BA.2 (imagines-viewable) only getting probable

[Desperate-Dan]

Hello! Firstly, thanks for the update! We were running our routine pipeline and noticed we now aren't getting any confirmed BA.2 (imagines viewable) calls. This is the case despite a number of samples having all 4 mutations detected and no ref alleles etc., and also all 15 mutations and no ref for the parent Omicron unassigned (plausible-scanner). I've attached a few screenshots to illustrate the situation. Any ideas what might be happening? Cheers.

Multiple samples not getting imagines-viewable confirmed.

4 mutations shown to be detected in the json, confirmed only needs 3 but not getting assigned.

[nickloman]

What pipeline are you using for the assignment? It looks like the definitions are matching correctly from what you have sent? Could it be an issue with the underlying pipeline?

[Desperate-Dan]

We use aln2type, as part of a docker container that has aln2type and pangolin, then table joins the two outputs together. The screenshot of the table is from the combined output but the pre-join output summary.csv has the same results. In this container aln2type was installed quite a while ago, but we routinely git pull the variant definitions repo. I didn't twig yesterday but this is more likely an aln2type problem rather than the definitions?

[nickloman]

I am not sure that aln2type necessarily supports the required tag which might be the problem. I'll ask the team at PHW.

[tomrconnor]

Have raised the issue with the team - and they are looking into it