Nature Microbiology

Colquhoun, R., Hinrichs, A.S., Hill, V. et al. A generalized lineage nomenclature for viral genomic epidemiology. Nat Microbiol 11, 2901–2910 (2026). https://doi.org/10.1038/s41564-026-02468-3

Pathogen genomics has become increasingly integrated into outbreak response, with recent virus epidemics better characterized by large numbers of viral genetic sequences. Effective international communication of viral diversity requires a scalable, adaptable nomenclature, and existing systems may not accommodate rapid sequence generation. The Pango lineage nomenclature system was designed to address these problems and has been applied to SARS-CoV-2 since early 2020. Here we generalize the underlying principles into a framework for virus surveillance. Lineages are defined as epidemiologically meaningful clusters on a phylogenetic tree, initiated from founding lineages and expanded across a phylogeny through a hierarchical system of alphanumeric sublineage names. Six years on from the inception of the Pango system, we discuss challenges and considerations for implementation. We present a Pango lineage framework for chikungunya virus, providing an alternative to the geography-based clade system and designating 21 lineages across 8 founding lineages. This generalization provides a foundation for future genomic surveillance of many viruses, including for emerging outbreaks and the surveillance of endemic pathogens.