Multiple lineages with S:L452Q

[NkRMnZr]

### Tracking multiple lineages with S:L452Q
- [ ] Branch 1: [XBB.1.5's T17124C > T23018C] > C7086T(ORF1a:T2274I) > A3249G(ORF1a:E995G), G3446T(ORF1a:A1061S) > A11206G > T8158C, T22917A(S:L452Q), A23535G(S:N658S) [Query: A11206G,T22917A, C7086T, 14 seqs, 07/27]
- [x] Branch 2: Designated as **XBB.1.16.14** _XBB.1.16 > A11782G > T22917A(S:L452Q)_
- [ ] Branch 3: [XBB.1.5's T17124C > T23018C] > G4712A(ORF1a:V1483I) > C15540T, T22917A(S:L452Q) [Query: C15540T, T22917A, G4712A, 17 seqs, 07/27]
- [ ] Branch 4: XBB.1.5.52 > C1267A > C3140T(ORF1a:P959S), A3234C(ORF1a:Q990P), C4782T(ORF1a:S1506L) > C15360T > C1263T(ORF1a:T333M) > T11084C(ORF1a:Y3607H) > T22917A(S:L452Q) [Query: T22917A, T11084C, C1263T, 10 seqs, 06/21]
- [x] Branch 5: Designated as **FP.2.1.1** _FP.2.1 (XBB.1.11.1.2.1) > T15357C > T22917A(L452Q)_

Branch 1:

Defining Mutations: [XBB.1.5's T17124C > T23018C] > C7086T(ORF1a:T2274I) > A3249G(ORF1a:E995G), G3446T(ORF1a:A1061S) > A11206G > T8158C, T22917A(S:L452Q), A23535G(S:N658S) Query: A11206G,T22917A, C7086T Earliest seq: 2023-04-20 (EPI_ISL_17608124, Spain) Latest seq: 2023-06-22 (EPI_ISL_17950823, Sweden) Sampled Countries: Spain (5), Germany (1), Sweden (1)

Genomes:

EPI_ISL_17608124, EPI_ISL_17679622, EPI_ISL_17776493, EPI_ISL_17788576, EPI_ISL_17788595, EPI_ISL_17838532, EPI_ISL_17950823

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3caf7_528e80.json?f_userOrOld=uploaded%20sample

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Branch 2

DESIGNATED AS XBB.1.16.14

via cov-lineages/pango-designation@5648ff2 **Defining Mutations:** XBB.1.16 > A11782G > T22917A(S:L452Q) > **Query:** T22917A, A11782G, A22101T **Earliest seq:** 2023-04-25 (EPI_ISL_17727276, Michigan, USA) **Latest seq:** 2023-06-21 (EPI_ISL_17964422, England, UK) **Sampled Countries:** France (6), USA (5, Michigan/2, Ohio/2, New York/1), Canada (5, Québec), UK (4, England/3, Scotland/1), India (1, Odisha), Netherlands (1), Spain (1)

Genomes:

EPI_ISL_17653273, EPI_ISL_17726763, EPI_ISL_17726926, EPI_ISL_17727006, EPI_ISL_17727276, EPI_ISL_17744350, EPI_ISL_17769629-17769633, EPI_ISL_17781582, EPI_ISL_17808965, EPI_ISL_17856330, EPI_ISL_17872566, EPI_ISL_17885000, EPI_ISL_17950881, EPI_ISL_17953465, EPI_ISL_17956123, EPI_ISL_17957941, EPI_ISL_17959243, EPI_ISL_17964407, EPI_ISL_17964422

**UShER:** https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_12e96_6ee270.json?f_userOrOld=uploaded%20sample 

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Branch 3

Defining Mutations: [XBB.1.5's T17124C > T23018C] > G4712A(ORF1a:V1483I) > C15540T, T22917A(S:L452Q) Query: C15540T, T22917A, G4712A Earliest seq: 2023-03-18 (EPI_ISL_17596920, Canary Islands, Spain) Latest seq: 2023-06-06 (EPI_ISL_17949210, Spain) Sampled Countries: Spain (11 Mainland/10, Canary Islands/1) France (3), Austria (2), Denmark (1)

Genomes:

EPI_ISL_17446259, EPI_ISL_17482703, EPI_ISL_17524658, EPI_ISL_17596920, EPI_ISL_17614594, EPI_ISL_17650839, EPI_ISL_17673685, EPI_ISL_17679619, EPI_ISL_17679652, EPI_ISL_17679665, EPI_ISL_17700036, EPI_ISL_17731372, EPI_ISL_17731437, EPI_ISL_17859706, EPI_ISL_17949132, EPI_ISL_17949210, EPI_ISL_17949340

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_15fb6_6f00f0.json?f_userOrOld=uploaded%20sample

---

Branch 4

Defining Mutations: XBB.1.5.52 > C1267A > C3140T(ORF1a:P959S), A3234C(ORF1a:Q990P), C4782T(ORF1a:S1506L) > C15360T > C1263T(ORF1a:T333M) > T11084C(ORF1a:Y3607H) > T22917A(S:L452Q) Query: T22917A, T11084C, C1263T [10] Earliest seq: 2023-05-02 (EPI_ISL_17680075, England) Latest seq: 2023-05-30 (EPI_ISL_17820741, England) Sampled Countries: England (10)

Genomes:

EPI_ISL_17680075, EPI_ISL_17693016, EPI_ISL_17731193, EPI_ISL_17731195, EPI_ISL_17731200, EPI_ISL_17731204, EPI_ISL_17742249, EPI_ISL_17787022, EPI_ISL_17820741, EPI_ISL_17820748

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_199f5_6f15c0.json?f_userOrOld=uploaded%20sample&label=id:node_6969757&showBranchLabels=all

---

Branch 5:

DESIGNATED AS FP.2.1.1

via cov-lineages/pango-designation@7c88225 **Defining Mutations:** FP.2.1 (XBB.1.11.1.2.1) > T15357C > T22917A(L452Q) **Query:** T15357C, T22917A, G25839T **Earliest seq:** 2023-05-31 (EPI_ISL_17831580, Puerto Rico, United States) **Latest seq:** 2023-06-27 (EPI_ISL_17962925, Austria) **Sampled Countries:** US (3, Ohio, Texas, Puerto Rico), Austria (2)

Genomes:

EPI_ISL_17831580, EPI_ISL_17950927, EPI_ISL_17956024, EPI_ISL_17962918, EPI_ISL_17962925

**UShER:** https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1e71d_6f43e0.json?f_userOrOld=uploaded%20sample 

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Trivia:

• S:N658S is a parent branch of many BA.4* like BA.4.6, BA.4.7 etc.
• S:L452Q is the definition of BA.2.12.1.

[FedeGueli]

452Q also defining of BH.1 (BA.2.38.3.1)

[FedeGueli]

S:L452Q seems estimated as especially beneficial on XBB.1.5 backbone by T. Starr

[NkRMnZr]

Tracking updates:

23-07-18: 2 seqs from Spain & Sweden: EPI_ISL_17995462, EPI_ISL_17990592 on Branch 1

23-07-28 : 2 seqs from Branch1, 6 seqs from Branch 5

[NkRMnZr]

23-07-28:

Branch 1:

2 seqs from Canary Islands: EPI_ISL_18015817, EPI_ISL_18044951

Branch 5:

6 seqs from Airzona and Texas: EPI_ISL_17998410, EPI_ISL_18045001, EPI_ISL_18045025, EPI_ISL_18045035, EPI_ISL_18045037, EPI_ISL_18045064

[FedeGueli]

i think it is worth proposing branch 5

[NkRMnZr]

i think it is worth proposing branch 5

designated as FP.2.1.1 through cov-lineages/pango-designation@7c88225 need milestones for XBB.1.16.14 and FP.2.1.1

[FedeGueli]

Ok i think we can close this. Please keep checked branch 1.