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on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence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 incl
npx skills add K-Dense-AI/scientific-agent-skills --skill pathogen-variant-surveillance --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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 **Prior knowledge gets retracted, not just outdated.** 294 names in the current `lineage_notes.txt` are withdrawn or redesignated. `PC.2` is now `LF.7.9`; `XFG.20` was withdrawn outright.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. ## Sco
- When to use
- The rule
- Scope
- Instances
- Scripts
- Start from the data, not from a remembered list
- Check a name before using it
- Prevalence and growth
- Mutations, and whether an assay still matches
- Decide how far back to trust
- Traps that produce silently wrong answers
- Reporting results
- References
cd skills/pathogen-variant-surveillance/scripts no names: discover what is actually circulating in the window python3 lineage_prevalence.py --top 5 --where country=USA --weeks 12 python3 resolve_lineage.py XFG.23.1.3 PQ.17 PC.2 NOTALINEAGE python3 lineage_prevalence.py "XFG.1.1*" "XFJ*" --where country=USA --weeks 16 --growth python3 mutation_profile.py "XFJ*" --versus "XFG*" --gene S --since 2026-01-01 python3 reporting_lag.py --where country=USA
What does the pathogen-variant-surveillance skill do?
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 incl
How do I install it?
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill pathogen-variant-surveillance --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From K-Dense-AI/scientific-agent-skills, a repository with 32,619 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.