JN.1.4+S:S31del,Orf8:E106Q+S:R346T(95 seqs, 6 countries, 12 with S:F456V)

[xz-keg]

From branch 35 of sars-cov-2-variants/lineage-proposals#1502

JN.1.4+T18453C+G28209C,del21653_21655(Orf8:E106Q, S:S31-)+G22599C(S:R346T)

Brazil just uploads a lot of seqs recently on 8-16, and many of seqs seem to be belonging to this branch.
Usher placement of this is very messy due to unable to handle deletions and low sequencing quality.

@AngieHinrichs

The most likely path shall be JN.1.4(T18453C branch) first getting Orf8:E106Q and S:S31del (66 seqs), and then getting S:R346T(59 seqs).

GISAID query: del21653,T18453C,G28209C,G22599C
GISAID supplementary query: ,T18453C,G28209C,G22599C,-del21653,-del21992
GISAID query for S:F456V sub-branch: C10525T,G28209C,G22599C,T22928G
No. of seqs: 59(Ireland 1 French Guiana 1 USA 4 Brazil 53)

First: EPI_ISL_19179859, Brazil, 2024-3-11
Latest: EPI_ISL_19310803, USA, 2024-7-23

Usher places this on different branches of JN.1.4. This a general figure including everything with Orf8:E106Q and S:S31del.

usher

[FedeGueli]

65 with 5 samples from Para Brazil and 1 from NY , timely proposed it seems!

[xz-keg]

74, Netherlands

[AngieHinrichs]

usher.bio runs only usher, not matOptimize, so placements of uploaded sequences may be messier than when the big tree is updated and optimized. It is still a little messy in the big tree because a couple sequences (pink nodes) that have C10525T appear to be missing G28209C, causing what should be one G28209C branch to be split into two now:

In case those sequences are just missing coverage at 28209, I will try a prune & replace.

[xz-keg]

+1 Spain

[DailyCovidCases]

Now 79 seqs
Tracked in 2738
usher

@corneliusroemer Is this branch worth a designation?

[FedeGueli]

The most recent sequence of this got S:F456V it is from Brazil collected on August 12

Query for this potential interesting singlet/branch: G3338A, T3877C, T24202C
It has also a PLPro mutation at PLPro_P129S

[FedeGueli]

@aviczhl2 absent from last brazilian batch i would close it

[Over-There-Is]

10 have no S:S31del.

[FedeGueli]

@xz-keg pls close this died off

[xz-keg]

Add a supplementary query to include seqs do not register deletions.
95 now.
There is also an S:F456V branch of this in Brazil.

Still circulating in Nov. @corneliusroemer