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Repository for suggesting new lineages that should be added to the current scheme
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EG.5.1 with ORF3a:M260K, ORF1b:K1383R (nsp13_K460R) and S:L455F (130 seqs, 17 countries) #2322

Closed NkRMnZr closed 11 months ago

NkRMnZr commented 1 year ago

Taken from Branch 33 of Multitask sars-cov-2-variants/lineage-proposals#537

Defining Mutations: EG.5.1 > T26171A(ORF3a:M260K) > A17615G(ORF1b:K1383R), G22927T(S:L455F) Query: G21718T, G22927T, T26171A Earliest seq: 2023-08-09 (EPI_ISL_18134871, Daknam, Belgium) Latest seq: 2023-10-03 (EPI_ISL_18372012, Ontario, Canada) Sampled Countries: Canada (27: ON), Belgium (9), France (6), Finland (4), USA (3; NY; RI; ex. Netherlands/1), Israel (2), Germany (1), Romania (1), UK (1: SC)

Genomes: `EPI_ISL_18134871, EPI_ISL_18229094, EPI_ISL_18252041, EPI_ISL_18254718, EPI_ISL_18264973, EPI_ISL_18277398, EPI_ISL_18295757, EPI_ISL_18304853, EPI_ISL_18304909, EPI_ISL_18304911-18304912, EPI_ISL_18304914-18304915, EPI_ISL_18304918, EPI_ISL_18304970, EPI_ISL_18304972, EPI_ISL_18304975, EPI_ISL_18305065, EPI_ISL_18305070-18305071, EPI_ISL_18305296, EPI_ISL_18305326, EPI_ISL_18325168, EPI_ISL_18325195, EPI_ISL_18327319, EPI_ISL_18338352, EPI_ISL_18342352, EPI_ISL_18343798, EPI_ISL_18344163, EPI_ISL_18344165, EPI_ISL_18344179, EPI_ISL_18344269, EPI_ISL_18344486, EPI_ISL_18344775, EPI_ISL_18344818, EPI_ISL_18345032, EPI_ISL_18347738, EPI_ISL_18347758, EPI_ISL_18347791, EPI_ISL_18347807, EPI_ISL_18357056, EPI_ISL_18358885, EPI_ISL_18363512, EPI_ISL_18366918, EPI_ISL_18370997, EPI_ISL_18371006, EPI_ISL_18371012, EPI_ISL_18371019, EPI_ISL_18371023, EPI_ISL_18371030, EPI_ISL_18371036, EPI_ISL_18372012, EPI_ISL_18372201`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2f576_6a39f0.json?f_userOrOld=uploaded%20sample&label=id:node_3460683 image

FedeGueli commented 1 year ago

It looks fast : https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=G21718T%2CG22927T%2CT26171A&analysisMode=CompareToBaseline& Some canadian targeted sequencing possible tough.

FedeGueli commented 1 year ago

wrong issue sorry

NkRMnZr commented 1 year ago

Tracking updates

10-14, 5 seqs from Belgium, Iceland and Netherlands EPI_ISL_18377342, EPI_ISL_18385186, EPI_ISL_18385458, EPI_ISL_18385465, EPI_ISL_18386770

10-20, 17 seqs from Belgium, Canada, Finland, France, Netherlands and USA https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1a8e7_2f4b50.json?f_userOrOld=uploaded%20sample&label=id:node_3487749 ![image](https://github.com/cov-lineages/pango-designation/assets/125747944/add403d0-9edd-4ab9-83a1-8ba1fe808324) `EPI_ISL_18389886, EPI_ISL_18394200, EPI_ISL_18395315, EPI_ISL_18395396, EPI_ISL_18395756, EPI_ISL_18396908, EPI_ISL_18396950, EPI_ISL_18396957, EPI_ISL_18396965, EPI_ISL_18403132, EPI_ISL_18403137-18403139, EPI_ISL_18403576, EPI_ISL_18403607, EPI_ISL_18412059, EPI_ISL_18412996`
10-28, 21 seqs from Belgium, Denmark, France, Germany, Netherlands, Portugal, UK, and USA `EPI_ISL_18419995, EPI_ISL_18420433, EPI_ISL_18422680, EPI_ISL_18423306, EPI_ISL_18423562, EPI_ISL_18427244, EPI_ISL_18428127, EPI_ISL_18428227-18428228, EPI_ISL_18428401, EPI_ISL_18428563, EPI_ISL_18429292, EPI_ISL_18429563, EPI_ISL_18433091, EPI_ISL_18441063, EPI_ISL_18441664, EPI_ISL_18441675, EPI_ISL_18441685, EPI_ISL_18441712, EPI_ISL_18441854, EPI_ISL_18442856`

11-05, 9 seqs from Austria, Belgium, Canada, Finland, France, Germany, Netherlands and Sweden EPI_ISL_18445457, EPI_ISL_18445533, EPI_ISL_18448732, EPI_ISL_18451713, EPI_ISL_18455064, EPI_ISL_18457684, EPI_ISL_18458448, EPI_ISL_18462425, EPI_ISL_18463325

11-18, 15 seqs from Australia, Belgium, France, Israel, Italy, Romania, Sweden and USA EPI_ISL_18469030, EPI_ISL_18469141, EPI_ISL_18473131, EPI_ISL_18476828, EPI_ISL_18490002, EPI_ISL_18490144-18490145, EPI_ISL_18493586, EPI_ISL_18502476, EPI_ISL_18509775, EPI_ISL_18512098, EPI_ISL_18513907, EPI_ISL_18517583, EPI_ISL_18519069, EPI_ISL_18519082

11-25, 10 seqs from France, Germany, Italy, Netherlands and USA EPI_ISL_18525134, EPI_ISL_18526438, EPI_ISL_18531568, EPI_ISL_18536037, EPI_ISL_18536041-18536042, EPI_ISL_18536065, EPI_ISL_18537194, EPI_ISL_18540976, EPI_ISL_18542820

FedeGueli commented 1 year ago

104 now

FedeGueli commented 11 months ago

Now designated EG.5.1.19 via https://github.com/cov-lineages/pango-designation/commit/0807c239597f9ab2d4bd86f7c789508877643be6