Individual skill
pathogen-variant-surveillance
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.
skills/pathogen-variant-surveillance/SKILL.md
Source commit 2d2065fb4520fa3f3f2bcf61cff26ec8b7eba4b5
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- Last checked
- Nov 10, 2026
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- 56,785
- Repository last updated
- Nov 9, 2026
- License
- MIT
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- ai-scientist Repository topic
- bioinformatics Repository topic
- chemoinformatics Repository topic
- claude Repository topic
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- clinical-research Repository topic
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SKILL.mdcore · 10,817 bytesSKILL.mdcore · 10,817 bytesSKILL.mdcore · 10,817 bytesSKILL.mdcore · 10,817 bytesSKILL.mdcore · 10,817 bytesSKILL.mdcore · 10,817 bytesSKILL.mdcore · 10,817 bytesSKILL.mdcore · 10,817 bytesSKILL.mdcore · 10,817 bytesreferences/lapis-api.mddoc · 10,992 bytesreferences/lineage-nomenclature.mddoc · 5,753 bytesreferences/surveillance-caveats.mddoc · 6,259 bytesscripts/lapis_client.pyruns · 30,484 bytesscripts/lineage_prevalence.pyruns · 15,201 bytesscripts/mutation_profile.pyruns · 10,616 bytesscripts/reporting_lag.pyruns · 8,232 bytesscripts/resolve_lineage.pyruns · 7,599 bytes
Read excerpt
# 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
