XBB.2.6 sublineage with S:P521S and Orf9b:P51Q circulating in Peru'/Chile/Brazil/USA, Netherlands, Canada (233 seqs - >20% prevalence in Peru' after April 1st.

[FedeGueli]

I have found a sublineage of XBB.2.6 defined by S:P521S that further acquired Orf9b:P51Q that has been sampled multiple times in US airport surveillance.

Defining mutations:
XBB.2.6 >> > S:P521S (C23123T) > T6895C, T9148C, A15192C, Orf9b:P51Q (C28435A )

Gisaid query: T9148C, A15192C, C28435A

Sequences: 7 (2 Chile, 2 Peru, 3 Us )
EPI_ISL_17168346, EPI_ISL_17271459, EPI_ISL_17286697,
EPI_ISL_17401628, EPI_ISL_17405026, EPI_ISL_17405045,
EPI_ISL_17411947

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2b381_3db880.json?c=userOrOld&label=id:node_6028006

[FedeGueli]

8 Sequences , last one from Chile.

[FedeGueli]

9 sequences last one from Chile

[FedeGueli]

12 sequences as today : 3 more samples two from Lima and one from Brazil, Minais Geras.

Usher shows 13 samples

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_26e0b_af3000.json?c=userOrOld&label=id:node_6091259

[FedeGueli]

Mores samples uploaded today from Peru' plus an airport surveillance from Virginia and one from Texas. total count is 20

[FedeGueli]

Odd but true this is growing fast , 7 new sequences (from March) uploaded by Peruvian scientists:
It is 14 seqs out of 99 collected in peru' after 1st of March .
pinging @corneliusroemer on this one, i would have not bet anything on this but it keeps going in South America.

[corneliusroemer]

Hmm, bit small, also 521S seems to be a bit too homoplasic in XBB.2.6 - maybe some QC issue?

[FedeGueli]

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20860_55bed0.json?c=userOrOld&label=id:node_6126969

Cornelius look at the tree it seems clean. S:P521S is larger than 521S +orf9b:P51Q

There is also a S:490P +S:P521Q that seems growing:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_20860_55bed0.json?label=id:node_6126511

[FedeGueli]

@corneliusroemer i see what you meant the whole xbb.2.6 tree is messy at S:P521S , right, we will see how evolves this sublineage

[corneliusroemer]

Yeah, I think Peru has some QC issues, so that makes Usher struggle distinguishing between real and artefactual homoplasy.

[FedeGueli]

Huge upload from Peru' in the last days it reached 110 sequences , it counts 31 out of 132 samples from Peru' collected after first of April . I am reopening it from the preproposal page asking for a review @corneliusroemer @InfrPopGen @thomasppeacock

New tree:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1a012_e38700.json?label=id:node_6963125

[corneliusroemer]

I've also seen this on a few nextstrain trees now - I'll have a look

[FedeGueli]

One more sequence from Florida

[FedeGueli]

142 seqs as today tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_8edb_60a3c0.json

[FedeGueli]

@corneliusroemer another bump to 166 sequences newly found in Canada and Netherlands.
I think the Orf9b:P51Q could be the key of its apparrent growth.
It is more than 20% of Samples in Peru' ahead of April although looking week by week i can see likely it is starting to go down in the second half of April.
Worth noticing that is one of the few no 486P lineages able to compete nowadays (FK.1/EL.1/XBB.1.31/XBB.1.33/XBB.1.28/FV.1 and ?)

[FedeGueli]

Another big upload from Peru' reaching 233 seqs. Prevalence in Peru' seems slightly less than 20% in the second half od April. Still i think it should be designated