pathogen-variant-surveillance

SUMMARY

What it does

This skill provides scripts to query live pathogen genomic surveillance data via the GenSpectrum LAPIS API. It resolves lineage names against the current Pango designation, computes lineage prevalence and growth from sequence counts, compares mutation profiles between lineages, and estimates reporting lag to determine trustworthy time windows. It emphasizes using live data over memory, handles per-instance schema differences, and warns against common pitfalls that lead to silently wrong answers. The skill is intended for research use and does not provide clinical or public-health guidance.