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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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XBB.1.16 Sublineage with S:F186S, S:E554Q, S:N556K, ORF1a:P286S (11 seq, 2 continents, Sept 7) #555

Closed ryhisner closed 11 months ago

ryhisner commented 1 year ago

Description

Sub-lineage of: XBB.1.16 Earliest sequence: 2023-6-13, France, Grand Est, Colmar — EPI_ISL_17837367 Most recent sequence: 2023-7-24, France, Occitanie, Haute Garonne — EPI_ISL_18070166 Countries circulating: Japan (4), France (2) Number of Sequences: 6 GISAID AA Query: Spike_E554Q, Spike_N556K GISAID Nucleotide Query: C26894T, T5335C, A29110T, T22119C, G4504A CovSpectrum Query: Nextcladepangolineage:XBB.1.16* & C23230A & [3-of: C1121T, G4504A, T5335C, T22119C, G23222C, C26894T, A29110T] Substitutions on top of XBB.1.16: Spike: F186S, E554Q, N556K ORF1a: P286S Nucleotide: C1121T, G4504A, T5335C, T22119C, G23222C, C23230A, C26894T, A29110T

Phylogenetic Order of Mutations: C26894T → T5335C, A29110T → T22119C (S:F186S) → C1121T, G23222C (ORF1a:P286S, S:E554Q) → G4504A, C23230A (S:N556K) →

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.16_F186S_E554Q_N556K.json

image

Evidence This has appeared on opposite sides of the world in short succession. A different branch of XBB.1.16 with S:E554Q was also noticed just today by @NkRMnZr, in issue #554.

Something isn't entirely right with the Usher Tree since ORF1b:R2613C (C21304T) appears and is almost immediately reverted. Not a big deal, and if this lineage grows, the tree might sort itself out.

Genomes

Genomes EPI_ISL_17837367, EPI_ISL_18056109, EPI_ISL_18056364, EPI_ISL_18056383, EPI_ISL_18056386, EPI_ISL_18070166
FedeGueli commented 1 year ago

Something isn't entirely right with the Usher Tree since ORF1b:R2613C (C21304T) appears and is almost immediately reverted. Not a big deal, and if this lineage grows, the tree might sort itself out.

cc @angiehinrichs

AngieHinrichs commented 1 year ago

21304 stuff cleaned up in the 2023-08-17 tree (on dev.usher.bio now, on usher.bio in a bit over 4 hours), thanks @ryhisner and @FedeGueli.

FedeGueli commented 1 year ago

so now we have 7 : Schermata 2023-08-18 alle 14 38 13

Schermata 2023-08-18 alle 14 37 47 https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_407ca_f65960.json?label=id:node_6826265

FedeGueli commented 11 months ago

It seems slow @ryhisner closing for now.