Double headed sublineage of XBB.2.3 with S:S494P one with Orf8:I58T likely emerged in Philippines (61 sequences) and its apparently sibling lineage defined by silent S:R498R (14 seqs- see what this means in the great comment by Ryan Hisner)

[FedeGueli]

Originally preproposed in: sars-cov-2-variants/lineage-proposals#58 (already tracked there for a while)

Despite never being sampled in Philippines this sublineage of XBB.2.3 likely emerged there cause three samples from travellers from Philippines were sampled by South Korea and Singapore.

Here i want to highlight this sublineage that stems out of XBB.2.3 politomy with S:S494P and then divides in two:
Lineage A defined by Orf8:I58T
Lineage B defined by the silent nuc mutation :C23054A

Defining mutations:
XBB.2.3>>> G29706T > C4234T > ORF1a:G2091S (G6536A) > S:S494P ( T23042C)

Lineage A (Philippines)> Orf8:I58T (28066C )
Lineage B (S:R498R,Ryan) >C23054A

Gisaid queries :
Lineage A
T23042C,T28066C finds 59seqs
Lineage B
T23042C,C23054A finds 14seqs

COMMENTARY on LINEAGE B by @ryhisner:
"Thanks for the reminder, Fede! I noticed that one branch of this lineage has a synonymous nucleotide mutation in S:498 (C23045A), as pictured below.

While this doesn't change the amino acid there, it does open the door to other S:498 mutations that were previously two nucleotide mutations away—R498I and R498T. Furthermore, R498K becomes easier to reach, requiring only a relatively common G->A mutation instead of the less common C->A. The path to R498G also becomes much easier, requiring a relatively common A->G mutation rather than a C->G, which is the rarest of all nucleotide mutations.

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_24c9_6e4ed0.json?label=id:node_7000738

Samples:
Lineage A
EPI_ISL_16549280, EPI_ISL_17168341, EPI_ISL_17168401,
EPI_ISL_17238701, EPI_ISL_17252364, EPI_ISL_17293312,
EPI_ISL_17326972, EPI_ISL_17374102, EPI_ISL_17465459,
EPI_ISL_17480762, EPI_ISL_17495941, EPI_ISL_17495998,
EPI_ISL_17537072, EPI_ISL_17539414, EPI_ISL_17539507,
EPI_ISL_17539555, EPI_ISL_17543402, EPI_ISL_17545449,
EPI_ISL_17548165, EPI_ISL_17549922, EPI_ISL_17550514,
EPI_ISL_17552197, EPI_ISL_17589231, EPI_ISL_17594924,
EPI_ISL_17596098, EPI_ISL_17606093, EPI_ISL_17615680,
EPI_ISL_17625670, EPI_ISL_17629944, EPI_ISL_17631450,
EPI_ISL_17631461, EPI_ISL_17649134, EPI_ISL_17651213,
EPI_ISL_17653113, EPI_ISL_17660042, EPI_ISL_17672349,
EPI_ISL_17672456, EPI_ISL_17672505, EPI_ISL_17678279,
EPI_ISL_17680288-17680289, EPI_ISL_17680469, EPI_ISL_17683647,
EPI_ISL_17683671, EPI_ISL_17685879, EPI_ISL_17685922,
EPI_ISL_17686994, EPI_ISL_17688864, EPI_ISL_17695041,
EPI_ISL_17698121, EPI_ISL_17704340, EPI_ISL_17718640,
EPI_ISL_17718874, EPI_ISL_17719157, EPI_ISL_17723677,
EPI_ISL_17724700, EPI_ISL_17726321, EPI_ISL_17727158,

Lineage B
EPI_ISL_9835845, EPI_ISL_11469711, EPI_ISL_11469841,
EPI_ISL_17190074, EPI_ISL_17236435, EPI_ISL_17326136,
EPI_ISL_17372484, EPI_ISL_17523639, EPI_ISL_17523650,
EPI_ISL_17565963, EPI_ISL_17588278, EPI_ISL_17666427,
EPI_ISL_17685936, EPI_ISL_17714613

[FedeGueli]

2 new for seqs lineage A from two different US states (California/Iowa)