sublineage of BQ.1.1+S:K182E (A22106G) +C16767T (82 seqs, mainly in Botswana and UK), including branches of S:K478R(A22995G) and S:S494P(T23042C)

[HynnSpylor]

Defining mutations: BQ.1.1>A22106G (S:K182E) >C16767T
then branch 1: >G3955A>A22995G (S:K478R)
branch 2: >A20019G>T23042C (S:S494P, all in USA)

GISAID query: Spike_R346T, Spike_K182E, Spike_K444T, C16767T

Earliest seq (for C16767T): 2022-06-06 (Botswana, EPI_ISL_16279080)
Most recent seq (for C16767T): 2023-03-20 (England, EPI_ISL_17317306)
Countries Detected: UK (37), Botswana (19), USA (14), South Africa (4), Austria (3), Reunion (2), Mauritius (1), Japan (1), India (1)
Usher Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_3a1b8_283e40.json

Description:
It is a "very old" BQ.1.1 sublineage- the first seq was detected in May 23th, 2022 (EPI_ISL_16279064 by Usher), which is also one of the earliest BQ.1.1 seqs. S:K182E is also seen in some BQ.1.1 sublineage (#1385 and #1713), but they are not in same branch as Usher shows.

Recently there are two main branches. One further acquires S:K478R, which is also popular recently (in XBB.1.16 and some BQ* sublineage). It became over half of latest updated seqs in Botswana (despite the collections are two months ago). Also, it spread in South Africa and UK, and notice that the updated seqs in UK are increased recently.
The other branch gets S: S494P and concentrated in USA since Jan 2023 (but only 14 seqs).

As the fast growth rate of S:K478R branch, the sublineage shows notable advantage to the parent lineage (BQ.1.1), even slightly faster than XBB.1.5.

https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=XBB.1.5*&aaMutations1=S%3AK182E%2CS%3AT478R&nextcladePangoLineage1=BQ.1.1*&analysisMode=CompareToBaseline&

Genomes:
Genomes of BQ.1.1 sublineage.txt

[InfrPopGen]

Thanks for submitting. So far the parent has been designated as lineage BQ.1.1.74 with 70 newly designated sequences, and 6 updated from BQ.1.1. Defining mutation A22106G (S:K182E) (following A17039G (ORF1b:N1191S)). The designation is from the closest non-silent mutation to the proposal above, which also has some apparent advantage over BQ.1.1 - over last 3 months: USA [21% Current adv. 13-29%]; UK [37% Current adv. 30-43%]; Canada [33% Current adv. 24-42%]; Indonesia [8% Current adv. -20-36%]; Australia [29% Current adv. 10-47%]; Sweden [83% Current adv. 58-108%] latest 50%. The child lineages are pending for the moment.