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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.<\/jats:p>","DOI":"10.1038\/s41564-026-02468-3","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T09:02:33Z","timestamp":1790758953000},"page":"2901-2910","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A generalized lineage nomenclature for viral genomic epidemiology"],"prefix":"10.1038","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5577-9897","authenticated-orcid":false,"given":"Rachel","family":"Colquhoun","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1697-1130","authenticated-orcid":false,"given":"Angie S.","family":"Hinrichs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Verity","family":"Hill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0977-5534","authenticated-orcid":false,"given":"Christopher","family":"Ruis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6138-6539","authenticated-orcid":false,"given":"Cornelius","family":"Roemer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver G.","family":"Pybus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4337-3707","authenticated-orcid":false,"given":"Andrew","family":"Rambaut","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8083-474X","authenticated-orcid":false,"given":"\u00c1ine","family":"O\u2019Toole","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"2468_CR1","doi-asserted-by":"publisher","first-page":"001840","DOI":"10.1099\/jgv.0.001840","volume":"104","author":"SG Siddell","year":"2023","unstructured":"Siddell, S. 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