Suggestion to alter KP.3.1.3 designation to only the G25644T branch

[xz-keg]

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1856

In the new usher update it moves most of the previous KP.3.1.3 seqs to KP.3.1+G25644T+S:S31F branch. This shall be the correct mutation trajectory for most of the KP.3.1.3 seqs.

usher

As @FedeGueli points out, the original KP.3.1.3 branch(designated directly as KP.3.1+S:S31F) is now very small. Hence I suggest to alter the designation of KP.3.1.3 to focus only on the G25644T branch.

@AngieHinrichs @corneliusroemer

[FedeGueli]

Agree, it is enough tightening KP.3.1.3 to start from G25644T

[xz-keg]

@AngieHinrichs @corneliusroemer please have a look at this when doing your next lineage definition update.

[AngieHinrichs]

I see the problem, and there are a lot more KP.3.1 > G25644T-only sequences than KP.3.1 > C21654T-only sequences, so if I move the G25644T+C21654T branch to KP.3.1 > C21654T then it may not stick. It also might be incorrect, i.e. we might be looking at two independent occurrences of C21654T (S:S31F).

@corneliusroemer what do you think -- should G25644T+C21654T be lumped together with C21654T despite there being 88 seqs with G25644T only? (199 with both; ~28~ 13 with C21654T only, as of the 2023-08-26 tree I'm looking at in taxonium)

If so, then I can add a label to that branch (KP.3.1.3_25644) that will cause those sequences to be assigned KP.3.1.3 by pangolin in future releases.

If not, then G25644T+C21654T could either be a new KP.3.1.X, or KP.3.1.3 could be changed as @aviczhl2 suggests although in general I don't like changing definitions after designation unless there's some kind of error.

[Over-There-Is]

G25644T=ORF3d:V41F

[DailyCovidCases]

This issue is completed, please close it @xz-keg