XBB.1 with S:P521S and S:R403K apparently circulating in Himachal Pradesh , India 14 sequences

[FedeGueli]

I spotted this little sublienage that may circulate in Himachal Pradesh India, being defined by two mutations expected to increase potentially viral fitness i propose it to keep it monitored while India is surging its sequencing efforts

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_16efd_c479a0.json?c=userOrOld&label=id:node_7686014

Defining mutations: XBB.1 >> > C11956T > C26522T > S:P521S (C23123T) >S:R403K ( G22770A)

Gisaid query : C11956T , C26522T ,C23123T,G22770A

Sequences : 7 hCoV-19/India/HP-NII-1586/2023|EPI_ISL_17257455|2023-02-27 India/HP-NII-1568/2023|EPI_ISL_17096481|2023-02-17 hCoV-19/India/HP-NII-1608/2023|EPI_ISL_17257476|2023-02-28 hCoV-19/India/HP-NII-1607/2023|EPI_ISL_17257475|2023-02-28 India/HP-INSACOG-NII-1539/2023|EPI_ISL_16649090|2023-01-06 hCoV-19/India/HP-NII-1606/2023|EPI_ISL_17257474|2023-02-27 India/HP-NII-1606/2023|EPI_ISL_17257474|2023-02-27

[FedeGueli]

A couple more of sequences of this sublineage are misplaced on Usher tree in one of that trashbin trees with many reversions. (cc @AngieHinrichs ) https://nextstrain.org/fetch/genome.ucsc.edu/t

rash/ct/subtreeAuspice3_genome_16efd_c479a0.json?label=id:node_9856447

So the total count should be 9.

[AngieHinrichs]

Those two sequences have such a high number of reversions that they have been excluded from the tree (they would form a bigger trash-magnet!) But point taken, that little branch that pulled them in is just XBB > 3 reversions, and is more harm than help in this case.

[FedeGueli]

Thx @AngieHinrichs !!

[FedeGueli]

10 as today

[FedeGueli]

12 as today: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1540f_3b2960.json?c=userOrOld&label=id:node_5827899

[FedeGueli]

PS: the S.Korean sequence is from airport surveillance (travel related with India)

[FedeGueli]

Notably some sequences has S:A344T @corneliusroemer could u give a look at this sublineage? Surely very small but in my view it seems another evolution route for XBB.1 convergent with other lineages

[FedeGueli]

One new sequence came from Delhi with 681R and 344T:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_37bd2_b8bdd0.json?label=id:node_5819304

[corneliusroemer]

Lacking 486P this is unlikely to grow much more against competition from XBB.1.16 - I'll close for now. Not enough good quality sequences to allow designation.