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A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

Andrew Rambaut, Edward C. Holmes, Verity Hill, Áine O’Toole, JT McCrone, Chris Ruis, Louis du Plessis, Oliver G. Pybus
doi: https://doi.org/10.1101/2020.04.17.046086
Andrew Rambaut
1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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  • For correspondence: a.rambaut@ed.ac.uk edward.holmes@sydney.edu.au oliver.pybus@zoo.ox.ac.uk
Edward C. Holmes
2Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
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  • For correspondence: a.rambaut@ed.ac.uk edward.holmes@sydney.edu.au oliver.pybus@zoo.ox.ac.uk
Verity Hill
1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Áine O’Toole
1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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JT McCrone
1Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Chris Ruis
4Department of Medicine, University of Cambridge, UK
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Louis du Plessis
3Department of Zoology, University of Oxford, Oxford, UK
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Oliver G. Pybus
3Department of Zoology, University of Oxford, Oxford, UK
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  • For correspondence: a.rambaut@ed.ac.uk edward.holmes@sydney.edu.au oliver.pybus@zoo.ox.ac.uk
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Abstract

The ongoing pandemic spread of a novel human coronavirus, SARS-COV-2, associated with severe pneumonia disease (COVID-19), has resulted in the generation of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. We present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and declassifying virus lineages that become unobserved and hence are likely inactive. By focusing on active virus lineages and those spreading to new locations this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/hCoV-2019/pangolin

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 19, 2020.
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A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology
Andrew Rambaut, Edward C. Holmes, Verity Hill, Áine O’Toole, JT McCrone, Chris Ruis, Louis du Plessis, Oliver G. Pybus
bioRxiv 2020.04.17.046086; doi: https://doi.org/10.1101/2020.04.17.046086
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A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology
Andrew Rambaut, Edward C. Holmes, Verity Hill, Áine O’Toole, JT McCrone, Chris Ruis, Louis du Plessis, Oliver G. Pybus
bioRxiv 2020.04.17.046086; doi: https://doi.org/10.1101/2020.04.17.046086

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