AY.12 looks incorrect

[alurqu]

Pango-designation ticket 170 which led to designation of AY.12 explicitly mentions occurrence in Israel, but https://outbreak.info/situation-reports?pango=AY.12&selected=ISR&loc=ISR shows zero of 1245 AY.12 sequences in Israel. Also, the pango-designation ticket explicitly references mutation S:T791I with an explicit comment associating AY.12 with RNA mutation C23934T which should yield S:T791I, but the mutation table at https://outbreak.info/situation-reports?pango=AY.12 doesn't show S:T791I, and https://outbreak.info/compare-lineages?pango=AY.12 also doesn't show S:T791I. With these mismatches, there seems to be a possible error either in outbreak.info or upstream in the lineage classifier.

Edit: for reference, the pango-designation ticket for AY.12 is cov-lineages/pango-designation#170.

[flaneuse]

Thanks @alurqu for mentioning this. @mindoftea can you please look into it?

[AlaaALatif]

Thanks @alurqu for detailing the issue and providing necessary supporting information. We took a look at sequences from the list of accession IDs referenced in the pango-designation ticket, and the mutation was correctly identified in all of them as part of our upstream mutation-calling pipeline (bjorn). The discrepancy you reported is most likely because the recent pango-update hasn't yet been added for re-classifying the lineages of those sequences, which we currently get directly from GISAID's feed.

This issue should be fixed as soon as the incoming data has updated lineage classifications, which will likely happen in the next few days. We are also working on adding updated pango-designations directly to our upstream pipeline, so that these delays can be more avoidable.

[alurqu]

An upstream pango-designation ticket related to this issue has recently been opened: cov-lineages/pango-designation#186

[flaneuse]

@mindoftea is this fixed?