pathogen-variant-surveillance SKILL.md skillA
pathogen-variant-surveillance from k-dense-ai/scientific-agent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add k-dense-ai/scientific-agent-skills/pathogen-variant-surveillance@v1.3Pins v1.3 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- k-dense-ai/scientific-agent-skills
- Path
skills/pathogen-variant-surveillance/SKILL.md- Versions recorded
- 4
- Latest version
- v1.3, committed Oct 1, 2026
- First version recorded
- Jul 27, 2026
- Size
- 10,817 bytes
- Repository stars
- 56,497
- License
- MIT
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…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# 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 Reviewed on 2026-10-01 against official documentation, live schemas for all 15 registered instances, and small public queries. SARS-CoV-2 served LAPIS 0.8.7/SILO 0.14.3; the other registered deployments served LAPIS 0.8.0/SILO 0.11.0. Do not assume identical feature support. Bundled standard-library scripts have synthetic regression tests and bounded live smoke checks. Nextclade, GenoFLU, authenticated APIs, and sequence-level assay validation are not executed here. | Instance | Host | Common lineage field | | --- | --- | --- | …
Read the whole file at its exact version.
How to install
mdr add k-dense-ai/scientific-agent-skills/pathogen-variant-surveillance@sha256:95510f890a47ab2eThe line at the top of this page pins the label v1.3, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_w4vnb3bfqvmh5jgk)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 4 versions of this file, between Jul 27, 2026 and Oct 1, 2026, about one every 22 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| v1.3 latest | 2026-10-01 | a92663a | 10,817 B | A | view · diff |
| v1.2 | 2026-09-30 | ce9e6e9 | 12,916 B | A | view · diff |
| v1.1 | 2026-09-02 | 1e5eeff | 12,312 B | A | view · diff |
| v1.0 | 2026-07-27 | e608baa | 11,354 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (10817 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
k-dense-ai/scientific-agent-skills · 56,497 stars · license MIT · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_w4vnb3bfqvmh5jgk GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/pathogen-variant-surveillance GET https://markdownregistry.com/api/v1/blob/95510f890a47ab2e2275832fe60e725eca34e5318dcde88b0940d9362b3ab590
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.