A(ORF8:D75N) [Query: C12815T, T19260C, G22985T, 12/20]dead

• England/CLIMB-CM7YGFKU/2023|EPI_ISL_18707988|2023-12-21 BA.2.86.1 [with C12815T] > C29445T(N:T391I) > C11681T, C22986T(S:A475V) [Query; C11681T, C12815T, C22986T, 15 02/10] dead

• Spain/MC-HCUVA-70091274/2023|EPI_ISL_18702353|2023-11-24 JN.2 > A27107T > C3317T(ORF1a:P1018S), C5956T > G22985T(S:A475S), T28688C [Query: C3317T, C5956T, G22985T, 2 seqs 12/29] dead

• Sweden/N-2A779331523/2023|EPI_ISL_18587536|2023-11-14 JN.2 > G28378T(ORF9b:R32L) > C3117T(ORF1a:T951I) > C20404T(ORF1b:P2313S), C22986T(S:A475V), C26789T [Query: A2127G, C3117T, C22986T, 12/05] dead

• France/PAC-HCL723001722701/2023|EPI_ISL_18677034|2023-12-02 JN.3 > C8991T(ORF1a:A2909V) > C3177T(ORF1a:P971L) > G22985T(S:A475S) [Query: C3177T, C8991T, G22985T, 12/22] dead

• Austria/AGES-1143115/2023|EPI_ISL_18596869|2023-11-24 JN.3 > C11575T > T27794C > G25455T(ORF3a:K21N) > C1102T, C22986T(S:A475V) [Query: C6525T, C11575T, C22986T, 12/08]dead

• France/HDF-IPP28021/2023|EPI_ISL_18577378|2023-11-20 JN.5 > A23566T(S:A688A) > C12897T(ORF1a:P4211L) > A8771G(ORF1a:T2836A), T17115C, G17790T(ORF1b:Q1441H), C26684T > S:I19T_reversion(rev_T21618C, A21619T) > A8206G, T9725C(ORF1a:Y3154H) > C22986T(S:A475V) [Query: A8206G, T9725C, C22986T, 12/04]dead

• Japan/PG-587453/2023|EPI_ISL_18744462|2023-12-11 JN.5 > A23566T(S:A688A) > C12897T(ORF1a:P4211L) > C11564T(ORF1a:P3767S), G28476C(N:R68P) > C22986T(S:A475V) [Query: C11564T, C12897T, C22986T, 2 seqs 01/11] dead

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Doublets

• USA/MD-MDH-9069/2023|EPI_ISL_18403841|2023-10-03 and USA/VA-VTVAS3-GSC44565/2023|EPI_ISL_18636777|2023-11-29 BA.2.86.1 [pre-C12815T] > C12733T, C27503T(ORF7a:S37F) > G2305T(ORF1a:K680N), C22978T(S:I472I), C27143T > C22986T(S:A475V) [Query: G2305T, C12733T, C22986T, 7 seqs, 02/10] dead

• Israel/SMC-7116374/2023|EPI_ISL_18706493|2023-12-18 JN.2 > G16221T > C11758A, C15738T, C22986T(S:A475V), C25460T(ORF3a:A23V), G29540A [Query: A2127G, G16221T, C22986T, 01/02]dead

• Portugal/PT50123/2023|EPI_ISL_18521981|2023-10-29 and Portugal/PT50186/2023|EPI_ISL_18642132|2023-11-22 JN.2 > G16221T > G28903A(N:M210I) > G22985T(S:A475S) [Query: A2127G, G16221T, G22985T, 2 seqs, 12/18]dead

• Scotland/CLIMB-CM7YGPDB/2023|EPI_ISL_18421633|2023-10-10 and Scotland/CLIMB-CM7YEKXX/2023|EPI_ISL_18705387|2023-12-18 JN.5 > C2668A, C6539T(ORF1a:H2092Y), G22985T(S:A475S) [Query: C2668A, C12815T, G22985T, 01/02]dead

• England/CLIMB-CM7Y8NKN/2023|EPI_ISL_18673357|2023-12-11 and England/CLIMB-CM7YFQMS/2023|EPI_ISL_18705242|2023-12-19 JN.6 > A1588G > C19269T > C22986T(S:A475V) [Query: A1588G, C19269T, C22986T, 2 seqs, 01/02]dead

• Denmark/DCGC-662924/2023|EPI_ISL_18498727|2023-10-23 and South_Korea/KDCA280446/2023|EPI_ISL_18751749|2023-12-14 JN.9 > G22985T(S:A475S) [Query: C12815T, G22985T, G25249A, 2 seqs, 01/12]dead

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Triplets

• USA/WI-WSLH-2302219/2023|EPI_ISL_18643915|2023-10-22; USA/WI-WSLH-2302513/2023|EPI_ISL_18644191|2023-11-12 and USA/WI-WSLH-2302596/2023|EPI_ISL_18644270|2023-11-19 BA.2.86.1 [with C12815T] > G7954T(ORF1a:Q2563H) > C5724T(ORF1a:T1820I), G22985T(S:A475S), C29370T(N:T366I) [Query: G7954T, C12815T, G22985T, 3 seqs, 12/18] dead

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Quadruplets

• England/CLIMB-CM7YEKN5/2023|EPI_ISL_18652526|2023-12-10; England/CLIMB-CM7YGJUG/2023|EPI_ISL_18694712|2023-12-15; England/CLIMB-CM7YE1K1/2023|EPI_ISL_18694788|2023-12-19 and England/CLIMB-CM7YEZPT/2023|EPI_ISL_18727455|2023-12-24 JN.3 > G28378T(ORF9b:R32L) > A27950G > C8481T(ORF1a:P2739L) > C1594T, C22986T(S:A475V) [Query: C6525T, C8481T, C22986T, 4 seqs, 01/08]dead

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Quintuplets

• France/NAQ-HCL723001539201/2023|EPI_ISL_18568555|2023-11-13; France/NAQ-HCL723001540101/2023|EPI_ISL_18568563|2023-11-13; France/NAQ-HCL723001540301/2023|EPI_ISL_18568565|2023-11-13; Spain/GA-33335542/2023|EPI_ISL_18560724|2023-11-14 and Switzerland/BS-UHB-USB-2009db68/2023|EPI_ISL_18639142|2023-11-15 BA.2.86.1 [with C12815T] > C22986T(S:A475V)

• Sweden/Y-34975091/2023|EPI_ISL_18587025|2023-11-21; Sweden/Y-35043027/2023|EPI_ISL_18587040|2023-11-23; Sweden/M-SUS0022458/2023|EPI_ISL_18636570|2023-11-30; Sweden/M-SUS0022459/2023|EPI_ISL_18636571|2023-11-30 and Sweden/D-6563059976/2023|EPI_ISL_18672391|2023-12-05 JN.2 > A18640G(ORF1a:I1725V) > A11559G(ORF1a:Y3765C) > C21846T(S:T95I), C22986T(S:A475V) [Query: A11559G, A18640G, C22986T, 19 seqs, 03/03]

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[NkRMnZr]

Tracking updates

10-18, 3 seqs from Spain EPI_ISL_18400565, EPI_ISL_18400567, EPI_ISL_18400584 10-27, 1 from UK 10-30, 3 seqs from Spain EPI_ISL_18445313, EPI_ISL_18445316-18445317 10-31, 3 seqs from Spain 11-14, 1 more from France, adding Branch 2 11-17, 3 seqs from Spain 11-20, Branch 1 +7; Branch 2 +5

[NkRMnZr]

10-27, 1 more from Wales EPI_ISL_18440020

[HynnSpylor]

+3 in Galicia, Spain

[Huachuan1120]

1 more from Spain,EPI_ISL_18445489

[Huachuan1120]

Spain+3, EPI_ISL_18453794, EPI_ISL_18453771, EPI_ISL_18453743

[Memorablea]

https://github.com/cov-lineages/pango-designation/commit/8c291c77c2451fdbd2c0e9a3ff6ce38ea734c66c ？

[NkRMnZr]

cov-lineages/pango-designation@8c291c7 ？

nope, it's the other issue #1009

[NkRMnZr]

11-14, 1 more from Seine-Saint-Denis EPI_ISL_18499504

Adding Branch 2 from former triplet

[FedeGueli]

11-14, 1 more from Seine-Saint-Denis EPI_ISL_18499504

Adding Branch 2 from former triplet

thank you sorry didnt see the addendum

[BorisUitham]

Branch 2 with 475s due to a recent designation now exists on jn.5 (N:T135I)

[FedeGueli]

Branch 2 with 475s due to a recent designation now exists on jn.5 (N:T135I)

corrected everywhere here

[FedeGueli]

B.1 +2

[NkRMnZr]

11-17, Branch 1 +3 (Asturias, Extremadura, Galicia) EPI_ISL_18506838, EPI_ISL_18506924, EPI_ISL_18514902

[NkRMnZr]

11-20 Branch 1, +7 (France, Portugal, Spain) EPI_ISL_18521096, EPI_ISL_18521189, EPI_ISL_18521993, EPI_ISL_18522037-18522038, EPI_ISL_18522045-18522046 Branch 2, +5 (UK) EPI_ISL_18521290, EPI_ISL_18521319, EPI_ISL_18521351, EPI_ISL_18521370, EPI_ISL_18521390

[FedeGueli]

Branch 1 designated JN.10 via https://github.com/cov-lineages/pango-designation/commit/0a75629f83ff54c756aa129e1aa74f18e01803d3

[FedeGueli]

Branch 2 designated JN.5.1

[xz-keg]

Sweden/AB-01_SE100_23CS503266/2023|EPI_ISL_18547191|2023-11-19 and Canada/ON-PHL-23-44848/2023|EPI_ISL_18582068|2023-11-28

This one is 4 now.

[Over-There-Is]

A14397G branch is 10 now, detected in Malaysia, Indonesia and China.

[FedeGueli]

• England/CLIMB-CM7YJPWA/2023|EPI_ISL_18473823|2023-10-28; USA/IL-USAFSAM-S21652/2023|EPI_ISL_18566205|2023-11-01; USA/IL-USAFSAM-S21653/2023|EPI_ISL_18566206|2023-11-06; England/CLIMB-CM7YFA7T/2023|EPI_ISL_18525476|2023-11-13 and USA/DE-CDC-LC1071357/2023|EPI_ISL_18601884|2023-11-20 BA.2.86.1 [with C12815T] > A14397G > C22986T(S:A475V) [Query: A6183G, A14397G, C22986T, 5 seqs, 12/08]

This is now 10 added it as Branch 3

[FedeGueli]

Sweden/AB-01_SE100_23CS503266/2023|EPI_ISL_18547191|2023-11-19;Canada/ON-PHL-23-44848/2023|EPI_ISL_18582068|2023-11-28;Sweden/AB-01_SE100_23CS102741/2023|EPI_ISL_18642942|2023-12-07andSweden/AB-01_SE100_23CS102715/2023|EPI_ISL_18642928|2023-12-09 **JN.2** > G22985T(**S:A475S**) [Query:A2127G, C12815T, G22985T, -G16221T`, 6 seqs, 01/02]

now this reached 6 i would wait it reaches 10 to make it a branch

[FedeGueli]

Branch 3 went to 37 (propose if it will reach 50) Branch 4 went to 16 Several previous singlets/doublets/Triplets/Quintuplets are now dead and i ve flagged it to save your time. While some of them are now grown to 10, not urgent or important but maybe they should be upgraded to branches if still circulating at the end of this month. thx @NkRMnZr

[FedeGueli]

Sweden/AB-01_SE100_23CS503266/2023|EPI_ISL_18547191|2023-11-19;Canada/ON-PHL-23-44848/2023|EPI_ISL_18582068|2023-11-28;Sweden/AB-01_SE100_23CS102741/2023|EPI_ISL_18642942|2023-12-07andSweden/AB-01_SE100_23CS102715/2023|EPI_ISL_18642928|2023-12-09**JN.2** > G22985T(**S:A475S**) [Query:A2127G, C12815T, G22985T, -G16221T`, 6 seqs, 01/02]

now this reached 6 i would wait it reaches 10 to make it a branch

This is now 19 please i will track it privately. thxx @NkRMnZr closing this issue Branch 3 now 46 has been proposed in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1386 by @aviczhl2