XBB.2.3 sublineage with S:E654K and possible S:K478T reversion (44 seqs in India, US,France ,Canada )

[HynnSpylor]

Defining mutations:
XBB.2.3> C5622T (ORF1a:P1786L =NSP3_P968L = PLPro_P223L)> C7303A> C10776T (ORF1a:P3504L), C22624T, G23522A (S:E654K) (Edited)
GISAID query: C7303A, C10776T, G23522A
Earliest seq: 2023-06-20 (Maharashtra, India- EPI_ISL_18052802)
Most recent seq: 2023-08-24 (Maharashtra, India- EPI_ISL_18209977)
Countries detected: India (24, including 1 detected in US International Airport), US (1)

Usher Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_10b57_1ed5f0.json?c=gt-S_654

It is a branch with S:G184V ( proposed but undesignated in cov-lineages/pango-designation#1945) but without another defining mutation of XBB.2.3.2 (ORF1a:R2159W), hence it is not classified as XBB.2.3.2

Another notable feature is the almost seqs are possible S:K478T reversion. If we show the S:478 on neighbored branches, the other branch are not the concentrative reversion. Moreover, if we query the other samples updated in the same batch on GISAID, the samples outside the branch are all showing the S:T478X mutation. Therefore, I suggest the reversion is possibly true instead of artefacts.

*The branch accounts for >30% of samples updated in India today, and over half of them are collected in last 10 days.

Genomes:
EPI_ISL_18052798, EPI_ISL_18052802, EPI_ISL_18120273, EPI_ISL_18120276, EPI_ISL_18125007, EPI_ISL_18126472,
EPI_ISL_18209930-18209931, EPI_ISL_18209936, EPI_ISL_18209945, EPI_ISL_18209947-18209948, EPI_ISL_18209950-18209951, EPI_ISL_18209954, EPI_ISL_18209959, EPI_ISL_18209961, EPI_ISL_18209967, EPI_ISL_18209969, EPI_ISL_18209973,
EPI_ISL_18209976-18209977, EPI_ISL_18209980-18209981, EPI_ISL_18209983

[FedeGueli]

Thx for proposing also @ryhisner noticed it.
S:T478T is a trend i was trying to tracking and does not surprise me that is now blooming out. thank you.

[FedeGueli]

That branch is a long time pending proposal by @aviczhl2 cov-lineages/pango-designation#1945

cc @corneliusroemer could you take a look an undesignated branch is giving birth to fast (apparently) lineages.

[FedeGueli]

Being at 35% in MH and already went from 1 to 25 in one month in a very low sequencing area. i think it is better to propose directly. great spot @HynnSpylor and @ryhisner

[HynnSpylor]

Thx @FedeGueli!

[FedeGueli]

44 seqs now. it slowed down but it was found in 2 more countries i think it is worth a proposal once it has reached 50.

It has to be noticed that Orf1a:P1786L is NSP3_P968L > PLPro_P223L

[FedeGueli]

Designated JY.1 via cov-lineages/pango-designation@e4f431b