Mercury for Flu enhancement - label lineage pdm09 for H1N1 samples

[kapsakcj]

🆒

📌 Explain the Request

We recently added functionality (via PR #506 and PR3 over in Mercury repo: theiagen/mercury#3) in Mercury to automatically generate the NCBI BioSample metadata field isolate in the following format:

# format:
type/state/submission_id/year (subtype)

# example:
A/California/sample-0001/2024 (H1N1)

A user requested that the string pdm09 is appended to the string auto-generated in the isolate column, so for example A/California/sample-0001/2024 (H1N1)pdm09. This is to designate that samples are descendants/related to the pandemic 2009 strain.

However, we currently do not have a way in TheiaCoV wfs to determine if samples are truly descendants or not.

Also, not all H1N1 strains are descendants (like those collected prior to 2009) or H1N1 samples collected in the future could potentially not be part of the pdm09 lineage.

It would be beneficial to our users if this designation could be determined (perhaps via Nextclade or another mechanism/algorithm like something involving collection dates) and appended to the string auto-generated in Mercury code.

The current workaround is to run Mercury and manually edit the BioSample metadata TSV output from the workflow to include this lineage designation prior to NCBI submission

[kapsakcj]

This wasn't completed, so I'm reopening it

[sage-wright]

sorry! this was a misclick