Sublineage of XBB.2.3 (S:F486P) with Orf1b:A241T,Orf7a:H47Y,S:D80Y circualting in India and Uk- 80 sequences

[FedeGueli]

There may be a sublineage of XBB.2.3 that has convergently acquired S:H47Y (BF.5/BF.7.14 ) plus a couple more of AA mutations (S:D80Y and Orf1b:A241T) , it has likely started to circulate in England, but it has originated from India. It may be relevant cause XBB.2.3 is scoring quite high in the last #Collection24 updates

Defining mutations: XBB.2.3 >G29706T> C6031T, C11824T, Orf1b:A241T (G14188A = NSP12_A250T) , G19254A, S:D80Y (G21800T), Orf7a:H47Y (C27532T)

Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_54e3_59aed0.json?c=gt-ORF7a_47&label=id:node_7810443

Gisaid query:NSP12_A250T ,NS7a_H47Y,Spike_D80Y

Sequences : 67 on Usher but just 59 on Gisaid: here a 52 seqs list from CovSepctrum (filtered for good quality) contributors (2).csv

[aviczhl2]

C11824T is the defining mutation of DY.3

[FedeGueli]

80 as today, most of last samples uploaded by England

[c19850727]

@FedeGueli I found 83 sequences by querying spike mutations only. There are 3 with NNNs at ORF7a.

[FedeGueli]

now designated XBB.2.3.1

https://github.com/cov-lineages/pango-designation/commit/c49a12ad2ed34b5de602baddba834c7167b8076e