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Repository for suggesting new lineages that should be added to the current scheme
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LB.1 (JN.1.9.2.1) with ORF1a:M2606I (nsp3_M1788I ) S:T240I and S:T478R (93 seqs, 3+1 countries) #2792

Open NkRMnZr opened 1 month ago

NkRMnZr commented 1 month ago

Transferred from sars-cov-2-variants/lineage-proposals#1852

Defining Mutations: LB.1 > G8083A(ORF1a:M2606I), C22281T(S:T240I), C22995G(S:T478R) Query: G8083A, C22281T, C22995G Earliest seq: 24-05-24 (EPI_ISL_19188794, Texas, USA) Latest seq: 24-09-16 (EPI_ISL_19435177, British Columbia, Québec) Sampled Countries: USA (40: TX/20; CA/3; IL/3; CO/2; AL; AZ; MN; NC; NE; NJ; NY; SC; UT; GBW ex. Mexico/2; Japan), Canada (27: BC/25; ON; QC), Mexico (9: CMX/5; MOR/3; QUE)

Genomes: for `lineages.csv` commit: ``` Canada/BC-BCCDC-722475/2024 Canada/BC-BCCDC-723309/2024 Canada/BC-BCCDC-723310/2024 Canada/BC-BCCDC-723311/2024 Canada/BC-BCCDC-723333/2024 Canada/BC-BCCDC-723351/2024 Canada/BC-BCCDC-723358/2024 Canada/BC-BCCDC-723359/2024 Canada/BC-BCCDC-723360/2024 Canada/BC-BCCDC-723361/2024 Canada/BC-BCCDC-724820/2024 Canada/BC-BCCDC-724897/2024 Canada/BC-BCCDC-724898/2024 Canada/BC-BCCDC-727186/2024 Canada/BC-BCCDC-732737/2024 Canada/BC-BCCDC-732738/2024 Canada/BC-BCCDC-732739/2024 Canada/BC-BCCDC-732741/2024 Canada/BC-BCCDC-732742/2024 Canada/BC-BCCDC-732743/2024 Canada/BC-BCCDC-732744/2024 Canada/BC-BCCDC-732789/2024 Canada/BC-BCCDC-732790/2024 Canada/BC-BCCDC-732791/2024 Canada/BC-BCCDC-733100/2024 Canada/ON-PHL-202413231/2024 Canada/QC-L00787629001/2024 Mexico/CMX_InDRE_FB1204/2024 Mexico/CMX-INER-INMEGEN-3031/2024 Mexico/CMX-INER-INMEGEN-3081/2024 Mexico/CMX-INER-INMEGEN-3100/2024 Mexico/CMX-INER-INMEGEN-3126/2024 Mexico/MOR_InDRE_FB1139/2024 Mexico/MOR_InDRE_FB1185/2024 Mexico/MOR_InDRE_FB1200/2024 Mexico/QUE_InDRE_FB1195/2024 USA/AL-CDC-LC1118476/2024 USA/AZ-ASPHL-1391/2024 USA/CA-CDPH-500141542/2024 USA/CA-LACPHL-AY08043/2024 USA/CA-SEARCH-140901/2024 USA/CO-CDPHE-42226292/2024 USA/CO-CDPHE-42240642/2024 USA/IL-CDC-LC1120893/2024 USA/IL-RIPHL_123341_G/2024 USA/IL-RIPHL_21931_G/2024 USA/MN-MDH-42737/2024 USA/NC-CDC-LC1114474/2024 USA/NE-NM_L379194558/2024 USA/NJ-CDC-LC1116284/2024 USA/NY-GBW-GKISBBBC77155/2024 USA/NY-GBW-GKISBBBD25943/2024 USA/NY-URMC-O7S1P380-1/2024 USA/SC-CDC-LC1121085/2024 USA/TX-DSHS-26564/2024 USA/TX-HMH-M-141249/2024 USA/TX-HMH-M-141305/2024 USA/TX-HMH-M-142191/2024 USA/TX-HMH-M-142592/2024 USA/TX-HMH-M-143616/2024 USA/TX-HMH-M-143633/2024 USA/TX-HMH-M-143830/2024 USA/TX-HMH-M-144878/2024 USA/TX-HMH-M-144881/2024 USA/TX-HMH-M-145493/2024 USA/TX-HMH-M-145516/2024 USA/TX-HMH-M-145674/2024 USA/TX-HMH-M-145693/2024 USA/TX-HMH-MCoV-143171/2024 USA/TX-HMH-MCoV-143204/2024 USA/TX-HMH-MCoV-143427/2024 USA/TX-PHH-SPID1004434694/2024 USA/TX-TAMGHRC-SHS-111901/2024 USA/TX-UHS-UTHSA11355-P0/2024 USA/UT-UPHL-240920593220/2024 USA/WA-GBW-GKISBBBC45984/2024 ``` epi_isl accessions: `EPI_ISL_19188794, EPI_ISL_19259328, EPI_ISL_19286685, EPI_ISL_19294017, EPI_ISL_19295175, EPI_ISL_19298808, EPI_ISL_19306296, EPI_ISL_19317839, EPI_ISL_19318158, EPI_ISL_19318241-19318243, EPI_ISL_19318263, EPI_ISL_19318279, EPI_ISL_19318289-19318292, EPI_ISL_19325510, EPI_ISL_19326062, EPI_ISL_19326080, EPI_ISL_19326105, EPI_ISL_19334790, EPI_ISL_19334805, EPI_ISL_19335110, EPI_ISL_19337025, EPI_ISL_19337084-19337085, EPI_ISL_19341259, EPI_ISL_19348835, EPI_ISL_19349002, EPI_ISL_19349033, EPI_ISL_19350068, EPI_ISL_19354105, EPI_ISL_19365047, EPI_ISL_19366302, EPI_ISL_19366305, EPI_ISL_19369937-19369938, EPI_ISL_19369970, EPI_ISL_19373404, EPI_ISL_19373502-19373504, EPI_ISL_19373607, EPI_ISL_19379370, EPI_ISL_19382846, EPI_ISL_19391394, EPI_ISL_19392133, EPI_ISL_19394832, EPI_ISL_19417025, EPI_ISL_19423687, EPI_ISL_19425361, EPI_ISL_19425391, EPI_ISL_19425975, EPI_ISL_19426000, EPI_ISL_19428737, EPI_ISL_19429411, EPI_ISL_19432814, EPI_ISL_19433674, EPI_ISL_19435177, EPI_ISL_19438166-19438168, EPI_ISL_19438170-19438173, EPI_ISL_19438214-19438216, EPI_ISL_19438493, EPI_ISL_19438978, EPI_ISL_19439436, EPI_ISL_19445617, EPI_ISL_19445825`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_13dce_8d7890.json?label=id:node_7333924 image

FedeGueli commented 1 month ago

Thx for proposing. please don't keep GbW countires separated

FedeGueli commented 1 month ago

it has slowed down and circulation is quite limited to US and some Canadian clusters