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Repository for suggesting new lineages that should be added to the current scheme
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XBB.1.16.15 (S:K147N, P521S) Sublineage with ORF9b:P3L, ORF1a:S2024L, ORF1b:N2328S (94 seq, 25 countries, Sept 23) #2294

Closed ryhisner closed 2 months ago

ryhisner commented 1 year ago

Description — transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/695 Sub-lineage of: XBB.1.16.15 (XBB.1.16 + S:K147N, S:P521S) Earliest sequence: 2023-7-10, Shanghai, China — EPI_ISL_18074327 Most recent sequence: 2023-8-21, Spain, Basque Country — EPI_ISL_18134790 Countries circulating: England (3), Sweden (3), Denmark (2), Spain (2), USA (2), China (1), France (1—traveler to USA), Germany (1), Israel (1), Netherlands (1) Number of Sequences: 17 GISAID AA Query: NSP3_S1206L, NSP15_N277S, -Spike_D138H, -Spike_ins925FRYAM GISAID Nucleotide Query: C6336T, T10756C, T14067C, C28291T CovSpectrum Query: Nextcladepangolineage:XBB.1.16* & C6336T & [2-of: A20450G, A24121G, C28291T] Substitutions on top of XBB.1.16.15: ORF9b: P3L ORF1a: S2024L ORF1b: N2328S Nucleotide: C6336T, T10756C, A20450G, A24121G, C28291T

Phylogenetic Order of Mutations: T10756C → C28291T (ORF9b:P3L) → A20450G, A24121G (ORF1b:N2823S) → C6336T (ORF1a:S2024L)

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.16.15_9bP3L_1aS2024L_1bN2328S.json?c=gt-nuc_6336&label=id:node_6826659

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. Evidence ORF1a:S2024L/NSP3_S1206L is modestly convergent in chronic-infection sequences. C28291T (ORF9b:P3L) slightly increases the extended homology for what I believe is a suboptimal ORF9b TRS. It has very gradually increased in prevalence during the XBB era and might be slightly advantageous.

ORF1b:N2328S/NSP15_N277S is an uncommon mutation. NSP15 seems to be a pretty conserved part of the genome in general, and this mutation has been in <800 sequences in the entire pandemic.

Genomes

Genomes EPI_ISL_18074327, EPI_ISL_18095053, EPI_ISL_18097303, EPI_ISL_18099903, EPI_ISL_18099909, EPI_ISL_18099941, EPI_ISL_18112044, EPI_ISL_18112170, EPI_ISL_18115821, EPI_ISL_18123736, EPI_ISL_18124221, EPI_ISL_18126764, EPI_ISL_18126765, EPI_ISL_18130459, EPI_ISL_18130705, EPI_ISL_18134790, EPI_ISL_18135290
FedeGueli commented 1 year ago

This is now 225 . Still far from FLip but one of the fastest not flip :https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=HK.3*&nucMutations1=C6336T%2CT10756C%2CT14067C%2CC28291T&analysisMode=CompareToBaseline&

DailyCovidCases commented 5 months ago

Please close this issue