Sublineage of FK.1.2 with multiple ORF1a changes (53 seqs as of 2023/04/25)

[c19850727]

Description

Sublineage of: #1718 (CH.1.1.17 with ORF1a:L3829F, S:D215G, S:Q613H, M:S212G)
Earliest sequence: 2023/02/15 (New Zealand)
Most recent sequence: 2023/03/13 (New Zealand)
Countries circulating: France (1/18), US (2/8, from 2 different states), Australia (3/18, from 3 different states), New Zealand (12/18)

Mutations on top of #1718 : C18657T > C1415T (ORF1a:L384F), C27389T > G1914A (ORF1a:R550H) > G680A (ORF1a:D139N) > G942A (ORF1a:R226K), C1931A (ORF1a:Q556K), C25583A (ORF3a:T64N)

Taken all AA changes together: ORF1a:D139N + ORF1a:R226K + ORF1a:L384F +ORF1a:R550H + ORF1a:Q556K + ORF3a:T64N.
In total there are 5 AA changes concentrated in NSP1 and NSP2, including ORF1a:Q556K, a defining mutation of BQ.1*.

Also the most recent batch of upload from New Zealand have an additional A22184T (S:T208S).

GISAID and Cov-spectrum query: G680A, C1931A, C25583A

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_19d46_9b6380.json?c=gt-nuc_1931&label=id:node_8049538

Genomes:

EPI_ISL_17058090, EPI_ISL_17150291, EPI_ISL_17226512, EPI_ISL_17229161, EPI_ISL_17237791, EPI_ISL_17251918, EPI_ISL_17252091, EPI_ISL_17252099, EPI_ISL_17252162-17252163, EPI_ISL_17252223, EPI_ISL_17252273-17252275, EPI_ISL_17252277, EPI_ISL_17252299, EPI_ISL_17252657, EPI_ISL_17259103

[c19850727]

19 seqs now, found in another US state (WI)

[c19850727]

24 sequences as of 2023-03-30.
Newly found in US-TX and UK-England.

[FedeGueli]

@c19850727 you should update the title to FK.1 sublineage, isnt it?

[c19850727]

Thanks Fede! already updated.

[c19850727]

29 sequences as of 2023-04-04. Newly found in Australia-QLD and Canada-ON.

[c19850727]

37 seqs as of 2023-04-08. Newly found in Australia-TAS.

[c19850727]

44 seqs as of 2023-04-15. Newly found in Korea and US-CA.

[c19850727]

45 seqs as of 2023-04-17. Newly found in US-NY.

[corneliusroemer]

Parent of this is now FK.1.2

[c19850727]

53 seqs as of 2023-04-25. Newly found in Hong Kong and Ireland.

[InfrPopGen]

Thank you for proposing this lineage. It did show promise back in early April, but it's two month relative growth advantages are now are all negative (NZ, Australia, US, and regional). It is still growing, but not particularly fast compared with other lineages, nor is it part of any epidemiological event of concern. Consequently, this can be closed for now, but please request a re-opening should this lineage reawaken and show clear advantages.