Lineages with S:255-257 deletions: BR.1 = KP.2.8 (S:S60P) 23seqs , BR.2 = LB.1.3 - 16 seqs

[NkRMnZr]

Multiple lineages with S:SSG255-257Δ

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1. Branch 1 : Transferred to KP.2.8 with S:255-257 deletions (34 seqs, 12 countries) cov-lineages/pango-designation#2773 KP.2.8 > A1819G > C29095T > del22325_22333,
2. Branch 2 : LB.1.3 > G943A > A2389G, del22325_22333, query: G943A, A2389G, C18131T, 16 seqs, 5 countries as of 08/15

Branch 1

Transferred to main repo

Transferred to cov-lineages/pango-designation#2773

Defining Mutations: KP.2.8 > A1819G > C29095T > del22325_22333 (S:SSG255-257Δ)
Query: A1819G, del22325_22333
Earliest seq: 2024-03-29 (EPI_ISL_19037182, South Australia)
Latest seq: 2024-07-06 (EPI_ISL_19286145, Coquimbo, Chile)
Sampled Countries: Australia (7: SA/4; QLD/3), Spain (4), USA (2: CO; OH), Chile (1)

Genomes:

for lineages.csv commit:

Australia/QLD0x014426/2024
Australia/QLD0x01446A/2024
Australia/QLD0x01446C/2024
Australia/SA1368591/2024
Australia/SA1370772/2024
Australia/SA1372155/2024
Australia/SA1390078/2024
Chile/CO-53362/2024
Spain/CT-HUB09097/2024
Spain/CT-HUGTiP-G8R182/2024
Spain/CT-HUVH-E54791/2024
Spain/CT-HUVH-E67625/2024
USA/CO-CDPHE-42011782/2024
USA/OH-PLMI-6GN-25209/2024

epi_isl accessions:
EPI_ISL_19037182, EPI_ISL_19055759, EPI_ISL_19085178, EPI_ISL_19085317, EPI_ISL_19150328, EPI_ISL_19169441, EPI_ISL_19169445, EPI_ISL_19191188, EPI_ISL_19203552, EPI_ISL_19223501, EPI_ISL_19243908, EPI_ISL_19269209, EPI_ISL_19286108, EPI_ISL_19286145

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_32bd6_777330.json?label=id:node_7038842

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Branch 2

Defining Mutations: LB.1.3 > G943A > A2389G, del22325_22333 (S:SSG255-257Δ)
Query: G943A, A2389G, C18131T
Earliest seq: 24-05-30 (EPI_ISL_19198089, England)
Latest seq: 24-07-05 (EPI_ISL_19276404, England)
Sampled Countries: UK (5: EN), France (1), Ireland (1)

Genomes:

for lineages.csv commit:

England/CLIMB-CM7YJR3M/2024
England/CLIMB-CM7YJZHC/2024
England/CLIMB-CM7YKJ3Y/2024
England/CLIMB-CM7YKZA4/2024
England/CLIMB-CM7YR8R1/2024
France/BFC-RELAB-IPP07658/2024
Ireland/G-GUH-N2672/2024

epi_isl accessions:
EPI_ISL_19198089, EPI_ISL_19232448, EPI_ISL_19262153, EPI_ISL_19267156, EPI_ISL_19276372, EPI_ISL_19276404, EPI_ISL_19276460

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3b8c2_77b2e0.json?label=id:node_7231919

note: only the GBW samples under this branch are without 255-257 deletions

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Trivia:

• Of all the NTD deletions, S:Δ255-257 is something much less common than Δ69-70 (SGTF), Δ142-146, Δ185-189, Δ210-212, Δ241-243, to name a few.
  

[FedeGueli]

There is also the large del between S:184-190 that should be monitored

[FedeGueli]

17 seqs for br.1
10 for branch 2

[FedeGueli]

Branch 1 likely dying off while branch 2 went to 13

[FedeGueli]

20
16

[NkRMnZr]

B1 slowed but landing on new areas; B2 seems dying

[FedeGueli]

Br.1 > 25

[FedeGueli]

Br.1 went to 34 @NkRMnZr please propose it

[NkRMnZr]

B1 transferred to cov-lineages/pango-designation#2773, B2 seems inactive for now

[FedeGueli]

Thx @NkRMnZr