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pathogen-variant-surveillance

by Scientific Skills

Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies. Use for variant surveillance, Pango lineage validation, dominant submitted lineages, Nextclade assignment provenance, SARS-CoV-2, influenza/H5N1 clades, RSV, mpox, measles, dengue, or LAPIS queries. Distinguishes sequence prevalence from infection prevalence, clades from genotypes, missing calls from reference matches, and sampling changes from biological growth advantage.

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Run this command in your terminal. No account required — it auto-detects your AI tool and installs the skill file.

npx @skills-hub-ai/cli install scientific-skills-pathogen-variant-surveillance
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npx @skills-hub-ai/cli install scientific-skills-pathogen-variant-surveillance --target claude-code
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Frequently asked questions about pathogen-variant-surveillance

What does the pathogen-variant-surveillance skill do?

Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies. Use for variant surveillance, Pango lineage validation, dominant submitted lineages, Nextclade assignment provenance, SARS-CoV-2, influenza/H5N1 clades, RSV, mpox, measles, dengue, or LAPIS queries. Distinguishes sequence prevalence from infection prevalence, clades from genotypes, missing calls from reference matches, and sampling changes from biological growth advantage. It's a reusable SKILL.md instruction set that loads into your AI coding assistant on demand, no prompt engineering, no copy-pasting every session.

How do I install the pathogen-variant-surveillance skill?

Run `npx @skills-hub-ai/cli install scientific-skills-pathogen-variant-surveillance` from your terminal. The CLI writes the SKILL.md to the correct location for your AI tool (e.g. ~/.claude/skills/scientific-skills-pathogen-variant-surveillance/ for Claude Code or ~/.cursor/skills/ for Cursor with --target cursor) and adds it to your project's .skills.json lockfile.

Which AI tools does pathogen-variant-surveillance work with?

pathogen-variant-surveillance runs in Claude Code. It follows the open Agent Skills standard (SKILL.md), so the same skill works in every supported tool without modification.

Is the pathogen-variant-surveillance skill free?

Yes. Every skill on skills-hub.ai is free and open-source. There are no premium tiers, paywalls, or usage limits. You only pay for whatever AI assistant you're already using.

How do I use pathogen-variant-surveillance after installing it?

In Claude Code, type `/scientific-skills-pathogen-variant-surveillance` (or whatever slash command the skill registers) and the AI follows the skill's instructions immediately. You can also reference it by name in natural language, your AI loads the skill into context when relevant.

Can I share the pathogen-variant-surveillance skill with my team?

Yes. Commit your project's .skills.json lockfile and teammates run `npx @skills-hub-ai/cli install` (no args) to install every skill at the exact version you pinned. Organization-scoped installs work via skills-hub.ai organizations.