BF.7.14 with additional S:V445A, S:P561S and ORF3a:A72S (21 seqs as of 2023-04-20, China)

[c19850727]

Description

Sublineage of: BF.7.14 Earliest sequence: 2023/02/20 (China-Heilongjiang) Most recent sequence: 2023/03/07 (China-Heilongjiang) Countries circulating: China

Mutations on top of BF.7.14: G210T > C6781T > T22896C (S:V445A), C23243T (S:P561S), G23608A, G25606T (ORF3a:A72S)

GISAID and Cov-spectrum query: T22896C, C23243T, G23608A, G25606T

Evidence

Usher tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2d6fd_14af20.json?c=gt-nuc_6781,25606&label=id:node_6662246

Genomes:

EPI_ISL_17199725-17199727, EPI_ISL_17199781, EPI_ISL_17199815-17199817, EPI_ISL_17199850, EPI_ISL_17199911

[thomasppeacock]

Think is this is worth prioritising for designation if any more sequences come up in the next week or two. Let me know and I'll change from monitoring to recommending! thanks!

[xz-keg]

9 more seqs found on GenBase, sampling time as late as 2023-3-30.

[xz-keg]

For new Genbase seqs:

C_AA00 sampling time location 3762 2023-3-30, Harbin(Heilongjiang) 3748 2023-3-27, Harbin 3747 2023-3-27,Harbin 3247 2023-3-20, Harbin 3246 2023-3-20, Harbin 3192 2023-3-14, Harbin 3191 2023-3-11, Harbin 3190 2023-3-8, Harbin 3189 2023-3-13, Harbin

Still inside Heilongjiang though.

[xz-keg]

@AngieHinrichs is it possible to add GenBase seqs to usher database? Most Chinese seqs are on that platform and not on GISAID since March.

[AngieHinrichs]

is it possible to add GenBase seqs to usher database?

@aviczhl2 I'm looking into it. Thanks for pointing that out and for updating issues with GenBase sequences. The pango-designation lineages.csv file and pangoLEARN training are set up to use GISAID sequences, but I should be able to add the GenBase sequences to the UShER tree as soon as I work out how to automatically download them and integrate them into my daily build pipeline.

[xz-keg]

21 seqs and also detected in Tianjin now.

[DailyCovidCases]

This branch is dead, please close this issue