Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology (original) (raw)

Nature Microbiology volume 6, page 415 (2021) Cite this article

Subjects

An Addendum to this paper has been published: https://doi.org/10.1038/s41564-021-00872-5.

Addendum to: Nature Microbiology https://doi.org/10.1038/s41564-020-0770-5, published online 15 July 2020.

Here we provide clarification regarding the name of the dynamic nomenclature system for SARS-CoV-2 lineages published in our Article. Our nomenclature system should be referred to as the ‘Pango’ nomenclature system (from the first-person Latin verb meaning ‘I set’, ‘I fix’ or ‘I record’). It should not be referred to as the ‘Rambaut et al.’ or ‘Pangolin’ nomenclature system. Lineages defined by this nomenclature system should be referred to as ‘Pango lineages’.

We emphasize that the Pango nomenclature is distinct from, and independent of, any algorithms that are used to implement the system. A growing set of computational tools for working with the Pango nomenclature are provided at https://cov-lineages.org/ and the corresponding GitHub repository, https://github.com/cov-lineages. One popular tool hosted at https://cov-lineages.org/ for classifying SARS-CoV-2 genome sequences is named Pangolin (an acronym for Phylogenetic Assignment of Named Global Outbreak LINeages). The term ‘Pangolin lineage’ in particular should be avoided because it may be misinterpreted as referring to viral host species, rather than to lineages defined by the Pango nomenclature system.

Author information

Authors and Affiliations

  1. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
    Andrew Rambaut, Áine O’Toole, Verity Hill & John T. McCrone
  2. Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
    Edward C. Holmes
  3. Department of Medicine, University of Cambridge, Cambridge, UK
    Christopher Ruis
  4. Department of Zoology, University of Oxford, Oxford, UK
    Louis du Plessis & Oliver G. Pybus

Authors

  1. Andrew Rambaut
  2. Edward C. Holmes
  3. Áine O’Toole
  4. Verity Hill
  5. John T. McCrone
  6. Christopher Ruis
  7. Louis du Plessis
  8. Oliver G. Pybus

Corresponding authors

Correspondence toAndrew Rambaut, Edward C. Holmes or Oliver G. Pybus.

Rights and permissions

About this article

Cite this article

Rambaut, A., Holmes, E.C., O’Toole, Á. et al. Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.Nat Microbiol 6, 415 (2021). https://doi.org/10.1038/s41564-021-00872-5

Download citation

This article is cited by