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on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence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.
Security AStatic scan found no risk patternsHow grading works ›
What this skill does
Pathogen Variant Surveillance is a community-contributed Claude Code skill in the general-misc sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/pathogen-variant-surveillance/ and loads when your prompt matches the skill's trigger.
When to invoke it: 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on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence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.
Who uses this skill
The Pathogen Variant Surveillance Claude Code skill is built for Claude Code users and developers across all disciplines looking for general-purpose AI assistance. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 196,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).
How to install
Free
Manual install (2 steps)
mkdir -p ~/.claude/skills/pathogen-variant-surveillance
curl -L https://claudskills.com/skills/pathogen-variant-surveillance/SKILL.md \
-o ~/.claude/skills/pathogen-variant-surveillance/SKILL.md
Or just download SKILL.md directly and drop it into ~/.claude/skills/pathogen-variant-surveillance/. Claude Code auto-discovers it on next session.
Skills live at ~/.claude/skills/pathogen-variant-surveillance/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\pathogen-variant-surveillance\SKILL.md on Windows. See the full install guide for step-by-step instructions.
Telegram
📱 Install from your phone or desktop Telegram
Open @claudskills_bot on Telegram, tap Open Desktop App, and the desktop app installs this skill for you. Or share the bot link with a colleague — they get the same one-tap install. Learn more →
Pro
One-click install via the desktop app
The ClaudSkills desktop app installs any skill directly into ~/.claude/skills/ with one click — no terminal required. Pro starts at $9/mo or $149 lifetime.
Pro
For the full experience including quality scoring and one-click install features for each skill — upgrade to Pro.
Frequently asked questions
How do I install the Pathogen Variant Surveillance Claude Code skill?
Install via the ClaudSkills desktop app (one click) or copy
SKILL.md from the source repository to
~/.claude/skills/pathogen-variant-surveillance/SKILL.md and restart Claude Code. Both flows are detailed at
claudskills.com/install/.
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 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.
Is this skill free to install?
Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.
When should I use the Pathogen Variant Surveillance skill?
Use Pathogen Variant Surveillance when your Claude Code task falls under the General category — specifically in the general misc area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use Pathogen Variant Surveillance" or describe the task and let Claude pick). Browse related skills at
/category/general/.
What is a Claude Code skill and how does the Pathogen Variant Surveillance skill fit in?
A Claude Code skill is a
SKILL.md file that lives under
~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. Pathogen Variant Surveillance is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the General category. Learn more at
/learn/what-is-a-claude-skill/.
Attribution & license
Cite this skill
If you reference this skill in a blog post, paper, or documentation, you can cite it as:
APA
K-Dense-AI. (2026). Pathogen Variant Surveillance [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/pathogen-variant-surveillance/
BibTeX
@misc{pathogen-variant-surveillance-2026,
author = {K-Dense-AI},
title = {Pathogen Variant Surveillance [Claude Code skill]},
year = {2026},
publisher = {ClaudSkills},
url = {https://claudskills.com/skills/pathogen-variant-surveillance/}
}Embed this skill
Promote, attribute, or link this skill from your own README, blog post, or documentation. All three snippets are free to use — no sign-up, no API key. More distribution surfaces →
Badge
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Security scan
Grade A · scanned 2026-09-28 — free static scan against the OWASP Agentic Skills Top 10.
The scan flagged 1 of 10 categories (network), including lower-severity patterns. Patterns shown inside code fences are weighted as examples rather than instructions — read the grading methodology for what this does and does not guarantee.
- ✓ Prompt injection
- ✓ Data exfiltration
- ✓ Supply chain
- ✓ Reverse shell
- ✓ Credentials
- ✓ Execution
- ✓ Filesystem
- ✓ Persistence
- ✓ Obfuscation
- ⚠ Network
Show this grade on your repo (click to copy):
[](https://claudskills.com/skills/pathogen-variant-surveillance/#security)
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