search

sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
42 stars 2 forks source link

EG.5.1 Sublineage w/new S2' FCS—S:P812R, ORF3a:A98V, ORF1a:F2334L, ORF1b:S997L (Denmark, 6 seq, Sept 09) #682

Closed ryhisner closed 11 months ago

ryhisner commented 1 year ago

Description

Sub-lineage of: EG.5.1 Earliest sequence: 2023-7-31 — EPI_ISL_18130335, EPI_ISL_18130353 Most recent sequence: 2023-8-7 — EPI_ISL_18130314, EPI_ISL_18135305, EPI_ISL_18135340 Countries circulating: Denmark (5) Number of Sequences: 5 GISAID Nucleotide Query: C15763T, C16457T, C23997G CovSpectrum Query: Nextcladepangolineage: Substitutions on top of EG.5.1: Spike: P812R ORF3a: A98V ORF1a: F2334L ORF1b: S997L Nucleotide: T7265C, C15763T, C16457T, C23997G, C25685T

Phylogenetic Order of Mutations: T7265C, C25685T (ORF3a:A98V, ORF1a:F2334L) → C16457T (ORF1b:S997L) → C15763T, C23997G (S:P812R)

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/EG.5.1_P812R__S2'_FCS.json?c=gt-nuc_23997&label=id:node_6908166

image

Evidence This is the second multiple-sequence, S:P812R lineage in the past week to emerge from Europe. As I understand it, S:P812R often emerges in cell culture studies, but it has been quite rare in circulating lineages. As stated previously, @ThomasPeacock explained to use that S:P812R creates a new furin-cleavage site (FCS) but at the S2' location in spike instead of the S1/S2 spot. See his explanation at Pango Github issue #1627 here: https://github.com/cov-lineages/pango-designation/issues/1627 . In that issue, the only heretofore known S:P812R lineage with significant circulation was designated.

Do recent XBB lineages perhaps create a spike environment more favorable to S:P812R and the novel FCS it creates? Or perhaps there is something about the current level and type of population immunity that favors S:P812R? Too soon to tell, really. This could be a random blip. But the independent evolution of S:P812R in two unrelated XBB* lineages (the other being XBB.2.3.3) is certainly unexpected.

Genomes

Genomes EPI_ISL_18130314, EPI_ISL_18130335, EPI_ISL_18130353, EPI_ISL_18135305, EPI_ISL_18135340
FedeGueli commented 11 months ago

It seems super slow! (or super mild ?) closing for now

ryhisner commented 11 months ago

Yeah, agree. Weird how two lineages with P812R popped up all at once, then almost instantly disappeared.