> ## Documentation Index
> Fetch the complete documentation index at: https://kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# pathogen-variant-surveillance — AI agent skill for life sciences

> Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API to find which viral lineages are circulating now, how fast they are growin…

# `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on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence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.

**Category:** [life-sciences](/skills#life-sciences) · **License:** MIT · **Version:** 1.1

## Install

```bash theme={null}
npx research-agent-skills install pathogen-variant-surveillance
npx skills add KalarisLabs/research-agent-skills --skill pathogen-variant-surveillance
```

## When to use it

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on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence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.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/pathogen-variant-surveillance/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.