XBB.1.5* with S:R403K and S:L582F (8 sequences - South Africa)

[FedeGueli]

There may be a XBB..5 sublineage circulating in Gauteng that have gained further two spike mutations: S:R403K,S:L582F.

It is just two samples so not necessarily could have any relevance. Put here to check for a while and eventually closing it.
the predicted composite fitness is increased by ACE2 binding going up, but i have to say i still never saw any mayor boost in transmissibility as with S:Y453F.

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e3d5_59ac0.json?c=gt-S_403&label=id:node_7752195

Defining mutations:
XBB.1.5 > C21811T > T10204C >C6031T, C22498A , S:RT403K (G22770A),S:L582F (C23306T)
(Note that i exclude a bunch of reversions here, we will see if they are real)

Sequences:EPI_ISL_17222285, EPI_ISL_17285135

Gisaid query: Spike_F486P,Spike_L582F,Spike_R403K

[FedeGueli]

Third sequence came from Gauteng

[FedeGueli]

4 sequences now.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice10_genome_2af10_de6b30.json?c=gt-nuc_6031&label=id:node_7802750

[FedeGueli]

5 sequences as today:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice18_genome_43bea_b994c0.json?c=userOrOld&label=id:node_5921827

[FedeGueli]

4 new sequences uploaded from South Africa and one from Canada but this last one is not placed in the same tree by Usher due to presence of 12919 and absence of 10204 and 6031

total count 9

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_55066_3e9a20.json?c=userOrOld&label=id:node_5949306

[FedeGueli]

Now designated XBB.1.5.53 via c5a06b0

[InfrPopGen]

Hi @corneliusroemer these appear to be duplicated in lineages.csv (and can see similar effect in the first pair of sequences, at top, of the first tree in this issue above); for example (in lineages.csv),
SouthAfrica/NICD-N54078/2023,XBB.1.5.53
South_Africa/NICD-N54078/2023,XBB.1.5.53
...
South_Africa/NICD-N54038/2023,XBB.1.5.53
SouthAfrica/NICD-N54038/2023,XBB.1.5.53

These cryptic duplicates could easily creep in, as they appear to be present at source.