Pathogen Variant Surveillance (LAPIS)

Queries live GenSpectrum LAPIS instances to report which pathogen lineages are circulating now, how fast they grow, and which mutations they carry — always with provenance.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

Queries public LAPIS instances (cov-spectrum, genspectrum, pathoplexus) for SARS-CoV-2, H5N1, seasonal influenza, RSV, mpox, measles, dengue and more.
Refuses to write lineage names from memory: resolve_lineage.py checks whether a name still exists, what it unaliases to, and whether it was withdrawn or redesignated (exit code 1 gates a manuscript list).
lineage_prevalence.py gives week-by-week proportions with Wilson intervals plus a descriptive log-odds growth slope, flagging weeks whose denominators have not filled in.
mutation_profile.py diffs gained/lost mutations between lineage sets; nucleotide mode answers primer/probe questions.
reporting_lag.py tells you how far back collection dates can be trusted before quoting recent prevalence.
Documents per-instance traps (e.g. clade=2.3.4.4b* returning 0 on H5N1) that otherwise yield silently wrong answers.

Who it's for

Genomic surveillance and infectious-disease researchers, epidemiology/public-health data analysts.
Diagnostic assay developers validating primer and probe targets against circulating sequence.
Anyone who must verify lineage names and prevalence figures before publishing them.

Example uses

"What's circulating in the USA over the last 12 weeks?" → lineage_prevalence.py --top 5 --where country=USA --weeks 12, discovering names instead of assuming them.
Audit a manuscript's lineage list → resolve_lineage.py XFG.23.1.3 PQ.17 PC.2 catches withdrawn names (PC.2 is now LF.7.9).
Check whether a PCR assay still matches → mutation_profile.py "XFJ*" --versus "XFG*" --nucleotide.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/pathogen-variant-surveillance/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)

Download the ZIP with the button below.
In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.

↓ Download ZIP

Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/pathogen-variant-surveillance folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/pathogen-variant-surveillance/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/pathogen-variant-surveillance ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

Open a terminal and confirm your Python version: python3 --version (3.11+ required; no third-party packages needed).
Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
Create the skills directory: mkdir -p ~/.claude/skills
Copy the skill in: cp -r scientific-agent-skills/skills/pathogen-variant-surveillance ~/.claude/skills/
Verify network access to the public API: curl -s https://lapis.cov-spectrum.org/open/v2/sample/databaseConfig | head
Restart Claude Code and ask something like "Which SARS-CoV-2 lineage is dominant in the USA right now?" to trigger the skill.
Keep the provenance the scripts print to stderr (instance, data version, filters, window) with any figure you report.

View source on GitHub ↗License: MIT