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Designate XBB.1.5.99 (S:E554K, ORF1a:T1168I, C823T, Ecuador) with 70 …
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sars-cov-2-variants/lineage-proposals#170
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@corneliusroemer check : sars-cov-2-variants/lineage-proposals#362 (comment)
it was correct to put it as a separate sublineage.
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https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1345_fa610.json?c=gt-ORF1ab_1168&label=id:node_6929431
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Looks like this version of XBB.1.5.99 was renamed to HQ.1 in 8ecd6a4 and then a different lineage was named XBB.1.5.99 in 34eb52f. Thanks @FedeGueli for linking in that comment!
However there is still a loose end to tie up. @corneliusroemer lineage_notes.txt has this description of XBB.1.5.92:
However, all of the designated sequences for XBB.1.5.92 are on a different branch: just XBB.1.5 > C3768T (ORF1a:T1168I), without C823T. There are 184 samples on that branch. (e.g. Canada/QC-L00600692001/2023)
There are more sequences (213) with XBB.1.5 > C823T only, not ORF1a:T1168I (and some are from late 2022, e.g. USA/VA-CDC-LC0975692/2022). So C823T-first seems very plausible to me. Then XBB.1.5 > C823T has a child branch with both C3768T (ORF1a:T1168I) and C10615T, that has 144 sequences, and HQ.1 is a child of that branch with 70 sequences.
To me those look like separate occurrences of C3768T [or possibly recombination that got rid of C823T]. lineages.csv has samples only for the first branch (XBB.1.5 > C3768T only, no C823T), but the lineage_notes description and the designation of HQ.1 are for the second branch (XBB.1.5 > C823T > C3768T,C10615T). If you prefer the second branch that's fine but then I think lineages.csv should be updated to use samples that do have C823T as described in lineage_notes.txt.