Individual skill
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on remembered facts - which SARS-CoV-2 variant is dominant, whether a Pango lineage is still designated or has been withdrawn, what clade or genotype of H5N1 is in a host or region, whether a PCR primer or assay target still matches circulating sequence, or how a lineage's prevalence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.
backend/cli/skills/biology/pathogen-variant-surveillance/SKILL.md
Source commit a08e0ad0ad3d6448123039ee4659163eb2e35d99
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- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
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- No
- Observed behavior
- Network or broad shell
- Last checked
- Nov 2, 2026
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Repository context
- Repository stars (not skill ratings)
- 4,351
- Repository last updated
- Nov 6, 2026
- License
- Apache-2.0
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SKILL.mdcore · 12,591 bytesSKILL.mdcore · 12,591 bytesSKILL.mdcore · 12,591 bytesSKILL.mdcore · 12,591 bytesSKILL.mdcore · 12,591 bytesSKILL.mdcore · 12,591 bytesSKILL.mdcore · 12,591 bytesSKILL.mdcore · 12,591 bytesreferences/lapis-api.mddoc · 9,712 bytesreferences/lineage-nomenclature.mddoc · 6,417 bytesreferences/surveillance-caveats.mddoc · 8,506 bytesscripts/lapis_client.pyruns · 30,496 bytesscripts/lineage_prevalence.pyruns · 13,003 bytesscripts/mutation_profile.pyruns · 9,403 bytesscripts/reporting_lag.pyruns · 8,605 bytesscripts/resolve_lineage.pyruns · 7,198 bytes
Read excerpt
# Pathogen Variant Surveillance
## When to use
Any time an answer depends on what a pathogen population looks like **now**: which lineages are
circulating, whether one is growing, what a lineage name currently means, or whether an assay
target still matches.
## The rule
**Never state what is circulating, and never write a lineage name, from memory.**
Three things go wrong at once, and only the first is an ordinary knowledge-cutoff problem:
