XBB.1 sublineage with S:F486A (32 seq, Denmark, Turkey, Germany, Israel, Austria, USA , Singapore, Australia, Netherlands, Switzerland)

[agamedilab]

Proposal for a sublineage of XBB.1
Earliest sequence: 21.11.2022 (Turkey)
Countries detected: Denmark, Turkey, Germany, Israel, Austria, USA

This sublineage of is defined by S:F486A and was found in five countries so far. It clusters badly in usher because of S:F486A. Subclade also carries S:R346T.

Defining mutation:
T23019C
T23018G = S:F486A

[OLD Gisaid query: T23018G, T23019C, A20262G]
Better query: T23018G, T23019C, C6388T

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_9ed_6573d0.json?c=userOrOld&label=id:node_7983111

EPI_ISL_16330609, EPI_ISL_16414341, EPI_ISL_16414465, EPI_ISL_16423847, EPI_ISL_16424061, EPI_ISL_16591836, EPI_ISL_16591959, EPI_ISL_16646954, EPI_ISL_16739023, EPI_ISL_16813268, EPI_ISL_16831851, EPI_ISL_16831851, EPI_ISL_16847478

OQ351058.1

[AnonymousUserUse]

I do not think the clade with reversion S:T346R is real. Probably it is just bought by dropout of Turkish sequences at the codon S:346.

[agamedilab]

17 as of 20.02.23.

[FedeGueli]

22 as today

[FedeGueli]

28 sequences as today. @corneliusroemer @thomasppeacock @InfrPopGen maybe worth thinking of designate this one.

[agamedilab]

31 on usher, 32 on GISAID as of 09.03.23.
Better query: T23018G, T23019C, C6388T

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_155b_984a40.json?c=gt-nuc_6388

[corneliusroemer]

I'll have a look, but I'm a little cautious because Turkish sequences have had big quality problems in the past.

Based on dates of samples this isn't explosive so not urgent.

There's a lot of diversity. Hence old most recent common ancestor.

[agamedilab]

Many thanks @corneliusroemer

Note only a about five sequences are from Turkey. Sequence quality for most is fine.

[FedeGueli]

38 as today

[corneliusroemer]

Designated - it's actually quite clean - there are lots of other mutations that are correlated in this lineage so not an issue. It seems to be particularly common in Turkey.