HK.13.2 (S:F797L, S:D1153H) with further rare mutations: S:Q474K, ORF9b:A57V, ORF1b:Y1648C (18 seq, England, 2023-10-13) EDITED

[ryhisner]

This is a sublineage of cov-lineages/pango-designation#2250 (Edited) spotted and tracked by @NkRMnZr

@ryhisner i ve edited the proposal to keep the S:Q474K subbranch of HK.13.2 proposed.

First spotted by Dave Olias and Fede Gueli last week

Description
Sub-lineage of: EG.5.1.1
Earliest sequence: 2023-9-16, England — EPI_ISL_18325995
Most recent sequence: 2023-10-3, England — EPI_ISL_18373661
Countries circulating: England (16)
Number of Sequences: 16
GISAID Nucleotide Query: A19782T, G25019C
CovSpectrum Query: Nextcladepangolineage:EG.5.1* & [4-of: C17703T, A18410G, A19782T, C22982A, C28453T]
Substitutions on top of EG.5.1.1:
Spike: (L455F > HK.13, F797L, D1153H > HK.13.2) S:Q474K
ORF9b: A57V
ORF1b: Y1648C (NSP15_Y124C)
Nucleotide: C6016T, C17703T, A18410G, A19782T, G22927C, C22982A, T23953A, G25019C, C28453T

Phylogenetic Order of Mutations: HK.13.2 = [ G22927C (S:L455F) → C6016T, T23953A, G25019C (S:F797L, S:D1153H)] → C17703T, A18410G, A19782T, C22982A, C28453T (S:Q474K, ORF9b:A57V, ORF1b:Y1648C)

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/EG.5.1.1_L455F_Q474K_F797L_D1153H.json?c=gt-S_474&gmax=25384&gmin=21563&label=id:node_3450445

Evidence
This lineage, which first picked up FLip with S:L455F, proceeded to accumulate several rare mutations.

• ORF1b:Y1648C (NSP15_Y124C) – 156 seq (only 36 since 2022 and zero in past 5 months)
• S:Q474K – 161 seq ever
• S:F797L – 308 seq ever
• S:D1153H – 500 seq ever

Genomes

Genomes

EPI_ISL_18325919, EPI_ISL_18325924, EPI_ISL_18325995, EPI_ISL_18337725, EPI_ISL_18356199, EPI_ISL_18356201, EPI_ISL_18356204, EPI_ISL_18356209, EPI_ISL_18362273, EPI_ISL_18362283, EPI_ISL_18362289, EPI_ISL_18362305, EPI_ISL_18373643, EPI_ISL_18373649, EPI_ISL_18373656, EPI_ISL_18373661, EPI_ISL_18373662, EPI_ISL_18373664

[FedeGueli]

thank you Ryan for putting together a proposal : i ve edited it cause it is a sublineage of an already proposed flip sublineage: cov-lineages/pango-designation#2250
proposed by @NkRMnZr in the main repo

ping @corneliusroemer i suggest to designate parental and this descendant together.

[FedeGueli]

( given the huge amount if homoplasy of 455F could be also an independent branch but without anything supporting that.

[FedeGueli]

18 now

[xz-keg]

Designated HK.13.2 via cov-lineages/pango-designation@b123561

[Over-There-Is]

Designated HK.13.2

HK.13.2 is the whole branch with S:F797L, S:D1153H.

[FedeGueli]

Designated HK.13.2

HK.13.2 is the whole branch with S:F797L, S:D1153H.

Edited the proposal to keep it open with the HK.13.2 sublineage with S:Q474K

[FedeGueli]

i think it is near dead closing it now