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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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XBB.1.5 Sublineage with S:V36I, S:P272H, S:Q836K, N:I292T, ORF1b:M2322I (Puerto Rico, USA, Uk, 45 seq, Sept 9) #403

Closed ryhisner closed 11 months ago

ryhisner commented 1 year ago

Description

Sub-lineage of: XBB.1.5 Earliest sequence: 2023-4-21, Puerto Rico, EPI_ISL_17700246 Most recent sequence: 2023-6-27, USA, Florida, EPI_ISL_17979245 Countries circulating: Puerto Rico (16), USA (9) Number of Sequences: 25 GISAID AA Query: Spike_V36I, Spike_P272H, N_I292T GISAID Nucleotide Query: G21668A, C22377A, T29148C CovSpectrum Query: Nextcladepangolineage: XBB.1.5* & [3-of: G20433A, G21668A, C22377A, C24068A, T29148C] Substitutions on top of XBB.1.5: Spike: V36I, P272H, Q836K N: I292T ORF1b: M2322I Nucleotide: G20433A, G21668A, C22377A, C24068A, T29148C

Phylogenetic Order of Mutations: G21668A (S:V36I) → C24068A (S:Q836K) → G20433A (ORF1b:M2322I), T29148C (N:I292T) → C22377A (S:P272H)

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.5_V36I_P272H_Q836K__N-I292T__ORF1b-M2322I.json

image

Evidence An earlier study found S:P272L to be a T-cell-escape mutation, so it seems likely S:P272H is one as well. S:Q836K is in an interesting region of S2 and seems likely to be consequential in some way. https://www.cell.com/cell/pdf/S0092-8674(22)00849-2.pdf

This lineage makes up about 2% of sequences from Puerto Rico collected since May 15, and has been detected in five US states (Connecticut, Florida, Mississippi, New Jersey, New York).

XBB.1.5 seems like a dying lineage, so this one will probably die with it, but it seems worth noting nonetheless.

Genomes

Genomes EPI_ISL_17700246, EPI_ISL_17700255, EPI_ISL_17700262, EPI_ISL_17810315, EPI_ISL_17821251, EPI_ISL_17830891, EPI_ISL_17830947, EPI_ISL_17830953, EPI_ISL_17830956, EPI_ISL_17831082, EPI_ISL_17853080, EPI_ISL_17853153, EPI_ISL_17853307, EPI_ISL_17856365, EPI_ISL_17885206, EPI_ISL_17885222, EPI_ISL_17885226, EPI_ISL_17953730, EPI_ISL_17955545, EPI_ISL_17965558, EPI_ISL_17965563, EPI_ISL_17965596, EPI_ISL_17965601, EPI_ISL_17979117, EPI_ISL_17979245
FedeGueli commented 1 year ago

it seems expanding again after a slight slowdown. better to keep this tracked

FedeGueli commented 1 year ago

Also samples from July so ongoing circulation.

FedeGueli commented 11 months ago

Only 3 samples from August closing it