JN.1 with N:Q240L, ORF9b:I5T, ORF1a:G519S (107 seq, May 3)

[ryhisner]

Transferred from sars-cov-2-variants/lineage-proposals#1342
Description
Sub-lineage of: JN.1
Earliest sequence: 2023-12-8, England — EPI_ISL_18652267
Most recent sequence: 2024-1-14, England — EPI_ISL_18809846
Continents circulating: Europe (12), North America (12)
Countries circulating: USA (12), England (9), Italy (2), Mexico (1), Netherlands (1), Scotland (1), Spain (1)
Number of Sequences: 24
GISAID Nucleotide Query: A28992T, T28297C, C28958A
CovSpectrum Query: Nextcladepangolineage:JN.1* & T28297C & [3-of: G1820A, C8299T, G8578A, A13063G, C26499G, A28992T]
Substitutions on top of JN.1:
N: Q240L
ORF9b: I5T
ORF1a: G519S
Nucleotide: G1820A, C8299T, G8578A, A13063G, C26499G, T28297C, A28992T

Phylogenetic Order of Mutations: G8578A → C26499G → A28992T (N:Q240L) → G1820A (ORF1a:G519S) → C8299T, A13063G → T28297C (ORF9b:I5T)

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/JN.1_N.Q240L_ORF9b.I5T.json?c=gt-nuc_28297&gmax=29297&gmin=27297&label=id:node_6854307

Evidence
This is surprisingly geographically widespread perhaps indicating that it originates in a region with no sequencing. Like Germany, for example.

There is one sequence from England and one sequence from the US on the Usher tree but not yet on GISAID.

Genomes

Genomes

EPI_ISL_18652267, EPI_ISL_18668187, EPI_ISL_18668195, EPI_ISL_18688910, EPI_ISL_18699137, EPI_ISL_18701770, EPI_ISL_18721176, EPI_ISL_18721203, EPI_ISL_18722984, EPI_ISL_18723009, EPI_ISL_18731528, EPI_ISL_18763944, EPI_ISL_18763949, EPI_ISL_18763951, EPI_ISL_18771708, EPI_ISL_18774842, EPI_ISL_18775066, EPI_ISL_18793807, EPI_ISL_18799435, EPI_ISL_18809175, EPI_ISL_18809846, EPI_ISL_18809849, EPI_ISL_18822360-18822361

[FedeGueli]

Thank you!