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XBB.1 sublineage with S:F490P : 68 sequences - Usa , Czechia, Uk, Malaysia, Austria -EDITED as 09/02/23 #1487
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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? |
@corneliusroemer F486P ≠ F490P |
Oh god, I'm blind. Sorry! |
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
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I fully edited this proposal Here i want to propose just the one found by: -G1466A,-C12439T, -T24796C, - C4999T, -C745T,T23031C , G22895C, T22896C ,C22664A , G22317T , G27915T, T23030C cc @thomasppeacock @corneliusroemer @InfrPopGen please take a look. |
9 sequences uploaded today from Alaska and Georgia in the US and newly found in Czechia (4 samples which cluster with an austrian sample) @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& |
60 seqeunces as today growing steadily last samples from Texas, and Georgia |
62 viruses as today . It is spreading quite well in Georgia . @corneliusroemer i think it could be designated at this point |
On Usher it is already 79 sequences: |
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: |
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,The text was updated successfully, but these errors were encountered: