KD.5 Retraction Request

[Over-There-Is]

22289-22294 sites of XBC is deleted, and it causes S:del243-244. As both S:242 and S:244 are Leucine residue, it is always also described as S:del242-243.
Sometimes, TT on 22287-22288 sites is duplicated and causes artefactual frameshift. These sequences are analyzed as having del22286-22289 and A22294T, and even got analyzed as "S:L244F" further.
In UShER, 55 sequences are assigned as KD.5. Some of its subbranches share mutations with other branches. The largest subbranch with 30 sequences has 2 private synonymous mutations: C4456T, A10621G, I do not consider this subbranch worth designated.

[aviczhl2]

@AngieHinrichs suggest to put a branch-specific mask for XBC.1.3.1

[Over-There-Is]

and the note text of XBC.1.1.2 should also be modified.

[Over-There-Is]

@corneliusroemer

[corneliusroemer]

Thanks for the nice analysis of why we see those 244 artefacts!

I already wondered why KD.5 doesn't have any defining mutations on my Nextclade reference tree, looks like this was a bad designation then. Will have a look!

https://nextstrain.org/staging/nextclade/sars-cov-2/21L?label=spike_mutations:-24L,%20-25S,%20-26P,%20S27A,%20Y144-,%20E156-,%20F157-,%20R158G,%20P209L,%20L212S,%20G213V,%20D215H,%20A222V,%20L242-,%20A243-,%20S256L,%20D339G,%20G446S,%20F486P,%20R493Q,%20N703I

[AngieHinrichs]

Thanks @Over-There-Is. I will mask the deleted range in all of XBC. (starting with 2023-12-22 build)

[AngieHinrichs]

Confirmed the UShER tree no longer has a KD.5 branch as of 2023-12-22, due to masking the deleted range in XBC. I agree with @Over-There-Is's comment above that the description of XBC.1.1.2 in lineage_notes.txt should be updated to no longer include S:L244F because that was an artefact.

[Memorablea]

Confirmed the UShER tree no longer has a KD.5 branch as of 2023-12-22

The file has not been updated.

[AngieHinrichs]

@corneliusroemer I am going to do a PR to remove KD.5 from lineages.csv and lineage_notes.txt unless you object soon. 🙂

[corneliusroemer]

Fixed in #2443