XDV.1.9+S:30-31del, F32I (14 seqs, 6 countries, 10 with S:A435S)

[xz-keg]

XDV.1.9+G4255A, del21650_21655, T21656A (S:N30-, S31-,F32I)

GISAID query: G4255A,C6855T,T22930A
No. of seqs: 9(China 6 Japan 1 USA 1 New Zealand 1 )
GISAID query for S:A435S sub-branch: G4255A,C6855T,T22930A,G22865T(5 seqs)

First: EPI_ISL_19242074, Yunnan, 2024-4-1
Latest: EPI_ISL_19362962, New Zealand, 2024-8-5

Usher doesn't display the S:N30-, S31-, F32I thing. @AngieHinrichs, can you check the alignment of usher? why it isn't displaying T21656A/F32I?

usher

[Mydtlwn]

The S:A435S mutation also appears on #1946 and #1949.

[FedeGueli]

I was tracking this too, thx i didnt notice that it got 435S good to track it then

[AngieHinrichs]

Usher doesn't display the S:N30-, S31-, F32I thing. @AngieHinrichs, can you check the alignment of usher? why it isn't displaying T21656A/F32I?

I'm using nextclade to align the sequences now. nextclade finds a deletion at 21651-21656 for all of those sequences -- no nucleotide substitutions in that range. And usher ignores deletions.

GISAID reports the deletion one base to the left (del21650_21655) and the substitution T21656A. That seems less optimal than just a deletion.

[xz-keg]

Usher doesn't display the S:N30-, S31-, F32I thing. @AngieHinrichs, can you check the alignment of usher? why it isn't displaying T21656A/F32I?

I'm using nextclade to align the sequences now. nextclade finds a deletion at 21651-21656 for all of those sequences -- no nucleotide substitutions in that range. And usher ignores deletions.

GISAID reports the deletion one base to the left (del21650_21655) and the substitution T21656A. That seems less optimal than just a deletion.

It seems GISAID prefers in-place deletions that most likely align deletions to aa places?

Since there is a real AA change here besides the deletion, is usher able to display it?

[xz-keg]

+1 South korea +1 Taiwan

[FedeGueli]

Usher doesn't display the S:N30-, S31-, F32I thing. @AngieHinrichs, can you check the alignment of usher? why it isn't displaying T21656A/F32I?

I'm using nextclade to align the sequences now. nextclade finds a deletion at 21651-21656 for all of those sequences -- no nucleotide substitutions in that range. And usher ignores deletions.
GISAID reports the deletion one base to the left (del21650_21655) and the substitution T21656A. That seems less optimal than just a deletion.

It seems GISAID prefers in-place deletions that most likely align deletions to aa places?

Since there is a real AA change here besides the deletion, is usher able to display it?

Now S:32 = ATC so I itshould be seen as happened with S:F186I after S:N185del

[AngieHinrichs]

usher works entirely in the nucleotide space. usher.bio has code to translate substitutions in the subtrees into amino acid substitutions for display, but deletions are invisible for non-uploaded sequences (unless full alignments for all sequences would be incorporated into usher.bio, a large volume of additional data and a significant amount of development work that I don't have time for).

[xz-keg]

usher works entirely in the nucleotide space. usher.bio has code to translate substitutions in the subtrees into amino acid substitutions for display, but deletions are invisible for non-uploaded sequences (unless full alignments for all sequences would be incorporated into usher.bio, a large volume of additional data and a significant amount of development work that I don't have time for).

I would love to help if necessary. I think the task can be done in two steps.

1: Record alignment for each seq and put them in usher generated json file.

2: Detect branch specific alignment change if alignment of most seqs on certain branches are different than others.

If usher can do 1(just put those alignments in generated json file is fine) I can incorporate 2 into my analyse tool. Then you can detect whether to merge it to usher.

[xz-keg]

+1 Liaoning

[xz-keg]

+1 Singapore

[FedeGueli]

Designated XDV.1.9.1 via cov-lineages/pango-designation@0d17efb

[Over-There-Is]

some became S:NSF30-32TI in the recent batch from Yunnan. Artefact?

[FedeGueli]

S:NSF30-32TI in the recent batch from Yunnan

i see them as 28-31del but i think they are artifacts

[xz-keg]

S:NSF30-32TI in the recent batch from Yunnan

i see them as 28-31del but i think they are artifacts

Maybe it further gets S:28- and S:29- after S:30-, 31-, F31I?

[FedeGueli]

Maybe it further gets S:28- and S:29-

mm thx , i looked at samples and i found now that there wera also one from Heilongjiang with that , but unrelated being a XDV.1.9.1 sample.
but the tree could suggest that the extended deletion could be real:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_b8d_824220.json?f_userOrOld=uploaded%20sample&label=id:node_11789734

if you expand you see the Heil.sample

If real this means S:23-32 is just QAI instead of QLPPAYTNSF , what a change from WT. if you put the insertion too that could mean that there were a S:1-32 2AA shorter and around only 80% of homology with WT (4 changes + 2del out of 32AA)