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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.2.3 (S:∆S31) + S:V382L, ORF1a:I3090V (152 seq, 16 countries , Sep 4) #2761

Closed ryhisner closed 2 days ago

ryhisner commented 1 week ago

Description Transferred from: https://github.com/sars-cov-2-variants/lineage-proposals/issues/1619 Sub-lineage of: KP.2.3 (S:∆S31, H146Q, R346T, F456L, V1104L) Earliest sequence: 2024-5-14, USA, Utah — EPI_ISL_19175796 Most recent sequence: 2024-8-19, Denmark - EPI_ISL_19378108 Continents circulating: Asia, Europe, North America, Oceania Countries circulating: Many Number of Sequences: 152 GISAID Nucleotide Query: G22706T, A9533G CovSpectrum Query: Nextcladepangolineage:KP.2* & G22706T & [1-of: A9533G, C29095T] Substitutions on top of KP.2.3: Spike: V382L ORF1a: I3090V Nucleotide: A9533G, G22706T, C29095T

USHER Tree Only a temporary link here as I doubt this is of lasting importance. https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_c2da_8f1960.json?label=id:node_7052115

image

Evidence Mainly of interest due to recency of collection, wide geographic spread, and the fact that one sequence is from a traveler from India.

Update: Not a particularly fast lineage, to tell the truth, but it's still alive and over 150 sequences, so I'm moving the proposal here. Like the vast majority of proposals here, it's probably not worthy of designation. Only a matter of time until it gets the automated "Please close this issue" from DailyCovidCases I suppose.

Genomes

Genomes EPI_ISL_19159306, EPI_ISL_19159308, EPI_ISL_19159313-19159314, EPI_ISL_19159318, EPI_ISL_19162365, EPI_ISL_19162491, EPI_ISL_19162535, EPI_ISL_19175796, EPI_ISL_19189066, EPI_ISL_19195199, EPI_ISL_19195604, EPI_ISL_19195626, EPI_ISL_19195695, EPI_ISL_19195862, EPI_ISL_19196392, EPI_ISL_19196399, EPI_ISL_19197410, EPI_ISL_19205306, EPI_ISL_19208190, EPI_ISL_19208481, EPI_ISL_19210045, EPI_ISL_19210055, EPI_ISL_19210077, EPI_ISL_19210088, EPI_ISL_19210583, EPI_ISL_19213662, EPI_ISL_19213670, EPI_ISL_19213743, EPI_ISL_19213748, EPI_ISL_19213758, EPI_ISL_19213761, EPI_ISL_19213763-19213764, EPI_ISL_19213766, EPI_ISL_19213786, EPI_ISL_19213788, EPI_ISL_19213790, EPI_ISL_19213796-19213797, EPI_ISL_19214304, EPI_ISL_19224189, EPI_ISL_19224191-19224192, EPI_ISL_19225320, EPI_ISL_19225397, EPI_ISL_19228748, EPI_ISL_19231544, EPI_ISL_19232419, EPI_ISL_19232543, EPI_ISL_19238103, EPI_ISL_19240106, EPI_ISL_19240259, EPI_ISL_19243533, EPI_ISL_19244245, EPI_ISL_19244641, EPI_ISL_19253040, EPI_ISL_19254942, EPI_ISL_19254948, EPI_ISL_19255025, EPI_ISL_19255243, EPI_ISL_19256801, EPI_ISL_19256820, EPI_ISL_19256835, EPI_ISL_19256854, EPI_ISL_19256874, EPI_ISL_19256888, EPI_ISL_19265034, EPI_ISL_19265044, EPI_ISL_19265654, EPI_ISL_19266419, EPI_ISL_19267943, EPI_ISL_19267962, EPI_ISL_19267970, EPI_ISL_19267997, EPI_ISL_19268012, EPI_ISL_19268014, EPI_ISL_19269059, EPI_ISL_19269952, EPI_ISL_19271147, EPI_ISL_19274031, EPI_ISL_19276090, EPI_ISL_19276413, EPI_ISL_19276633, EPI_ISL_19276691, EPI_ISL_19278931, EPI_ISL_19278947, EPI_ISL_19281686, EPI_ISL_19284981, EPI_ISL_19285045, EPI_ISL_19285671, EPI_ISL_19285698, EPI_ISL_19285752, EPI_ISL_19285772, EPI_ISL_19285826, EPI_ISL_19286123, EPI_ISL_19286768, EPI_ISL_19288116, EPI_ISL_19289025, EPI_ISL_19289167, EPI_ISL_19289263, EPI_ISL_19291974, EPI_ISL_19291976, EPI_ISL_19293055, EPI_ISL_19293446, EPI_ISL_19294946, EPI_ISL_19299856, EPI_ISL_19304795, EPI_ISL_19306740, EPI_ISL_19309942, EPI_ISL_19310516, EPI_ISL_19313067, EPI_ISL_19313132, EPI_ISL_19313378-19313380, EPI_ISL_19313401, EPI_ISL_19314959, EPI_ISL_19314978, EPI_ISL_19316684, EPI_ISL_19316748, EPI_ISL_19319026, EPI_ISL_19319958, EPI_ISL_19323623, EPI_ISL_19323704, EPI_ISL_19325931, EPI_ISL_19327149, EPI_ISL_19327230-19327231, EPI_ISL_19329255, EPI_ISL_19332770, EPI_ISL_19332987, EPI_ISL_19343748, EPI_ISL_19343830, EPI_ISL_19344987, EPI_ISL_19346356, EPI_ISL_19347817, EPI_ISL_19349834, EPI_ISL_19349867, EPI_ISL_19350110, EPI_ISL_19352803, EPI_ISL_19354820, EPI_ISL_19357959, EPI_ISL_19359097, EPI_ISL_19361955, EPI_ISL_19365073, EPI_ISL_19368183, EPI_ISL_19368756, EPI_ISL_19371118, EPI_ISL_19373162, EPI_ISL_19378108, EPI_ISL_19378351
DailyCovidCases commented 4 days ago

ping @corneliusroemer worth a designation this one

ryhisner commented 2 days ago

ping @corneliusroemer worth a designation this one

I disagree. Only 166 sequences total and it seems basically dead. There's no point in designating relatively unremarkable lineages like this that have nothing particularly interesting about them, haven't made a serious impact, and are irrelevant going forward.

Closing.