XBB.1.5 Sublineage with S:Q146K, S:S704L, ORF6:D6G, ORF1b:V1607I (29 seq, Apr 7)

[ryhisner]

Description

Sub-lineage of: XBB.1.5
Earliest sequence: 2023-1-16, France — EPI_ISL_16677358; 2023-1-16, Guinea — EPI_ISL_17305639
Most recent sequence: 2023-3-29, Guinea, 3 seq — EPI_ISL_17418963-17418965
Countries circulating: Guinea (20), France (3), Scotland (2), England (1), Spain (1), USA-Hawaii (1), USA w/travel in Liberia (1)
Number of Sequences: 29
GISAID AA Query: Spike_S704L, NS6_D6G, NSP14_V83I
GISAID Nucleotide Query: T772A, G18286A, A27218G
CovSpectrum Query: [3-of: T772A, G18286A, C23673T, A27218G, T23018C] & !T17124C
Substitutions on top of XBB.1.5:
Spike: Q146K, S704L
ORF6a: D6G
ORF1b: V1607I (NSP14_V83I)
Nucleotide: T772A, C17124T (Reversion), G18286A, C21998A, C23673T, A27218G

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB.1.5_H146K_S704L_ORF6D6G_subtreeAuspice1_genome_140c4_5fce0.json

Downsampled Global Tree (temporary link)
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_140c4_5fce0.json?label=id:node_3770121

Evidence
Of the 28 sequences collected in Guinea in 2023, 20 have been from this lineage. All 20 were hospitalized, as it seems Guinea only sequences hospitalized cases. There are virtually no sequences from the countries in the region of Africa that Guinea is in, but there is one sequence from the USA with travel history in Liberia. It seems likely that this lineage has been circulating extensively in western Africa for some time.

Consistent with this hypothesis is the surprising diversity and prevalence of fairly long branches in this branch. Spike mutations present in this branch include R21T (1), K146N (1), ∆178-183, S254F (1), S256L (1), G257D (1), F456L (2), K478T (1), G485S (2), P521S (1), T549I (1), E554K (3 seq), N556K (3), H681R (1), P1263L (1)

Genomes (Note: I've excluded two pooled samples from Ginkgo Bioworks from the USA. There is also 1 seq from Scotland on the Usher tree but not yet on GISAID.)

Genomes

EPI_ISL_16677358, EPI_ISL_16878591, EPI_ISL_16979767, EPI_ISL_17008049, EPI_ISL_17109755, EPI_ISL_17168364, EPI_ISL_17188152, EPI_ISL_17239777, EPI_ISL_17305639, EPI_ISL_17305641-17305646, EPI_ISL_17418804, EPI_ISL_17418951-17418957, EPI_ISL_17418959-17418960, EPI_ISL_17418963-17418965