Consensus statement: Virus taxonomy in the age of metagenomics

doi:10.1038/nrmicro.2016.177

. 2017 Mar;15(3):161-168.

doi: 10.1038/nrmicro.2016.177. Epub 2017 Jan 3.

Consensus statement: Virus taxonomy in the age of metagenomics

Peter Simmonds¹, Mike J Adams, Mária Benkő², Mya Breitbart³, J Rodney Brister⁴, Eric B Carstens⁵, Andrew J Davison⁶, Eric Delwart^{7

8}, Alexander E Gorbalenya^{9

10}, Balázs Harrach², Roger Hull¹¹, Andrew M Q King¹², Eugene V Koonin⁴, Mart Krupovic¹³, Jens H Kuhn¹⁴, Elliot J Lefkowitz¹⁵, Max L Nibert¹⁶, Richard Orton⁶, Marilyn J Roossinck¹⁷, Sead Sabanadzovic¹⁸, Matthew B Sullivan¹⁹, Curtis A Suttle^{20

21}, Robert B Tesh²², René A van der Vlugt²³, Arvind Varsani²⁴, F Murilo Zerbini²⁵

Affiliations

¹ Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.
² Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, 21 Hungária krt., Budapest H-1143, Hungary.
³ University of South Florida, College of Marine Science, 140 7th Avenue South, Saint Petersburg, Florida 33701, USA.
⁴ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
⁵ Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, Ontario K7L 3N6, Canada.
⁶ UK Medical Research Council (MRC)-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK.
⁷ Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, California 94118, USA.
⁸ Department of Laboratory Medicine, 521 Parnassus Avenue, University of California, San Francisco, California 94118, USA.
⁹ Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, E4-P, room E4-72, 2300 RC Leiden, The Netherlands.
¹⁰ Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899 Moscow, Russia.
¹¹ The John Innes Centre, Norwich, Norfolk, UK.
¹² The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
¹³ Department of Microbiology, Institut Pasteur, 25 Rue du Dr Roux, 75015 Paris, France.
¹⁴ National Institute of Allergy and Infectious Diseases (NIAID), Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, Maryland 21702, USA.
¹⁵ Department of Microbiology, University of Alabama at Birmingham (UAB), Bevill Biomedical Research Building (BBRB) Suite 276, 845 19th Street South, Birmingham, Alabama 35294-2170, USA.
¹⁶ Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.
¹⁷ Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
¹⁸ Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Highway 12 Mail Stop 9775, Mississippi State, Mississippi 39762, USA.
¹⁹ Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, USA.
²⁰ Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada.
²¹ Canadian Institute for Advanced Research (CIFAR), 180 Dundas Street West, Toronto, Ontario M5G 1Z8, Canada.
²² Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0609, USA.
²³ Wageningen Plant Research, Wageningen University and Research Centre (WUR-PRI), Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
²⁴ The Center for Fundamental and Applied Microbiomics, The Biodesign Institute and School of Life Sciences, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281-2115, USA.
²⁵ Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil.

PMID: 28134265
DOI: 10.1038/nrmicro.2016.177

Free article

Consensus statement: Virus taxonomy in the age of metagenomics

Peter Simmonds et al. Nat Rev Microbiol. 2017 Mar.

Free article

. 2017 Mar;15(3):161-168.

doi: 10.1038/nrmicro.2016.177. Epub 2017 Jan 3.

Authors

Affiliations

¹ Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford OX1 3SY, UK.
² Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, 21 Hungária krt., Budapest H-1143, Hungary.
³ University of South Florida, College of Marine Science, 140 7th Avenue South, Saint Petersburg, Florida 33701, USA.
⁴ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
⁵ Department of Biomedical and Molecular Sciences, Queen's University, 18 Stuart Street, Kingston, Ontario K7L 3N6, Canada.
⁶ UK Medical Research Council (MRC)-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK.
⁷ Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, California 94118, USA.
⁸ Department of Laboratory Medicine, 521 Parnassus Avenue, University of California, San Francisco, California 94118, USA.
⁹ Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, E4-P, room E4-72, 2300 RC Leiden, The Netherlands.
¹⁰ Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899 Moscow, Russia.
¹¹ The John Innes Centre, Norwich, Norfolk, UK.
¹² The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
¹³ Department of Microbiology, Institut Pasteur, 25 Rue du Dr Roux, 75015 Paris, France.
¹⁴ National Institute of Allergy and Infectious Diseases (NIAID), Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, Maryland 21702, USA.
¹⁵ Department of Microbiology, University of Alabama at Birmingham (UAB), Bevill Biomedical Research Building (BBRB) Suite 276, 845 19th Street South, Birmingham, Alabama 35294-2170, USA.
¹⁶ Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.
¹⁷ Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
¹⁸ Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Highway 12 Mail Stop 9775, Mississippi State, Mississippi 39762, USA.
¹⁹ Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, USA.
²⁰ Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, University of British Columbia, Vancouver, V6T 1Z4, Canada.
²¹ Canadian Institute for Advanced Research (CIFAR), 180 Dundas Street West, Toronto, Ontario M5G 1Z8, Canada.
²² Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0609, USA.
²³ Wageningen Plant Research, Wageningen University and Research Centre (WUR-PRI), Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
²⁴ The Center for Fundamental and Applied Microbiomics, The Biodesign Institute and School of Life Sciences, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281-2115, USA.
²⁵ Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil.

PMID: 28134265
DOI: 10.1038/nrmicro.2016.177

Abstract

The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.

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A sea change for virology.
[No authors listed] [No authors listed] Nat Rev Microbiol. 2017 Feb 13;15(3):129. doi: 10.1038/nrmicro.2017.13. Nat Rev Microbiol. 2017. PMID: 28190884 No abstract available.

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[1] Nature. 2016 Aug 25;536(7617):425-30 - PubMed

[2] Nature. 2016 Aug 25;536(7617):425-30 - PubMed

[3] J Virol. 2015 Oct 21;90(2):659-69 - PubMed

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[10] Arch Virol. 2016 Sep;161(9):2633-43 - PubMed

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Consensus statement: Virus taxonomy in the age of metagenomics

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