pathogen-variant-surveillancelisted

# Pathogen Variant Surveillance ## When to use Any time an answer depends on what a pathogen population looks like **now**: which lineages are circulating, whether one is growing, what a lineage name currently means, or whether an assay target still matches. ## The rule **Never state what is circulating, and never write a lineage name, from memory.** Three things go wrong at once, and only the first is an ordinary knowledge-cutoff problem: 1. **Names post-date training.** The Pango designation list carries over 6,200 names and grows continuously. 2. **The nomenclature is a live data structure, not a convention.** `XFG` is a recombinant that only resolves through `alias_key.json`; `PQ.17` unaliases to `XDV.1.5.1.1.8.1.17`. Neither expansion is derivable by reasoning — the mapping is a file that changes. 3. **Prior knowledge gets retracted, not just outdated.** 294 names in the current `lineage_notes.txt` are withdrawn or redesignated. `PC.2` is now `LF.7.9`; `XFG.20` was withdrawn outright. A remembered lineage fact is not merely stale, it can be actively wrong. Every number this skill reports is a count returned by a live instance, stamped with the data version it came from. ## Scope Surveillance data analysis for research. This skill describes sequences that were collected and submitted; it does not produce clinical interpretations, outbreak-response recommendations, or public-health guidance, and sequence counts are not case counts. ## Instances On