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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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KP.2.8 with S:255-257 deletions (34 seqs, 12 countries) #2773

Open NkRMnZr opened 2 weeks ago

NkRMnZr commented 2 weeks ago

Taken from Branch 1 of sars-cov-2-variants/lineage-proposals#1794

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: 2024-08-15 (EPI_ISL_19380520, British Columbia, Canada) Sampled Countries: Canada (9: BC), Australia (7: SA/4; QLD/3), Spain (6), USA (4: CO; OH; TN; TX), Austria (1), Chile (1), France (1), Germany (1), Netherlands (1), Norway (1), UK (1: SC), South Korea (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 Austria/MUW_1744831/2024 Canada/BC-BCCDC-726278/2024 Canada/BC-BCCDC-727446/2024 Canada/BC-BCCDC-727461/2024 Canada/BC-BCCDC-728152/2024 Canada/BC-BCCDC-728206/2024 Canada/BC-BCCDC-728268/2024 Canada/BC-BCCDC-728337/2024 Canada/BC-BCCDC-728338/2024 Canada/BC-BCCDC-728371/2024 Chile/CO-53362/2024 France/OCC-RELAB-HCL724000274901/2024 Germany/BY-USAFSAM-S22702/2024 Netherlands/GE-RIVM-139891/2024 Norway/4947/2024 Scotland/CLIMB-CM7Y8F8T/2024 SouthKorea/KDCA294282/2024 Spain/CT-HUB09097/2024 Spain/CT-HUB09136/2024 Spain/CT-HUB09154/2024 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 USA/TN-SPHL-4205/2024 USA/TX-HMH-M-142396/2024 ``` 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, EPI_ISL_19292287, EPI_ISL_19293234, EPI_ISL_19293432, EPI_ISL_19317633, EPI_ISL_19328611, EPI_ISL_19328629, EPI_ISL_19344720, EPI_ISL_19346218, EPI_ISL_19352493, EPI_ISL_19365270, EPI_ISL_19365285, EPI_ISL_19368836, EPI_ISL_19378300, EPI_ISL_19380339, EPI_ISL_19380385, EPI_ISL_19380448, EPI_ISL_19380494-19380495, EPI_ISL_19380520, EPI_ISL_19393856`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_ccf5_27e2e0.json?label=id:node_7020070 image

FedeGueli commented 3 days ago

35 but slowed down a lot. worth closing this