HF.1.1 (XBB.1.16.13.1.1 = S:H1101Y) with S:D1163Y, N:A35T, ORF1a:T2121I, ORF1b:V1228L, ORF1b:A176V (22 seq, Aug 6)

[ryhisner]

Description

Sub-lineage of: HF.1 (XBB.1.16.13.1)
Earliest sequence: 2023-7-4, USA, North Carolina, EPI_ISL_17996289
Most recent sequence: 2023-7-22, Canada, Ontario, EPI_ISL_18055273, EPI_ISL_18055274
Countries circulating: Canada (21), USA (1)
Number of Sequences: 22
GISAID AA Query: Spike_H1101Y, Spike_D1163Y, Spike_K304N
GISAID Nucleotide Query: C6627T, C24863T, G25049T (catch 1 old unrelated seq- EDITED)
CovSpectrum Query: Nextcladepangolineage:XBB.1.16* & G25049T & [3-of: C6627T, C7006T, C13994T, C24863T]
Substitutions on top of HF.1:
Spike: H1101Y, D1163Y
N: A35T
ORF1a: T2121I
ORF1b: A176V, V1228L
Nucleotide: C6627T, C7006T, C13994T, G17149T, C24863T, G25049T, G28376A

Phylogenetic Order of Mutations: G17149T, G28376A (ORF1b:V1228L, N:A35T) → C7006T, C13994T, C24863T (ORF1b:A176V, S:H1101Y) → C6627T (ORF1a:T2121I)→ G25049T (S:D1163Y)
Note—20/22 sequences also have → C28290T (N:P6L/ORF9b:P3S)

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/HF.1__XBB.1.16.13.1__H1101Y_D1163Y.json

Evidence
All sequences with very recent collection dates, and the sequence from North Carolina shows this is more than an outbreak in one facility in Canada. HF.1 is already quite a fast lineage, so this bears watching. Note that 20/22 sequences here also have N:P6L/ORF9b:P3S. I've noted before that ORF9b:P3S slightly improves the already impressive extended homology for a suboptimal ORF9b TRS.

Genomes

Genomes

EPI_ISL_17996289, EPI_ISL_18030497-18030499, EPI_ISL_18030522, EPI_ISL_18030547-18030549, EPI_ISL_18055171, EPI_ISL_18055173, EPI_ISL_18055176-18055177, EPI_ISL_18055217, EPI_ISL_18055221-18055222, EPI_ISL_18055261, EPI_ISL_18055264-18055265, EPI_ISL_18055273-18055274, EPI_ISL_18055324, EPI_ISL_18055347

[FedeGueli]

it doesnt sem to have spread further closing this for now,

[FedeGueli]

Designated HF.1.1 the parental S:H1101Y i dont know ryan if you want to keep open the issue or u re satisfied this way.
via cov-lineages/pango-designation@5e035b4.

I ve edited the title already. proposal untouched.

[ryhisner]

There were a couple geographically distant sequences recently in the US (Arkansas and New York), but for the most part, this seems like a classic Canadian cluster. I'd leave closed, and if more pop up, we can always reopen.