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Pathogen Variant Surveillance

Lets an agent query live public genomic databases for variant lineage trends and mutation patterns.

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
9 files

What it does

When installed, the agent answers questions about which pathogen lineages (such as SARS-CoV-2 variants or H5N1 clades) appear in publicly submitted sequences, by fetching current counts from public GenSpectrum/LAPIS databases instead of relying on memory. It produces weekly proportions with uncertainty intervals, checks whether lineage names are current, estimates how long submissions typically lag behind sample collection, and summarises common mutations. It is careful to state that these are counts of submitted sequences, not case counts or evidence of harm.

Great for

  • Researchers doing descriptive genomic surveillance of public sequence data
  • Students learning how variant tracking and lineage nomenclature work
  • Analysts who need current, sourced lineage counts with stated denominators and exclusions

Skip it if

  • Clinical or public-health decisions, since counts reflect submitted sequences rather than cases or infections and the skill is explicitly descriptive
  • Claims about transmissibility, fitness or forecasts, which the tools do not estimate beyond a descriptive log-odds slope
  • Assay validation or Nextclade/GenoFLU-based calling, which the skill states it does not execute

Try asking

  • “Which SARS-CoV-2 lineages were most common in submitted sequences from the USA over the last 12 weeks?”
  • “Check whether the lineage name XFG.1.1 is still current in Pango nomenclature”
  • “How long is the typical delay between sample collection and submission for USA records?”
  • “Which mutations distinguish lineage XFG.23.1.3 from XFG.1.1 in the S gene?”
Step-by-step guide: how to use Pathogen Variant SurveillanceInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 9 original files, the MIT licence and an attribution note.

    pathogen-variant-surveillance.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip pathogen-variant-surveillance.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip pathogen-variant-surveillance.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Always specify a country or date window with --where and --weeks so results are scoped and reproducible.
  • Read the coverage column before quoting mutation proportions, since low coverage can inflate them.
  • Cite the data version and attribution printed with results, and respect Pathoplexus terms for non-SARS-CoV-2 data.

What's inside

  • references/lapis-api.md
  • references/lineage-nomenclature.md
  • references/surveillance-caveats.md
  • scripts/lapis_client.py
  • scripts/lineage_prevalence.py
  • scripts/mutation_profile.py
  • scripts/reporting_lag.py
  • scripts/resolve_lineage.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.