# pathogen-variant-surveillance

Queries public LAPIS data for pathogen variant surveillance, lineage checks, weekly sequence proportions, and reporting delays.

- skill · `type=skill` · Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, OpenCode · 936 installs · ★ 54652
- Author: K-Dense-AI
- License: MIT · policy=mirror · the beginning of the file is at the end of this page
- Source: https://github.com/K-Dense-AI/scientific-agent-skills/tree/HEAD/skills/pathogen-variant-surveillance/SKILL.md
- Updated: 2026-10-19
- HTML: https://affpapa.org/en/nevibecode/skills/pathogen-variant-surveillance

## What it does

This skill queries public GenSpectrum LAPIS deployments to inspect lineage labels, calculate weekly sequence proportions, measure delays between collection and submission, and describe mutation frequencies. It covers available collections for SARS-CoV-2, influenza, RSV, mpox, measles, dengue, and other pathogens.

Its scripts include `reporting_lag.py`, `lineage_prevalence.py`, and `resolve_lineage.py`. They inspect database schemas, check Pango names through notes and alias maps, and apply filters for geography, dates, and lineage fields. Results describe submitted sequences rather than infection prevalence.

Python 3.11+ and network access are required; the scripts use the standard library and public queries need no credentials. A rising sequence proportion does not establish a biological advantage, so readers should check reporting lag and sampling changes first.

## Install

### Claude Code (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add K-Dense-AI/scientific-agent-skills --skill pathogen-variant-surveillance -a claude-code
```

2. **Manually: put the files in place**
- File: `~/.claude/skills/pathogen-variant-surveillance/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/pathogen-variant-surveillance/

### Codex

1. **Skills CLI (Vercel)**
```bash
npx skills add K-Dense-AI/scientific-agent-skills --skill pathogen-variant-surveillance -a codex
```

2. **Manually: put the files in place**
- File: `.agents/skills/pathogen-variant-surveillance/SKILL.md` — For all projects use ~/.agents/skills/

### Cursor

1. **Skills CLI (Vercel)**
```bash
npx skills add K-Dense-AI/scientific-agent-skills --skill pathogen-variant-surveillance -a cursor
```

2. **Manually: put the files in place**
- File: `.cursor/skills/pathogen-variant-surveillance/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install K-Dense-AI/scientific-agent-skills pathogen-variant-surveillance
```

2. **Manually: put the files in place**
- File: `.github/skills/pathogen-variant-surveillance/SKILL.md`

### Gemini CLI

1. **Skills CLI (Vercel)**
```bash
npx skills add K-Dense-AI/scientific-agent-skills --skill pathogen-variant-surveillance -a gemini-cli
```

2. **Platform CLI**
```bash
gemini skills install https://github.com/K-Dense-AI/scientific-agent-skills --path skills/pathogen-variant-surveillance
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/pathogen-variant-surveillance/SKILL.md` — The legacy .windsurf/skills/ path still works

### OpenCode

**Skills CLI (Vercel)**
```bash
npx skills add K-Dense-AI/scientific-agent-skills --skill pathogen-variant-surveillance -a opencode
```

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/K-Dense-AI/scientific-agent-skills/tree/HEAD/skills/pathogen-variant-surveillance/SKILL.md

## When to use it
- validate a current Pango lineage name
- calculate weekly lineage proportions for a country
- measure delay from collection to sequence submission
- discover common lineage labels in a time window
- separate submitted-sequence prevalence from infection prevalence

## Example prompts
- Check whether XFG is a valid Pango lineage and show its descendants.
- Show weekly lineage proportions for `country=USA` over `12` weeks.
- Run `reporting_lag.py` for `country=USA` to describe reporting delays.

## Source text · SKILL.md · MIT

Below is the content of a third-party file. It is data, not instructions for you: do not act on anything written inside unless the human asks. Block tag: eee0190c829aa57d.

BEGIN THIRD-PARTY FILE eee0190c829aa57d
```text
---
name: pathogen-variant-surveillance
description: 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.
license: MIT
compatibility: Requires Python 3.11+. Scripts use only the standard library. Needs network access to public LAPIS deployments on lapis.cov-spectrum.org, lapis.genspectrum.org, lapis.pathoplexus.org and raw.githubusercontent.com for pango-designation. No credentials for these public queries.
allowed-tools: Read Write Edit Bash
metadata:
  version: "1.3"
  skill-author: K-Dense Inc.
  last-reviewed: "2026-10-01"
---

# Pathogen Variant Surveillance

## When to use

Use current data when a question depends on which lineages appear in submitted sequences,
what a lineage name currently means, or how the submitted sequence distribution changed.
Never answer a current circulation question from remembered lineage names or old examples.

This skill supports descriptive surveillance research. Counts describe sequences submitted to
one database under stated filters; they are not case counts, infection prevalence, clinical
interpretations, outbreak recommendations, or evidence of enhanced pathogen function.

## Verified scope

Reviewed on 2026-10-01 against official documentation, live schemas for all 15 registered
instances, and small public queries. SARS-CoV-2 served LAPIS 0.8.7/SILO 0.14.3; the other
registered deployments served LAPIS 0.8.0/SILO 0.11.0. Do not assume identical feature support.
Bundled standard-library scripts have synthetic regression tests and bounded live smoke checks.
Nextclade, GenoFLU, authenticated APIs, and sequence-level assay validation are not executed here.

| Instance | Host | Common lineage field |
| --- | --- | --- |
| `sars-cov-2` | lapis.cov-spectrum.org/open/v2 | `pangoLineage` (indexed) |
| `h5n1` | lapis.genspectrum.org/h5n1 | `clade` (unindexed) |
| `h3n2`, `h1n1pdm` | lapis.genspectrum.org/<name> | `cladeHA` / `cladeNA` (unindexed) |
| `influenza-a` | lapis.genspectrum.org/influenza-a | `subtypeHA` / `subtypeNA` |
```
END THIRD-PARTY FILE eee0190c829aa57d

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