Influenza: highlight mutations of interest (annotation)

[anna-parker]

For influenza there are known NA and HA amino acid substitutions associated with reduced inhibition by antivirals, e.g. https://www.who.int/teams/global-influenza-programme/laboratory-network/quality-assurance/antiviral-susceptibility-influenza/neuraminidase-inhibitor

• Mark mutations of interest in H5N1
• Mark mutations of interest in waste-water
• Mark mutations of interest in H3N2
• Mark mutations of interest in B/vic
• Mark mutations of interest in H1N1pdm
• Highlight mutations in known epitopes: example of known file: https://github.com/nextstrain/seasonal-flu/blob/master/config/distance_maps/h1n1pdm/ha/canton.json

[fengelniederhammer]

We need more refinement.

[anna-parker]

Yesterday I asked Richard Neher which formats are typically used for marking epitope sites and mutations of interest and he said that they primarily just have lists (e.g. JSON, YAML) for this and don't use GFF3 etc.

As we have these lists it would be good to create a simple version of this that takes JSON or YAML as input with these lists.

[anna-parker]

Additionally we should annotate the highlighted here: https://pubmed.ncbi.nlm.nih.gov/39636969/