New XBB.1 branch with S:F490P circulating in Indonesia, Malaysia, South Korea ,Singapore , Vietnam, Turkey, Russia (64 seqs)

[FedeGueli]

I was checking S:F490P as mutation and i met this undesignated lineage of XBB.1 that seems to have some circulation in Indonesia after emerging earlier at the end of 2022 in Malaysia.
S:F490P doesnt seem to be competitive vs lineage carrying S:F486P and doesnt seem to act synergically when popping up in a S:F486P carrying lineage.
Still being from an undersampled area maybe worth keeping track of it

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice10_genome_3b97f_9dc250.json?c=country&label=id:node_7685578

Defining mutations:

XBB.1> Orf8:G8*> A14427G > C4999T > S:F490P (T23030C)

Gisaid query: A14427G ,C4999T ,T23030C

Sequences: 49 (last sample uploaded yesterday from NZL)
EPI_ISL_15796050, EPI_ISL_16016295, EPI_ISL_16040754,
EPI_ISL_16073962, EPI_ISL_16098123, EPI_ISL_16159398,
EPI_ISL_16240912, EPI_ISL_16288248, EPI_ISL_16399430,
EPI_ISL_16412718, EPI_ISL_16469725, EPI_ISL_16486933,
EPI_ISL_16600605, EPI_ISL_16647624, EPI_ISL_16647660,
EPI_ISL_16647701, EPI_ISL_16676408, EPI_ISL_16807835,
EPI_ISL_16847574, EPI_ISL_16858176, EPI_ISL_16882169,
EPI_ISL_16899385, EPI_ISL_16899399, EPI_ISL_16905258,
EPI_ISL_16947606, EPI_ISL_16947608, EPI_ISL_16975289,
EPI_ISL_16975424-16975425, EPI_ISL_16975433-16975434, EPI_ISL_17012198,
EPI_ISL_17012200, EPI_ISL_17012222, EPI_ISL_17012237,
EPI_ISL_17016363, EPI_ISL_17045341, EPI_ISL_17045352,
EPI_ISL_17081697, EPI_ISL_17090224, EPI_ISL_17094203,
EPI_ISL_17156428, EPI_ISL_17189122, EPI_ISL_17189129,
EPI_ISL_17207379, EPI_ISL_17213330, EPI_ISL_17213341,
EPI_ISL_17213346, EPI_ISL_17252337

[FedeGueli]

Last samples came from Singapore and South Korea both local cases

[FedeGueli]

57 as today.

[FedeGueli]

It is not fast but uploading last samples to Usher it is easy to get that some branches are quite loaded of mutations, worth keeep this open for a while.

[FedeGueli]

64 sequences as today but the fact very interesting here is its geographical spread. Today we had two airport samples from S.Korea one with travel history from Turkey the other with travel history from Vietnam, plus a bunch of sequences from Moscow and one very recent from Malaysia.

At this point i would suggest to designate to keep it tracked easily: @InfrPopGen @thomasppeacock

[InfrPopGen]

Thanks for submitting. Although this clade is not showing any growth advantages at all, based on the assumption that it is circulating in a less well sampled region, and in order to facilitate tracking, we've added lineage XBB.1.36 with 26 newly designated sequences, and 18 updated. Defining mutation T23030C (S:S490P) (following C4999T).