BA.5.2.1 + ORF1a:T265I, ORF1a:T568I, ORF1a:A2587V, ORF1b:P1427L, ORF1b:K2557R, ORF8:I39V(41 seq)

[DoropFan]

Description
Sub-lineage of:BA.5.2.1
Earliest sequence:2023-01-18
Most recent sequence:2023-03-17
Countries circulating:Japan41(Gunma39, Tokyo1, Saitama1)
Sequences:41

Tokyo 2023-01-18
Saitama 2023-02-02
Gunma 2023-02-22^2023-03-17

Nucleotide mutations:C1059T, C1968T, C8025T, C12068T, A12820G, C16608T, C17747T, C21054T, A21137G, A28008G
Amino acid changes:ORF1a:T265I, ORF1a:T568I, ORF1a:A2587V, ORF1b:P1427L, ORF1b:K2557R, ORF8:I39V

UShER Tree

C21054T>C1059T(ORF1ab:T265I)>A12820G>C16608T>C17747T(ORF1ab:P5828L)>A21137G(ORF1ab:K6958R)>C1968T(ORF1ab:T568I), C8025T(ORF1ab:A2587V), C12068T>A28008G(ORF8:I39V)

CovSpectrum:ORF1a:T568I, ORF1a:A2587V, ORF8:I39V
GISAID:C1968T, C8025T, A28008G

Genomes

[InfrPopGen]

Thanks for submitting. We've added lineage BF.42 with 30 newly designated sequences, and 0 updated. Defining mutation A28008G (ORF8:I39V) (following C1968T (ORF1a:T568I), C8025T (ORF1a:A2587V), C12068T).

[corneliusroemer]

I'm quite curious why this was proposed and designated. It's a very small lineage that seems to have evolved quite normally, stepwise in a country with good surveillance - I can't see any interesting Spike mutation.

Why did you propose it @DoropFan? Any reason in particular you designated it @InfrPopGen?

If I were to designate anything, I would have picked the branch starting from C21054T - there's ~3k sequences below there, so that would mean the lineage would be broadly useful. Now it's just a tiny speck of 15M sequences.

<img width="1431" alt="image" src="https://user-images.githubusercontent.com/25161793/232481930-aaa94e6c-1413-45db-b5af-78493d4049d3.png"

The branch has a rather low mutation rate. 70 -> 77 mutations in 6 months (2022-09 to 2023-03) [could be that some are masked by Usher and or Ns though]. But that could just be a chance event. Haven't analyzed the Usher tree in that respect.

https://next.nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_37494_d35d90.json?branchLabel=Spike%20mutations&c=gt-S_934

https://next.nextstrain.org/fetch/gist.githubusercontent.com/corneliusroemer/ecf31a5d0fae2541968a0d3c753f1603/raw/8ed584790bbe4bda81924d3a00e30a2db0d5a020/bf42tree.json

[InfrPopGen]

Hi @corneliusroemer
I probably designated it because the last two months' growth relative to BA.5.2.1 was over 75% (worldwide, Asia, and Japan itself), and it over 5% of that lineage's detections in all of those areas too. I felt it was just borderline enough, and I assumed it was proposed because it was prominent in Japan and local public health wanted to distinguish it.