FL.4 + S:T478R (around 186 seqs) as 18/08/2023 with a recombinant sublineage (with BA.5?) from Hawaii carryind S:N556K (10Seqs)

FedeGueli commented 1 year ago

Just a ping to @corneliusroemer for next designathlon : in FL.4 there is a quite big indonesian only sublineage with S:T478R without any nuc mutations from the politomy. I Think it is easier just pinging you here than making a complete issue hence the query will catch other unrelated sequences (as the FL.4.1 preproposed today)

At the moment low priority since i dont think it has any special advantage

Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3aea6_328f20.json?c=gt-S_478&label=id:node_6714994

FL.4 (G16741T)> C22995G Gisaid query finds more than 200 while this one is around 90seqs G16741T,C22995G

NkRMnZr commented 1 year ago

Has this one been solved (don't think so)? It is still growing

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5ea7_c06110.json?c=country&label=id:node_6684336&showBranchLabels=all

view from FL.4 polytomy: FL 4+T478R

detailed: details

Genomes:

EPI_ISL_17469972, EPI_ISL_17469998, EPI_ISL_17470011, EPI_ISL_17470032, EPI_ISL_17561648, EPI_ISL_17654976, EPI_ISL_17655060, EPI_ISL_17655101, EPI_ISL_17681446, EPI_ISL_17681561, EPI_ISL_17681571, EPI_ISL_17686586, EPI_ISL_17696411, EPI_ISL_17696438-17696439, EPI_ISL_17696442, EPI_ISL_17696445, EPI_ISL_17696448, EPI_ISL_17696451, EPI_ISL_17696455, EPI_ISL_17696475, EPI_ISL_17696477, EPI_ISL_17696483-17696484, EPI_ISL_17696501, EPI_ISL_17696528, EPI_ISL_17696531, EPI_ISL_17696533, EPI_ISL_17696539, EPI_ISL_17696552, EPI_ISL_17696564-17696565, EPI_ISL_17696572, EPI_ISL_17696581, EPI_ISL_17704098, EPI_ISL_17704100, EPI_ISL_17719531, EPI_ISL_17719533, EPI_ISL_17719558-17719559, EPI_ISL_17719597, EPI_ISL_17721531, EPI_ISL_17724781, EPI_ISL_17724796, EPI_ISL_17730727, EPI_ISL_17736294, EPI_ISL_17736304-17736305, EPI_ISL_17736334-17736335, EPI_ISL_17736361, EPI_ISL_17736365, EPI_ISL_17736376, EPI_ISL_17741455, EPI_ISL_17761890, EPI_ISL_17763537, EPI_ISL_17763548, EPI_ISL_17778932, EPI_ISL_17779725, EPI_ISL_17779782, EPI_ISL_17788352, EPI_ISL_17797309, EPI_ISL_17803088, EPI_ISL_17803253, EPI_ISL_17807694, EPI_ISL_17807950, EPI_ISL_17813343, EPI_ISL_17813351, EPI_ISL_17813383, EPI_ISL_17813444, EPI_ISL_17815650, EPI_ISL_17815660, EPI_ISL_17816603, EPI_ISL_17831784, EPI_ISL_17833332, EPI_ISL_17833335, EPI_ISL_17833347, EPI_ISL_17833365, EPI_ISL_17833367, EPI_ISL_17833376, EPI_ISL_17833417, EPI_ISL_17835845, EPI_ISL_17835932, EPI_ISL_17836017, EPI_ISL_17836054, EPI_ISL_17836070, EPI_ISL_17836075, EPI_ISL_17836082, EPI_ISL_17836183, EPI_ISL_17837810, EPI_ISL_17837856

FedeGueli commented 1 year ago

@corneliusroemer @InfrPopGen as @NkRMnZr noticed this kept growing and reched aroudn 90 sequences, it is very hard to track cause it stems out directly from the politomy of FL.4. I suggest a designation for two reason: 1) Mutation of interest growing globally 2) semplification of the tree cause it is quite big and eaasy to meet having a name would be useful to track easily.

FedeGueli commented 1 year ago

This is now 130 sequences: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6830_5bcb00.json?c=userOrOld&label=id:node_6706291 Schermata 2023-07-05 alle 20 59 00

cc @InfrPopGen @corneliusroemer @thomaspeacock @AngieHinrichs i suggest to review and designate this one. here the sequences belonging to this lineage:

strain

FedeGueli commented 1 year ago

Schermata 2023-07-17 alle 02 08 28 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_d495_485f60.json?label=id:node_6730367

FedeGueli commented 1 year ago

I count now around 160 seqeunces of this one: Schermata 2023-08-01 alle 12 19 36 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d6c2_8d8a20.json?c=userOrOld&label=id:node_6792144

FedeGueli commented 1 year ago

183 sequences now. I noticed a recent branch that has further acquired S:N556K Schermata 2023-08-10 alle 00 26 10

The same branch interestingly has a double reversion of XBB.1.9 and BA.2 defining suggesting a possible recombination maybe with a BA.5 lineage. Schermata 2023-08-10 alle 00 33 57

FedeGueli commented 12 months ago

Designated FL.4.8 via https://github.com/cov-lineages/pango-designation/commit/1118b71b9c28e45592eb3ccb485dfc2ace12a877

Please add milestone.

cov-lineages / pango-designation

FL.4 + S:T478R (around 186 seqs) as 18/08/2023 with a recombinant sublineage (with BA.5?) from Hawaii carryind S:N556K (10Seqs) #2024

strain