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

[FedeGueli]

SO i ve changed the title of the issue consequently.

Multiple lineages as 12-01-23

1) Main post : Spike_V83A,Spike_L368I,Spike_F490P,Spike_G252V,-Spike_Q677L, NUC: -T24796C, - C4999T, -C745T

40 viruses

2) 2nd Lineage: Spike_V83A,Spike_L368I,Spike_F490P,Spike_G252V plus NUC: C4999T, A14427G

11 viruses

3) 3rd Lineage: NUC:C745T,T10939C,A28540G,A8897G, T23030C,

3 sequences

[FedeGueli]

I fully edited this proposal while there are multiple lineages with S:F490P popping up in XBB.1 and XBB.1.5

Here i want to propose just the one found by: -G1466A,-C12439T, -T24796C, - C4999T, -C745T,T23031C , G22895C, T22896C ,C22664A , G22317T , G27915T, T23030C finds 45 sequences as 24/01/2023

cc @thomasppeacock @corneliusroemer @InfrPopGen please take a look.

[FedeGueli]

9 sequences uploaded today from Alaska and Georgia in the US and newly found in Czechia (4 samples which cluster with an austrian sample) Given it is quite widespread from Usa to Uk, from Malaysia to Australia , and in central europe is uggest to designate it, as you can see there are more sequences on Usher than the ones uploaded to Gisaid:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_270c7_1ca1f0.json?c=country&label=id:node_7869707

@thomasppeacock @corneliusroemer @InfrPopGen consider it shows an early advantage versus parental XBB.1 ( considering in it also XBB.1.5) : https://cov-spectrum.org/explore/World/AllSamples/from=2022-11-15&to=2023-01-25/variants?nextcladePangoLineage=XBB.1*&nucMutations1=T23031C%2CG22895C%2CT22896C%2CC22664A%2CG22317T%2CG27915T%2CT23030C%2C24796T%2C4999C%2C745C%2C1466G%2C12439C&analysisMode=CompareToBaseline&

While it is not far from XBB.1.5 itself :

[FedeGueli]

60 seqeunces as today growing steadily last samples from Texas, and Georgia

[FedeGueli]

62 viruses as today . It is spreading quite well in Georgia .

@corneliusroemer i think it could be designated at this point

[FedeGueli]

On Usher it is already 79 sequences: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_a346_2da650.json?c=userOrOld&label=id:node_7976128

[FedeGueli]

68 sequences with 3 new samples from Czechia. i think it is worth designating it.

cc @corneliusroemer note that onUsher they are already 85 sequences: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1adb3_566c60.json?c=userOrOld&label=id:node_7988092