Problem with AY.43 assignment?

[enabieva]

There may be a problem with the AY.43 assignment, at least for samples from Russia. According to https://www.pango.network/new-ay-lineages-and-an-update-to-ay-4-ay-12/, the defining mutation in that lineage is A28299T (N:Q9L), yet of the 1,653 Russian samples that are assigned that lineage only one carries that mutation: . Manual examination confirms the presence of the reference base in that position in those sequences. (Globally, as of 11/07/2021, 126,903 sequences in GISAID that are assigned AY.43 carry the N_Q9L mutation, and 92,448 do not).

[FedeGueli]

I have tried to check one of your sequences:https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_aed2_7f5260.json?c=pango_lineage&label=nuc%20mutations:G1048T&tl=pango_lineage_usher

From the Usher tree it appears to be an issue in Pango assignments, Usher assigns that sequence as B.1.617.2 correctly: It appears to belong to the large undesignated clade proposed in #268 with ORF1ab: K261N

Edit: i checked back with 4 sequences and the results is the same , Pango missassigns sequences from the large undesignated clade with orf1ab:K216N to AY.43 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1770c_81daf0.json?label=nuc%20mutations:G1048T

@corneliusroemer @AngieHinrichs @

[FedeGueli]

I see that a lot of sequences of #268 are assigned as AY.43.

I think the designation of the branch with Orf1a:K216N will resolve a lot of this issue cc @AngieHinrichs @chrisruis @corneliusroemer

[FedeGueli]

The big orf1a:K261N lineage has been designates as AY.122 in #320

So thos issue will be solved soon

@enabieva

[chrisruis]

Thanks @enabieva and @FedeGueli It looks like these sequences are indeed now being assigned AY.122

[FedeGueli]

I just realized that AY.43 had also a orf9b mutation : N:Q9L = ORF9b:S6C

cc @ryhisner @thomaspeacock @corneliusroemer at that time we didnt notice that. it could explain the clear success of AY.43.