Multiple EG.5.1* Lineages with S:T732I

[NkRMnZr]

Multiple EG.5.1* lineages with S:T732I

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1. Branch 1: Transferred to EG.5.1 with S:T732I (183 seqs, 12 countries) cov-lineages/pango-designation#2189 EG.5.1 > C14625T, C23757T(S:T732I)
2. Branch 2: Designated as JG.1 , Transferred to EG.5.1.3 with S:T732I (31 seqs, 8 countries) cov-lineages/pango-designation#2218 EG.5.1.3 > C23757T(S:T732I) [Query: C1889T, C22570T, C23757T, 31 seqs, 08/26]

Branch 1

Transferred to Main Repo

Transferred to cov-lineages/pango-designation#2189

Defining Mutations: EG.5.1 > C14625T, C23757T(S:T732I)
Query: C14625T, C23757T
Earliest seq: 2023-05-15 (EPI_ISL_17761688, Denmark)
Latest seq: 2023-07-10 (EPI_ISL_18015610, England, Uk)
Sampled Countries: Portugal (13), Spain (2), Denmark (1), UK (1, England)

Genomes:

EPI_ISL_17761688, EPI_ISL_17786187-17786188, EPI_ISL_17786190, EPI_ISL_17786192, EPI_ISL_17954647, EPI_ISL_17954846, EPI_ISL_17954850, EPI_ISL_17954852, EPI_ISL_17954855, EPI_ISL_18015610, EPI_ISL_18042284, EPI_ISL_18042306, EPI_ISL_18052319, EPI_ISL_18052385-18052386, EPI_ISL_18052431

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3d69e_908960.json?f_userOrOld=uploaded%20sample

Trivia:

• On checking Cov-Spectrum, you'll soon realize how few samples we got these days.
  

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Branch 2

Transferred to main repo, Designated as JG.1 (EG.5.1.3.1)

Designated as JG.1 (EG.5.1.3.1) via cov-lineages/pango-designation@98c5e92

Transfered to main repo as cov-lineages/pango-designation#2218

Defining Mutations: EG.5.1.3 > C23757T(S:T732I)
Query: C1889T, C22570T, C23757T
Earliest seq: 2023-06-28 (EPI_ISL_17953331, Noord-Brabant, Netherlands)
Latest seq: 2023-07-22 (EPI_ISL_18070133, Aude, Occitanie, France)
Sampled Countries: France (6), Netherlands (1)

Genomes:

EPI_ISL_17953331, EPI_ISL_18048998-18048999, EPI_ISL_18070063, EPI_ISL_18070115, EPI_ISL_18070127, EPI_ISL_18070133

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_338b1_f75cd0.json?f_userOrOld=uploaded%20sample&label=id:node_6778223

[NkRMnZr]

Tracking updates:

08-05, 1 sequence on Branch 1 from Ohio, USA: EPI_ISL_18069155; Adding Branch 2
08-08, Branch 1, +3 (USA); Branch 2, +1 (Canada)
08-13: Branch 1, +1 (USA); Branch 2, +4 (France)
08-14, Branch 1 Transferred to Main Repo; Branch 2, +1 (Netherlands)
08-18, Branch2: 5 seqs from Canada and Spain
08-26, Branch 2: 13 seqs from Denmark, France, Italy, Israel, Spain and UK

[NkRMnZr]

08-08: Branch 1, +3 (USA); Branch 2, +1 (Canada)
Branch 1, 3 seqs from USA: EPI_ISL_18072232, EPI_ISL_18075840, EPI_ISL_18075871
Branch 2, 1 sequence from Canada: EPI_ISL_18074050

[NkRMnZr]

08-13: Branch 1, +1 (USA); Branch 2, +4 (France)
Branch 1, 1 more from USA: EPI_ISL_18080247
Branch 2, 4 seqs from France: EPI_ISL_18094652, EPI_ISL_18094706, EPI_ISL_18094710, EPI_ISL_18094715

[FedeGueli]

Interesting i am not sure if they are the fastest descendant of EG.5.1. the same i think given the role of EG.5.1 in the global evo right now, it is better to propose at least Branch 1 on the main page. Please let @corneliusroemer know that there are more than one lineage with it.

[NkRMnZr]

08-14, 1 more from Netherlands on Branch 2: EPI_ISL_18098324. Branch 1 transferred to main repo cov-lineages/pango-designation#2189

[NkRMnZr]

08-18, Branch 2: 5 seqs from Canada and Spain

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3611f_9f5e0.json?f_userOrOld=uploaded%20sample&label=id:node_6901532

4 from Québec: EPI_ISL_18114571, EPI_ISL_18114638, EPI_ISL_18114640, EPI_ISL_18114657
1 from Basque EPI_ISL_18112412

[NkRMnZr]

08-26, Branch 2: 13 seqs from Denmark, France, Italy, Israel, Spain and UK

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_116f8_a1aa20.json?f_userOrOld=uploaded%20sample&label=id:node_6909784

EPI_ISL_18115884, EPI_ISL_18118547, EPI_ISL_18118560-18118561, EPI_ISL_18118605, EPI_ISL_18118939, EPI_ISL_18123412, EPI_ISL_18124215-18124216, EPI_ISL_18124233, EPI_ISL_18124235, EPI_ISL_18135295, EPI_ISL_18135614

[FedeGueli]

Also branch 2 is clearly expanding as expected please propose it

[NkRMnZr]

Branch 2 transferred to cov-lineages/pango-designation#2218

[FedeGueli]

Branch 2 designated JG.1 via cov-lineages/pango-designation@98c5e92

[xz-keg]

There seems a large HK.3+S:T732I branch too.

Query: A28877T,G28878C,C23757T,T22849C (36 seqs)

[xz-keg]

[FedeGueli]

pkease make a proposal of it