Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add agentlas-ai/agentlas-desktop --skill pathogen-variant-surveillancegit clone --depth 1 https://github.com/agentlas-ai/agentlas-desktopWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/pathogen-variant-surveillance)<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/pathogen-variant-surveillance"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/pathogen-variant-surveillance/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/pathogen-variant-surveillance"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/pathogen-variant-surveillance.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00249 | $0.03388 |
| Opus 5.5 | $0.00100 | $0.01355 |
| Sonnet 5.5 | $0.00050 | $0.00678 |
| Haiku 4.5 | $0.00025 | $0.00339 |
Grade A, and why
pathogen-variant-surveillance scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
100% identical to pathogen-variant-surveillance — 252 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 226 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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:
- Names post-date training. The Pango designation list carries over 6,200 names and grows continuously.
- The nomenclature is a live data structure, not a convention.
XFGis a recombinant that only resolves throughalias_key.json;PQ.17unaliases toXDV.1.5.1.1.8.1.17. Neither expansion is derivable by reasoning — the mapping is a file that changes. - Prior knowledge gets retracted, not just outdated. 294 names in the current
lineage_notes.txtare withdrawn or redesignated.PC.2is nowLF.7.9;XFG.20was withdrawn outright. A remembered lineage fact is not merely stale, it can be actively wrong.
Every number this skill reports is a count returned by a live instance, stamped with the data version it came from.
Scope
Surveillance data analysis for research. This skill describes sequences that were collected and submitted; it does not produce clinical interpretations, outbreak-response recommendations, or public-health guidance, and sequence counts are not case counts.
Instances
One API shape covers every pathogen. --instance names a verified deployment; --base-url
reaches any other LAPIS instance.
| Instance | Host | Lineage column | Indexed |
|---|---|---|---|
sars-cov-2 |
lapis.cov-spectrum.org (open GenBank data) | pangoLineage |
yes |
h5n1, h3n2, h1n1pdm, influenza-a |
lapis.genspectrum.org | clade |
no |
rsv-a, rsv-b, mpox, measles, dengue, west-nile, hmpv, ebola-zaire, ebola-sudan, cchf |
lapis.pathoplexus.org | varies | varies |
What ships with it
8 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- references/lapis-api.md 9.5 KB
- references/lineage-nomenclature.md 6.3 KB
- references/surveillance-caveats.md 8.3 KB
- scripts/lapis_client.py 30 KB runs code
- scripts/lineage_prevalence.py 13 KB runs code
- scripts/mutation_profile.py 9.2 KB runs code
- scripts/reporting_lag.py 8.4 KB runs code
- scripts/resolve_lineage.py 7.0 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago First seen · 226 lines · 249 tokens per session scan A 9db864de6bf1
pathogen-variant-surveillance is a skill published in the GitHub repository agentlas-ai/agentlas-desktop (6 stars, last pushed yesterday), licensed Apache-2.0. It adds 249 tokens to every session and 3,388 once invoked, about $0.0010 per session on Opus 5.5. A static security scan graded it A with 0 findings. It is 100% identical to pathogen-variant-surveillance, differing in 252 lines, and is treated as a copy.
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