XBB.1 sublineage with S:F490P : 68 sequences - Usa , Czechia, Uk, Malaysia, Austria -EDITED as 09/02/23

[FedeGueli]

I totally edited this proposal.
I would like to highlight to Pango team that S:f490P has been actually picked up by plenty XBB.1 and XBB.1.5 lineages.

Here i propose the biggest one:
On Usher is already 60 Sequences while Gisaid finds only 45, so i will keep only the Gisaid number of sequences in the headline.

Tree:

/87669813/214245297-b996e9e6-c778-4c5b-ac06-3dc649a54f62.png"> https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1fd49_f96b60.json?c=gt-S_490&label=id:node_7864390

Countries

Defining mutations:
XBB.1+ Orf8:G8* (G27915T ) + S:490P (T23030C) from S:F490S

Gisaid query : -T24796C, - C4999T, -C745T,T23031C , G22895C, T22896C ,C22664A , G22317T , G27915T, T23030C finds 47 viruses:

Expand for EPI_ISLs

EPI_ISL_15779494, EPI_ISL_15783850, EPI_ISL_15850447, EPI_ISL_15922900, EPI_ISL_16062761, EPI_ISL_16081265, EPI_ISL_16082493, EPI_ISL_16098932, EPI_ISL_16108499, EPI_ISL_16158794, EPI_ISL_16174510, EPI_ISL_16206578, EPI_ISL_16212647, EPI_ISL_16212650, EPI_ISL_16251102, EPI_ISL_16252833, EPI_ISL_16266009, EPI_ISL_16307624, EPI_ISL_16307637, EPI_ISL_16320263, EPI_ISL_16343245, EPI_ISL_16345430, EPI_ISL_16380935, EPI_ISL_16398743, EPI_ISL_16412740, EPI_ISL_16439631, EPI_ISL_16439654, EPI_ISL_16439685, EPI_ISL_16477580, EPI_ISL_16482966, EPI_ISL_16484263, EPI_ISL_16489874, EPI_ISL_16507763, EPI_ISL_16510859, EPI_ISL_16511583, EPI_ISL_16525874, EPI_ISL_16533953, EPI_ISL_16557322, EPI_ISL_16572743, EPI_ISL_16575442, EPI_ISL_16580025, EPI_ISL_16583385, EPI_ISL_16598649, EPI_ISL_16619782, EPI_ISL_16629141,

[corneliusroemer]

How do we know this is not an ancestor of XBB.1.5? Does it have any nuc mutation that XBB.1.5 doesn't have?

Especially considering this lineage is being found in NY, why do we think this is not the ancestor of XBB.1.5 which simply gained another silent mutation and then got a lucky super spread around NYC?

[silcn]

@corneliusroemer F486P ≠ F490P

[corneliusroemer]

Oh god, I'm blind. Sorry!

[corneliusroemer]

Usher seems to have multiple clusters of XBB.1 + S:490P. Which one is this one here?

Here's the biggest, a very international, which branches off XBB.1 directly:

Then there's a predominantly Malaysian one after C4999T, A14427G

And then there's another deep US-NY on a branch with among others A8897G