XBC.1.6 sublineage with S:V445A circulating in South Australia (49) - 3% of prevalence in August

[FedeGueli]

Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/203

This lineage seemed deemd to dying off when in the new batch from South Australia uploaded there were 11 samples belonging to it. I updated the query cause it was not perfect:

Gisaid query : T8707C,T22896C,C10156T

Defining mutations: XBC.1.6 >>T8707C, C26735T > C10156T > C29762T > S:V445A (T22896C)

Samples: 39 all from S.Australia (prevalence during July around 5%) First: 2023-05-25 Last:2023-08-01

IDs

EPI_ISL_17793665, EPI_ISL_17793682, EPI_ISL_17793695, EPI_ISL_17793826, EPI_ISL_17793913, EPI_ISL_17849502, EPI_ISL_17849512, EPI_ISL_17849599, EPI_ISL_17849602, EPI_ISL_17849709, EPI_ISL_17849740, EPI_ISL_17999363, EPI_ISL_17999375, EPI_ISL_17999401, EPI_ISL_17999414, EPI_ISL_17999429, EPI_ISL_18000038, EPI_ISL_18000047, EPI_ISL_18000081, EPI_ISL_18000084, EPI_ISL_18000114, EPI_ISL_18000194, EPI_ISL_18000208, EPI_ISL_18000240, EPI_ISL_18000244, EPI_ISL_18000264, EPI_ISL_18000298, EPI_ISL_18000306, EPI_ISL_18109322, EPI_ISL_18109324-18109325, EPI_ISL_18109362, EPI_ISL_18109364, EPI_ISL_18109367-18109368, EPI_ISL_18109370, EPI_ISL_18109376, EPI_ISL_18109509, EPI_ISL_18109511

Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_27975_e9b960.json?c=gt-S_445&label=id:node_6399900

[FedeGueli]

Prevalence of this one is going down. lets wait the last updload of samples collected in August before closing it .

[FedeGueli]

only 6 samples in august closing it for now.

[NkRMnZr]

49 now

[FedeGueli]

Reopening. it seems slow to me.

[FedeGueli]

Designated JT.1 via https://github.com/cov-lineages/pango-designation/commit/0f50930c6ec5b433af5b343e169213871ef903ca