Sublineage of XBB.1.4 with S:S673G (52 seq)

[ryhisner]

Description

Sub-lineage of: XBB.1.4
Earliest sequence: 2022-10-10, Norway — EPI_ISL_15742609
Most recent sequence: 2022-11-13, Denmark — EPI_ISL_15800920
Countries circulating: Denmark (23), Sweden (16), Norway (9), Iceland (1), France (1), Austria (1), Israel (1)
Number of Sequences: 52
GISAID Query: Spike_S673G, Spike_T883I
CovSpectrum Query: Nextcladepangolineage:XBB* & S:S673G & S:T883I
Substitutions on top of XBB.1.4:
Spike: S673G
Nucleotide: A23579G, T26160C

USHER Tree
https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons/main/XBB%20%2B%20S673G%20%2B%20T883I%20-%20subtreeAuspice1_genome_39a0f_7fc520.json

Evidence
S:S673G is a rare mutation; there have only been 27 non-XBB sequences with S:S673G in the past six months according to CovSpectrum and just 11 sequences in the past two months. Of the 52 sequences, 34 have collection dates of November 2 or later, and 24 sequences have collection dates of November 7 or later. Over half of the sequences in this lineage (27/52) have been uploaded to GISAID in just the past five days (Nov 14-18). This seems to be a rapidly growing lineage.

I don’t know what the expected effect of this mutation would be, but it’s in the neighborhood of the FCS and might be consequential.

Genomes

Genomes

EPI_ISL_15550659, EPI_ISL_15616112, EPI_ISL_15632434, EPI_ISL_15633546, EPI_ISL_15634773, EPI_ISL_15635370, EPI_ISL_15650895, EPI_ISL_15651160, EPI_ISL_15668181, EPI_ISL_15668460, EPI_ISL_15685715, EPI_ISL_15714162, EPI_ISL_15715345, EPI_ISL_15715840, EPI_ISL_15716397, EPI_ISL_15739779, EPI_ISL_15739780, EPI_ISL_15742609, EPI_ISL_15742610, EPI_ISL_15742611, EPI_ISL_15742612, EPI_ISL_15742613, EPI_ISL_15742654, EPI_ISL_15742801, EPI_ISL_15742925, EPI_ISL_15757520, EPI_ISL_15758292, EPI_ISL_15766128, EPI_ISL_15766189, EPI_ISL_15776370, EPI_ISL_15786890, EPI_ISL_15786985, EPI_ISL_15800674, EPI_ISL_15800920, EPI_ISL_15801555, EPI_ISL_15811483, EPI_ISL_15811519, EPI_ISL_15813787, EPI_ISL_15813788, EPI_ISL_15813861, EPI_ISL_15813862, EPI_ISL_15813863, EPI_ISL_15813864, EPI_ISL_15813865, EPI_ISL_15813866, EPI_ISL_15813867, EPI_ISL_15813868, EPI_ISL_15813869, EPI_ISL_15813870, EPI_ISL_15820287, EPI_ISL_15820296, EPI_ISL_15820312

[FedeGueli]

A mutation in the FCS from S to G but at the other end (toward 3' end) of the furin cleavage site emerged experimentally and gave a 100x infectivity booster in vitro via Heparan Sulfate binding:
'The S686G mutation also transforms the FCS into the heparin-binding peptide.'
from
https://www.biorxiv.org/content/10.1101/2021.06.28.450274v1

@thomaspeacock

[ryhisner]

Thanks for the link, @FedeGueli! I wasn't aware of that study, but it's fascinating. It's perhaps worth noting that a BA.2.75.1 from Russia collected on October 4 appears to have had S:S686G. The sequence looks clean. EPI_ISL_15616824

[FedeGueli]

Thx @ryhisner !

[FedeGueli]

60 sequences.

@corneliusroemer @InfrPopGen in our chart this has a initial doubling between 5 and 7 days. it should be designated to be properly monitored

[InfrPopGen]

Thanks for submitting. We've added lineage XBB.1.4.1 with 8 newly designated sequences, and 3 updated designations from XBB.1.4. Defining mutations G2164A (S:S673G), A23579G (following T26160C).

[FedeGueli]

thx @InfrPopGen it reached 71 tonight it seems really fast @ryhisner @corneliusroemer @thomasppeacock