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.