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pathogen-variant-surveillance

Query live pathogen genomic surveillance data through the GenSpectrum LAPIS API.

41.1k|3.8k|Updated Oct 19, 2025
Search Tags:#mutation analysis#pathogen#lapis api#variant prevalence#genomic surveillance#sars-cov-2#pango lineage
One-click install
npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill pathogen-variant-surveillance
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pathogen-variant-surveillance
Source: https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/pathogen-variant-surveillance
Command: npx skills add https://github.com/K-Dense-AI/scientific-agent-skills --skill pathogen-variant-surveillance

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

Answers about which pathogen variants are circulating right now cannot come from model memory: lineage names post-date training, the Pango nomenclature changes continuously, and hundreds of names have been withdrawn or redesignated. This Skill queries live LAPIS instances so every reported number is a current count stamped with its data version.

Core Features & Use Cases

  • Lineage resolution: Check whether a Pango lineage name is current, withdrawn, or unknown, expand aliases, and find recombinant parents via the live pango-designation files.
  • Prevalence and growth tracking: Compute weekly lineage proportions with Wilson confidence intervals, low-coverage week flags, and descriptive log-odds growth slopes across SARS-CoV-2, influenza, RSV, mpox, and other pathogens.
  • Mutation profiling and assay checks: Diff mutation profiles between lineages at amino-acid or nucleotide level to verify whether a PCR primer or assay target still matches circulating sequence.
  • Reporting lag measurement: Measure how fast sequence cohorts fill in so you know how far back the data can be trusted before quoting recent prevalence.
  • Use Case: Ask which SARS-CoV-2 lineages are dominant in the USA this month, and receive the top circulating Pango lineages with weekly proportions, confidence intervals, and a provenance record of instance, data version, and filters.

Quick Start

Ask the agent to use the pathogen-variant-surveillance skill to report which SARS-CoV-2 lineages are currently circulating in the USA over the last 12 weeks.

Frequently Asked Questions about pathogen-variant-surveillance

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I check which SARS-CoV-2 variant is currently dominant?▼

Run lineage_prevalence.py with --top 5 and a country filter to discover the most common pangoLineage values in a recent window directly from the live LAPIS instance. This avoids naming lineages from memory, since designations change continuously.

How do I verify a Pango lineage name is still valid?▼

Use resolve_lineage.py with the lineage name to check its status against the live pango-designation files. It reports whether the name is current, withdrawn, or unknown, expands aliases, and exits with code 1 if any name is withdrawn or unknown.

Does this work for pathogens other than SARS-CoV-2?▼

Yes, the same scripts work across verified LAPIS instances including H5N1, H3N2, H1N1pdm, RSV-A/B, mpox, measles, dengue, West Nile, and Ebola. Field names differ per instance, so the scripts read each instance's databaseConfig at runtime rather than assuming a schema.

Why does a trailing asterisk return zero sequences on H5N1?▼

A trailing asterisk only expands to descendant lineages on columns with a lineage index. H5N1's clade column has no index, so clade=2.3.4.4b* matches literally and returns 0, while the same syntax on SARS-CoV-2's indexed pangoLineage column returns all descendants.

Why are recent weeks unreliable for prevalence estimates?▼

Recent collection weeks are still filling in because laboratories report at different speeds; only a fraction of a cohort arrives within the first weeks. Run reporting_lag.py first to measure the completeness curve and get a cutoff date before quoting any recent prevalence figure.

What dependencies does the pathogen surveillance skill need?▼

The scripts require Python 3.11 or later and use only the standard library, with no third-party packages. They need network access to public GenSpectrum LAPIS instances and raw.githubusercontent.com for pango-designation, and no API key is required.

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