A generalized lineage nomenclature for viral genomic epidemiology

Abstract 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.