A generalized lineage nomenclature for viral genomic epidemiology
10 affiliations
- 1Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
- 2University of California, Santa Cruz, CA USA
- 3Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- 4Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- 5Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- 6Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
- 7Biozentrum, University of Basel, Basel, Switzerland
- 8Swiss Institute of Bioinformatics, Basel, Switzerland
- 9Royal Veterinary College, University of London, London, UK
- 10Department of Biology, University of Oxford, Oxford, UK
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.
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BibTeX
@article{colquhoun2026generalized,
title = {{A generalized lineage nomenclature for viral genomic epidemiology}},
author = {Rachel Colquhoun and Angie S. Hinrichs and Verity Hill and Christopher Ruis and Cornelius Roemer and Oliver G. Pybus and Andrew Rambaut and Áine O’Toole},
journal = {Nature Microbiology},
year = {2026},
month = sep,
doi = {10.1038/s41564-026-02468-3},
url = {https://doi.org/10.1038/s41564-026-02468-3},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - A generalized lineage nomenclature for viral genomic epidemiology
AU - Rachel Colquhoun
AU - Angie S. Hinrichs
AU - Verity Hill
AU - Christopher Ruis
AU - Cornelius Roemer
AU - Oliver G. Pybus
AU - Andrew Rambaut
AU - Áine O’Toole
PY - 2026
DA - 2026/09/30
JO - Nature Microbiology
DO - 10.1038/s41564-026-02468-3
UR - https://doi.org/10.1038/s41564-026-02468-3
AB - 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.
SN - 2058-5276
ER -