← All skills

pathogen-variant-surveillance

92 / 100 · Low risk

Fine to try. Some of what it can do is expected: a data skill usually connects to databases or online services with your credentials.

By K-Dense-AI/claude-scientific-skills (GitHub) · data · 57,146 stars · scanned at commit 2d2065f

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…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'pathogen-variant-surveillance' ] || [ -L ~/.agents/skills/'pathogen-variant-surveillance' ]; then echo 'A skill folder named pathogen-variant-surveillance already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/K-Dense-AI/claude-scientific-skills' "$d" && git -C "$d" checkout --quiet '2d2065fb4520fa3f3f2bcf61cff26ec8b7eba4b5' -- 'skills/pathogen-variant-surveillance' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/pathogen-variant-surveillance' ~/.agents/skills/'pathogen-variant-surveillance' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'pathogen-variant-surveillance' ~/.claude/skills/'pathogen-variant-surveillance' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

Badge for your README

The badge for K-Dense-AI/claude-scientific-skills shows the score of its lowest-scoring skill.

[![SkillTrust](https://zalavijaysinh.github.io/skilltrust/badges/K-Dense-AI/claude-scientific-skills.svg)](https://zalavijaysinh.github.io/skilltrust/repos/K-Dense-AI/claude-scientific-skills/)

Score history

Also found in

Identical copies of this skill exist at:

• K-Dense-AI/scientific-agent-skills/skills/pathogen-variant-surveillance