XBB.1.41.1 with ORF1a:V1056L(nsp3_V238L) and S:G339R (G>D>H>R) through A22578G_reversion (56 seqs, mainly in Greece, 9 countries)

[NkRMnZr]

Defining Mutations: XBB.1.41 > C18877T > T1657C, G3431T(ORF1a:V1056L), A22578G_reversion(S:G339R)
Query: T1657C, G3431T, C18877T
Earliest seq: 2023-07-16 (EPI_ISL_18314292, Attica, Greece)
Latest seq: 2023-10-02 (EPI_ISL_18387126, Auvergne-Rhône-Alpes, France, OR EPI_ISL_18356714, Dublin, Ireland)
Sampled Countries: Greece (35), France (11), Finland (2), Israel (2), Italy (2), Denmark (1), Ireland (1), Sweden (1), UK (1: SC)

Genomes:

EPI_ISL_18218408, EPI_ISL_18226767, EPI_ISL_18229415, EPI_ISL_18294252, EPI_ISL_18294254, EPI_ISL_18300223, EPI_ISL_18314292-18314294, EPI_ISL_18314343-18314344, EPI_ISL_18314347, EPI_ISL_18314361, EPI_ISL_18314398, EPI_ISL_18314402, EPI_ISL_18314405, EPI_ISL_18314418, EPI_ISL_18314430, EPI_ISL_18314442, EPI_ISL_18314495, EPI_ISL_18314620-18314621, EPI_ISL_18314663, EPI_ISL_18314674, EPI_ISL_18314682-18314683, EPI_ISL_18314779, EPI_ISL_18314781, EPI_ISL_18314786, EPI_ISL_18314793, EPI_ISL_18314798, EPI_ISL_18314836, EPI_ISL_18314934-18314936, EPI_ISL_18315038, EPI_ISL_18315062, EPI_ISL_18315076, EPI_ISL_18315174, EPI_ISL_18315180, EPI_ISL_18315185, EPI_ISL_18326463, EPI_ISL_18326511, EPI_ISL_18326582, EPI_ISL_18338154, EPI_ISL_18338536, EPI_ISL_18347850, EPI_ISL_18347853, EPI_ISL_18356714, EPI_ISL_18360405, EPI_ISL_18362853, EPI_ISL_18366842, EPI_ISL_18387090, EPI_ISL_18387126, EPI_ISL_18387163, EPI_ISL_18387514

UShER:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3f816_ba9490.json?f_userOrOld=uploaded%20sample&label=id:node_3530104

Trivia:

• UShER seems to mask spike_339, as you can see multiple branches labeled with S:H339R only when you upload those sequences.
• This site seems heavily selected for, it is S:G339D(G22578A) introduced since B.1.1.529, then got further mutated into S:G339H(G22577C, G22578A) from BA.2.75 (also on BA.2.86), which got inherited by XBB, and this lineage reverts A22578G to make it S:G339R, if not artifact, that's some 3-step mutations from G to D to H to R.
• S:G339R only has about 310 seqs on GISAID to date, this lineage represents 20% of them.
  

[xz-keg]

Designated JC.2 @FedeGueli

[FedeGueli]

Designated JC.2 via cov-lineages/pango-designation@9b30a50

(flash issue!)

[FedeGueli]

I was looking at this one for a second time some thoughts:
it is no more a local lineage and have spread in multiple countries
could be S:L335S to enable S:G339R ?
Interesting the trend in positive charge from G to R at 339