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

The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor acce...

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Published in	Nature microbiology Vol. 5; no. 11; pp. 1403 - 1407
Main Authors	Rambaut, Andrew, Holmes, Edward C., O’Toole, Áine, Hill, Verity, McCrone, John T., Ruis, Christopher, du Plessis, Louis, Pybus, Oliver G.
Format	Journal Article
Language	English
Published	London Nature Publishing Group UK 01.11.2020 Nature Publishing Group
Subjects	45 631/114/1386 631/114/739 631/181/757 631/326/596/2554 631/326/596/4130 Betacoronavirus - genetics Betacoronavirus - isolation & purification Biomedical and Life Sciences Coronavirus Infections - epidemiology Coronavirus Infections - virology Coronaviruses COVID-19 Decision making Disease transmission Epidemiology Genome, Viral Genomes Genotype Humans Infectious Diseases Life Sciences Medical Microbiology Microbiology Molecular Epidemiology Nomenclature Pandemics Parasitology Phylogenetics Phylogeny Pneumonia, Viral - epidemiology Pneumonia, Viral - virology SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Virology
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Abstract	The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens 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. Here, 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 delabelling virus lineages that become unobserved and hence are probably 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. The authors propose a nomenclature of SARS-CoV-2 lineages to assist research on epidemiology and decision-making during the COVID-19 pandemic. This nomenclature is based on the SARS-CoV-2 phylogeny and designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide. The authors develop a set of rules to produce a hierarchical four-level nomenclature of labels that is flexible and dynamic.
AbstractList	The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens 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. Here, 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 delabelling virus lineages that become unobserved and hence are probably 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.The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens 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. Here, 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 delabelling virus lineages that become unobserved and hence are probably 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. The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens 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. Here, 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 delabelling virus lineages that become unobserved and hence are probably 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. 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 tens 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 de-labelling 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. The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens 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. Here, 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 delabelling virus lineages that become unobserved and hence are probably 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. The authors propose a nomenclature of SARS-CoV-2 lineages to assist research on epidemiology and decision-making during the COVID-19 pandemic. This nomenclature is based on the SARS-CoV-2 phylogeny and designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide. The authors develop a set of rules to produce a hierarchical four-level nomenclature of labels that is flexible and dynamic. The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens 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. Here, 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 delabelling virus lineages that become unobserved and hence are probably 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.The authors propose a nomenclature of SARS-CoV-2 lineages to assist research on epidemiology and decision-making during the COVID-19 pandemic. This nomenclature is based on the SARS-CoV-2 phylogeny and designed to provide a real-time bird’s-eye view of the diversity of the hundreds of thousands of genome sequences collected worldwide. The authors develop a set of rules to produce a hierarchical four-level nomenclature of labels that is flexible and dynamic.
Author	Ruis, Christopher McCrone, John T. du Plessis, Louis Rambaut, Andrew Pybus, Oliver G. Holmes, Edward C. O’Toole, Áine Hill, Verity
AuthorAffiliation	2 Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia 3 Department of Zoology, University of Oxford, Oxford, UK 1 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK 4 Department of Medicine, University of Cambridge, UK
AuthorAffiliation_xml	– name: 4 Department of Medicine, University of Cambridge, UK – name: 2 Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia – name: 1 Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK – name: 3 Department of Zoology, University of Oxford, Oxford, UK
Author_xml	– sequence: 1 givenname: Andrew orcidid: 0000-0003-4337-3707 surname: Rambaut fullname: Rambaut, Andrew email: a.rambaut@ed.ac.uk organization: Institute of Evolutionary Biology, University of Edinburgh – sequence: 2 givenname: Edward C. orcidid: 0000-0001-9596-3552 surname: Holmes fullname: Holmes, Edward C. email: edward.holmes@sydney.edu.au organization: Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney – sequence: 3 givenname: Áine orcidid: 0000-0001-8083-474X surname: O’Toole fullname: O’Toole, Áine organization: Institute of Evolutionary Biology, University of Edinburgh – sequence: 4 givenname: Verity surname: Hill fullname: Hill, Verity organization: Institute of Evolutionary Biology, University of Edinburgh – sequence: 5 givenname: John T. surname: McCrone fullname: McCrone, John T. organization: Institute of Evolutionary Biology, University of Edinburgh – sequence: 6 givenname: Christopher surname: Ruis fullname: Ruis, Christopher organization: Department of Medicine, University of Cambridge – sequence: 7 givenname: Louis surname: du Plessis fullname: du Plessis, Louis organization: Department of Zoology, University of Oxford – sequence: 8 givenname: Oliver G. orcidid: 0000-0002-8797-2667 surname: Pybus fullname: Pybus, Oliver G. email: oliver.pybus@zoo.ox.ac.uk organization: Department of Zoology, University of Oxford
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/32669681$$D View this record in MEDLINE/PubMed
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SubjectTerms	45 631/114/1386 631/114/739 631/181/757 631/326/596/2554 631/326/596/4130 Betacoronavirus - genetics Betacoronavirus - isolation & purification Biomedical and Life Sciences Coronavirus Infections - epidemiology Coronavirus Infections - virology Coronaviruses COVID-19 Decision making Disease transmission Epidemiology Genome, Viral Genomes Genotype Humans Infectious Diseases Life Sciences Medical Microbiology Microbiology Molecular Epidemiology Nomenclature Pandemics Parasitology Phylogenetics Phylogeny Pneumonia, Viral - epidemiology Pneumonia, Viral - virology SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Virology
Title	A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
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