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Repository for suggesting new lineages that should be added to the current scheme
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EG.5.1.1 with ORF1a:P2144S (nsp3_P1326S) and S:L455F, many with follow-up S:G482R (52 seqs, 13 countries) #2353

Closed NkRMnZr closed 10 months ago

NkRMnZr commented 10 months ago

Taken from Branch 24 of Multitask sars-cov-2-variants/lineage-proposals#537

Defining Mutations: EG.5.1.1 > C6695T(ORF1a:P2144S) > C9448A > C5575T, G22927T(S:L455F) Query: C6695T, C9448A, G22927T Earliest seq: 2023-08-13 (EPI_ISL_18114870, Shanghai Customs, travel history to Japan) Latest seq: 2023-10-20 (EPI_ISL_18448529, Ontario, Canada) Sampled Countries: China (13, SH/6; SC/4; FJ/1; ex. Japan/1; ex. S. Korea/1), USA (12: CA/8; AZ/1; OH/1; TX/1; ex. Nepal/1), Singapore (6: Local/5; ex. China/1), Italy (5), UK (3: EN), Australia (2: NSW; QLD), Canada (2: ON), Japan (2), South Korea (2), Switzerland (2), Denmark (1), France (1), Spain (1)

Genomes: `EPI_ISL_18114870, EPI_ISL_18208555, EPI_ISL_18208592, EPI_ISL_18208601, EPI_ISL_18232643, EPI_ISL_18246292, EPI_ISL_18284706, EPI_ISL_18285031, EPI_ISL_18285192, EPI_ISL_18306956, EPI_ISL_18307066, EPI_ISL_18320793, EPI_ISL_18328004, EPI_ISL_18352555, EPI_ISL_18354001, EPI_ISL_18355023, EPI_ISL_18360344, EPI_ISL_18360616, EPI_ISL_18361723, EPI_ISL_18366403, EPI_ISL_18370066, EPI_ISL_18370200, EPI_ISL_18371411, EPI_ISL_18376528, EPI_ISL_18385607, EPI_ISL_18386446, EPI_ISL_18386489, EPI_ISL_18387133, EPI_ISL_18397207, EPI_ISL_18403093, EPI_ISL_18407761, EPI_ISL_18409112, EPI_ISL_18411495, EPI_ISL_18415804, EPI_ISL_18421982, EPI_ISL_18423702, EPI_ISL_18425050, EPI_ISL_18428715, EPI_ISL_18429030, EPI_ISL_18430106, EPI_ISL_18433978, EPI_ISL_18435244, EPI_ISL_18442967, EPI_ISL_18443714, EPI_ISL_18443742-18443744, EPI_ISL_18443746, EPI_ISL_18444154, EPI_ISL_18446641, EPI_ISL_18448416, EPI_ISL_18448529`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_11cc_c2b40.json?label=id:node_3485632 image

NkRMnZr commented 10 months ago

Designated as HK.20 via cov-lineages/pango-designation@71cf97b ; follow-up S:G482R/G23006C designated as HK.20.1