XBB.1.5 (on T10204C) with S:Q1201K, S:V70F, deletion/frameshift around S:183-185 (S:Q183del, S:G184E S:N185D) and S:F456L (14 seqs, USA, Mexico, Australia, Canada)

[NkRMnZr]

Defining Mutations: XBB.1.5 [T17124C > T23018C] > C25163A(S:Q1201K) > C25162A > T10204C > T3520A, G21770T(S:V70F), T22928C(S:F456L)
Query: T3520A, G21770T, T22928C
Earliest seq: 2023-06-30 (EPI_ISL_18120766, California, USA)
Latest seq: 2023-08-04 (EPI_ISL_18098800, Texas, USA)
Sampled Countries: USA (8: Texas/4; Arizona/1; California/1; Florida/1; Louisiana/1), Mexico (1)

Genomes:

EPI_ISL_18037725, EPI_ISL_18057193, EPI_ISL_18057605, EPI_ISL_18057616, EPI_ISL_18098800, EPI_ISL_18104608, EPI_ISL_18120766, EPI_ISL_18133696, EPI_ISL_18137440

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_13191_9fe3d0.json?c=gt-nuc_10204,22928&label=id:node_7204018

Trivia:

• The tree is quite messy again, this time probably due to a deletion around S:183-185 causing frameshit, nextclade think it's S:Q183Δ, S:G184E and S:N185D. This is not the 1st case of deletion around that area, one other example being XBB.1.5 Sublineage with S:∆180-184, S:N185D, S:F456L, ORF1a:T1437I (36 seq, Aug 14) #592.
  

• UShER puts T10204C after some changes around S:1200-1201, one silent and one aa change, that could be some kind of mis-placement (or another cause of it).
  

[FedeGueli]

Very interesting lineage for mutations, deletions and also that double nuc spike mutation. cc @ryhisner if you have a time this could be interesting.

[ryhisner]

The 2-nuc change at S:1200-1201 has occurred again and again, and Marc Johnson has even noticed it in several cryptic wastewater lineages. Like many multi-nuc mutations, it's TRS related.

.

In BA.2.3.20, there were even a handful of sequences that went the whole distance to get the ideal TRS sequence, though this is far less common than the S:Q1201K version.

[ryhisner]

Definitely an interesting lineage though. Are deletions in the N4 NTD loop coming into favor? N4 is the only NTD loop that has so far not seen many deletions, but the fitness landscape is constantly changing, and there are at least three lineages now with deletions in N4.

I wonder if this one might me fairly prominent in Mexico or other Central American countries from which we've had almost no sequencing in the past two months.

[FedeGueli]

Thank you very much @ryhisner

[FedeGueli]

it seems slow. waiting a week more befoe closing.

[NkRMnZr]

09-08, 1 more from California: EPI_ISL_18232886

[NkRMnZr]

no more sequences

[NkRMnZr]

Landing in Queensland, Australia EPI_ISL_18324505