Agent skill · research science · k-dense-ai
pathogen-variant-surveillance
Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growing, and what mutations they carry. Use whenever a question depends on the current state of a pathogen population rather than on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence has moved week to week. Triggers include "variant surveillance", "genomic surveillance", "what variant is circulating", "dominant variant", "Pango lineage", "lineage prevalence", "growth advantage", "SARS-CoV-2 variant", "XFG", "clade 2.3.4.4b", "H5N1 genotype", "influenza clade", "RSV/mpox/measles/dengue lineage", "CoV-Spectrum", "LAPIS", "Nextclade", "pango-designation", and any request to report what a pathogen population looks like today.
Why this skill is useful
Adds executable scripts for querying live genomic surveillance data that provide real-time insights into pathogen populations.
What it needs
Requires python installed locally. About 7k tokens when loaded. Last updated 2026-08-03. 32,849 stars on the source repository.
What this skill does
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 aliaskey.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 Prior knowledge gets retracted, not just outdated. 294 names in the current lineagenotes.txt are withdrawn or redesignated. PC.2 is now LF.7.9; XFG.20 was withdrawn outright.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 One API shape covers every pathogen. --instance names a verified deployment; --base-url reaches any other LAPIS instance. Instance Host Lineage column Indexed --- --- --- --- sars-cov-2 lapis.cov-spectrum.org (open GenBank data) pangoLineage yes h5n1, h3n2, h1n1pdm, influenza-a lapis.genspectrum.org clade no rsv-a, rsv-b, mpox, measles, dengue, west-nile, hmpv, ebola-zaire, ebola-sudan, cchf lapis.pathoplexus.org varies varies Field names differ per instance and are never assumed. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills k-dense-ai/pathogen-variant-surveillance