Closed Over-There-Is closed 2 months ago
JN.1.1> C9142T> G2035A has been split into several branches
Thanks so much @Over-There-Is for reporting these.
- Most of JN.1.1 sequences are placed on JN.1> G21535C> C1762A> C11747T> C21535G and assigned as JN.1. Only a bit of JN.1.1 sequences placed on JN.1> C1762A> C25521T> C11747T> C5869T> T25521C are assigned as JN.1.1.
That's really bad! I should be able to fix it in tomorrow's build (2024-04-23).
- KP.1.1 is now placed under KP.2.
Unfortunately my usual trick of prune & re-optimize will probably not fix that one. usher and matOptimize use the maximum parsimony method, which sees no difference between G22599C > A24819G and A24819G > G22599C, even though a person with knowledge about convergent mutations (and sample dates, countries etc.) can make a more educated guess.
However, having the designated lineages means that at least sequences will have the correct lineage assignment, even if the tree structure is not quite right there.
- LA.2 is now placed under LA.1.
Yes, usher and matOptimize have a weird habit of wanting to serialize mutations that share position (22599C and 22599T in this case, which probably happened independently) -- probably a bug, I will report it. Again, having designated lineages helps to make up for the tree being wrong here.
JN.1.1> C9142T> G2035A has been split into several branches
I hope that fixing #1 above will fix some of those -- but I see a lot of C9142T out of place now that you mention it, I will work on those too, thanks.
@AngieHinrichs is it ok for you to keep this issue open to highlight to you the bugs we will find around?
@AngieHinrichs is it ok for you to keep this issue open to highlight to you the bugs we will find around?
Sure!
JN.1.1> C9142T> G2035A has been split into several branches
Now designated JN.1.1.9 via https://github.com/cov-lineages/pango-designation/commit/377e773e03462f2c51c0d0cb2eeb82da9dcc6a2a