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nextstrain / nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
https://clades.nextstrain.org
MIT License
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Bogus mutations in definition of BE.9 #1077

Closed silcn closed 1 year ago

silcn commented 1 year ago

Lineage BE.9 contains a huge deletion 27508-27751del. The Brazilian bioinformatics pipelines have had issues with this, producing the erroneous substitutions A27508C and A27749G. Since the lineage arose in Brazil, Nextclade lists these two substitutions as defining and so non-Brazilian BE.9 sequences are not getting recognised as BE.9. See https://github.com/cov-lineages/pango-designation/issues/1430

corneliusroemer commented 1 year ago

Thanks @silcn for digging into this! I'll do a manual override of these lineage defining mutations and it'll be fixed in the next release.

Are you aware of the same problem in any other lineages?

silcn commented 1 year ago

@corneliusroemer thanks! Not aware of any other cases like this but I haven't been looking out for them.