JB.2 (S:R403K,T478R) sublineage circulating in South Africa with S:H245Y & S:E554D (17 samples) and a further sublineage with S:T500A (4)

[FedeGueli]

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_38b57_dbb2d0.json?label=id:node_10275433

Gisaid query: C22295T, G23224T, G22770A

Samples: 1
EPI_ISL_17801585

Def mutations:
XBB.1.5.53 >> G22770A (S:r403K) C22295T (S:H245Y) A22995G (S:T478R), G23224T (S:E554D)

[FedeGueli]

Another sequence of this one popped up from South Africa, although quite old from the start of May (EPI_ISL_17859332)
This last sample gained S:T500A and S:L582F

[FedeGueli]

third sample of this came from SA but it is the oldest of them! (from April..) lets wait how is this going really on the ground.

[FedeGueli]

Parental lineage with S:K478R designated JB.2

[silcn]

Quite a few more in today's South Africa upload @FedeGueli

[FedeGueli]

Quite a few more in today's South Africa upload @FedeGueli

wow 17 now! i am ushering to understand if it makes sense to propose this as sublineage of JB.2 or not.
(Btw interesting to say a shadow convergence with BA.2.86 in 3 out 4 defining mutations, shadow cause we were tracking these ones but likely the same immunity landscape favored the emergence of the other much more heavily mutated lineage.

and thank you for noticing!

[FedeGueli]

Thanks to @silcn i have reopened this one cause it is recently circulating in South Africa and keeping acquiring spike mutations.
If you have time @corneliusroemer i think the whole tree could give a couple more of sublineage of JB.2:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_227c1_5513a0.json?label=id:node_7074602

[FedeGueli]

Designated JB.2.1 via cov-lineages/pango-designation@5140e40

cc @silcn thank you!