A generalized lineage nomenclature for viral genomic epidemiology.

A generalized lineage nomenclature system enables scalable viral genomic surveillance, exemplified by defining 21 chikungunya virus lineages across 8 founding lineages.

• Why it matters: Effective communication of viral diversity is crucial for outbreak response, but existing systems struggle to keep pace with rapid sequence generation and diverse pathogens.
• What they did: The authors expanded the Pango system, originally for SARS-CoV-2, into a hierarchical framework based on phylogenetic clusters, applying it to chikungunya virus with 21 lineages identified.
• The result: This adaptable framework supports real-time genomic surveillance of various viruses, aiding outbreak tracking and endemic pathogen monitoring across different contexts.