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 Prior knowledge gets retracted, not just outdated. 294 names in the current lineage_notes.txt are withdrawn or redesignated. PC.2 is now LF.7.9; XFG.20 was withdrawn outright.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 versio…