XBB.1.5 + S:I410V and S:P521S circulating in central europe 199 sequences as today (18-03-23)

[FedeGueli]

I spotted this sublineage of XBB.1.5 that seems accumulating fastly sequences in Germany, Austria (spike only samples), Netherlands and was sampled also in England, Scotalnd, Singapore (one local case and one in a traveller from Switzerland.

It captured my attention cause it is characterized by two spike mutation one in Rbd and the other right after RBD

Defining mutations:
XBB.1.5 > > C920T > C21910A > S:p521S (C23123T) > SPike:I410V (A22790G )

Tree ( note that 13 spike only sequences are missing from it):

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d83f_7e9b70.json?c=userOrOld&label=id:node_7652127

Gisaid query: Spike_I410V,Spike_P521S,Spike_F486P

Sequences: EPI_ISL_16874995, EPI_ISL_16899435, EPI_ISL_16905264,
EPI_ISL_16942932, EPI_ISL_16943133, EPI_ISL_16963356,
EPI_ISL_16978268, EPI_ISL_16996741, EPI_ISL_17004417,
EPI_ISL_17004420, EPI_ISL_17004519, EPI_ISL_17004533,
EPI_ISL_17004563, EPI_ISL_17006050, EPI_ISL_17006760,
EPI_ISL_17006837, EPI_ISL_17010099, EPI_ISL_17010112,
EPI_ISL_17010157, EPI_ISL_17010185, EPI_ISL_17010323,
EPI_ISL_17010543, EPI_ISL_17010552, EPI_ISL_17010691,
EPI_ISL_17011339, EPI_ISL_17011808

Predicted composite fitness is not better than original, but i dont know if any epistasis is at work here ( @thomaspeacock) :

[FedeGueli]

31 as today. all new samples from Austria (spike only seqs)

[FedeGueli]

34 sequences as today newly found in Denmark and Luxembourg beyond Germany, Austria, Netherlands, Uk, Singapore, Australia

[FedeGueli]

54 sequences as today, just from march uploads i see Iceland, Italy, Usa , Netherlands, Germany , Austria. I think this deserves a designation. @corneliusroemer @InfrPopGen

[FedeGueli]

New sequences are accumulating from central europe: last samples from Denmark Netherlands and Germany

[FedeGueli]

@corneliusroemer @thomasppeacock @InfrPopGen big jump of this sublineage in the last days:
It appears to be circulating in Germany , Austria, Denmark and Netherlands
More than half of its samples have been collected after 20th of february,
Its prevalence in the last 20 days in Austria Denmark and Netherlands is around 1%

I suggest to designate it .

[FedeGueli]

135 sequences with the last ones mostly coming from Austria with singlets from Denmark and Netherlands

[FedeGueli]

@thomasppeacock i think that differently from other XBB.1.5 sublineages proposed by me where the spike mutation seems to identify a local lineage with limited spread outside , this is circulating widely in at least 4 countries in Central Europe.

[FedeGueli]

@thomasppeacock @corneliusroemer @AngieHinrichs @InfrPopGen
Big upload yesterday from Austria it Jumped to 199, its last doubling estimated via Cornelius alternative method is 7 days ,
in comparison to 6 Days of XBB.1.16 and XBB.1+486PD215H from Africa.
Parent XBB.1.5 is far at 14 days and the XBB.1.9Twins and XBB.1+486P*Y200C (that has orf1b:5t too) are at 11 days.

I would designate this one.

[corneliusroemer]

Couldn't decide where to start so went all in with the 920T branch being XBB.1.5.26, S:521S being EU.1, and S:410V being EU.1.1

It's not clear if 410V is founder or not, hence makes sense to designate also the parent with just 521S.

[FedeGueli]

Thx @corneliusroemer for your great work. Agree wit your choice to differentiate it more than the proposed. thx.