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  References  ( placed on NEW HTML page < here >

  1. 1.

    Iwanowsky, D. Über die Mosaikkrankheit der Tabakspflanze. Bull. Acad. Imp. Sci. Saint-Pétersbourg 35, 67–70 (1892).

  2. 2.

    Beijerinck, M. W. Über ein Contagium vivum fluidum als Ursache der Fleckenkrankheit der Tabaksblätter. Verh. K. Ned. Akad. Wet. Afd. Natuurkd. Tweede Sect. 65, 1–22 (1898).

  3. 3.

    Loeffler, F. & Frosch, P. Berichte der Kommission zur Erforschung der Maul- und Klauenseuche bei dem Institut für Infektionskrankheiten in Berlin. Centralblatt für Bakteriologie, Parasitenkunde und Infektionskrankheiten Abt. I 23, 371–391 (1898).

  4. 4.

    Lustig, A. & Levine, A. J. One hundred years of virology. J. Virol. 66, 4629–4631 (1992).

  5. 5.

    Rott, R. & Siddell, S. One hundred years of animal virology. J. Gen. Virol. 79, 2871–2874 (1998).

  6. 6.

    Duffy, S., Shackelton, L. A. & Holmes, E. C. Rates of evolutionary change in viruses: patterns and determinants. Nat. Rev. Genet. 9, 267–276 (2008).

  7. 7.

    Holmes, E. C. The Evolution and Emergence of RNA Viruses: Oxford Series in Ecology and Evolution (Oxford Univ. Press, 2009).

  8. 8.

    Biek, R., Pybus, O. G., Lloyd-Smith, J. O. & Didelot, X. Measurably evolving pathogens in the genomic era. Trends Ecol. Evol. 30, 306–313 (2015).

  9. 9.

    Suttle, C. A. Marine viruses — major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801–812 (2007).

  10. 10.

    Cobián Güemes, A. G. et al. Viruses as winners in the game of life. Annu. Rev. Virol. 3, 197–214 (2016).

  11. 11.

    Gregory, A. C. Marine DNA viral macro- and microdiversity from pole to pole. Cell 177, 1109–1123 (2019).

  12. 12.

    Lefeuvre, P. et al. Evolution and ecology of plant viruses. Nat. Rev. Microbiol. 17, 632–644 (2019).

  13. 13.

    Zhang, Y.-Z., Chen, Y.-M., Wang, W., Qin, X.-C. & Holmes, E. C. Expanding the RNA virosphere by unbiased metagenomics. Annu. Rev. Virol. 6, 119–139 (2019).

  14. 14.

    Krupovic, M., Dolja, V. V. & Koonin, E. V. Origin of viruses: primordial replicators recruiting capsids from hosts. Nat. Rev. Microbiol. 17, 449–458 (2019).

  15. 15.

    Adams, M. J. et al. 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Arch. Virol. 162, 1441–1446 (2017).

  16. 16.

    Wildy, P. in Monographs in Virology Vol. 5 (ed. Melnick, J. L.) (S. Karger, 1971).

  17. 17.

    Francki, R. I. B., Fauquet, C. M., Knudson, D. L. & Brown, F. (eds) Classification and Nomenclature of Viruses: Fifth Report of the International Committee on Taxonomy of Viruses (ICTV, 1991).

  18. 18.

    Simmonds, P. et al. Consensus statement: virus taxonomy in the age of metagenomics. Nat. Rev. Microbiol. 15, 161–168 (2017).

  19. 19.

    Barylski, J. et al. Analysis of spounaviruses as a case study for the overdue reclassification of tailed phages. Syst. Biol. 69, 110–123 (2020).

  20. 20.

    Gorbalenya, A. E., Lauber, C. & Siddell, S. Taxonomy of Viruses, in Reference Module in Biomedical Sciences (Elsevier, 2019); https://doi.org/10.1016/B978-0-12-801238-3.99237-7.

  21. 21.

    Goldbach, R. W. Molecular evolution of plant RNA viruses. Annu. Rev. Phytopathol. 24, 289–310 (1986).

  22. 22.

    Strauss, J. H. & Strauss, E. G. Evolution of RNA viruses. Annu. Rev. Microbiol. 42, 657–683 (1988).

  23. 23.

    Gorbalenya, A. E. et al. The palm subdomain-based active site is internally permuted in viral RNA-dependent RNA polymerases of an ancient lineage. J. Mol. Biol. 324, 47–62 (2002).

  24. 24.

    Iyer, L. M., Aravind, L. & Koonin, E. V. Common origin of four diverse families of large eukaryotic DNA viruses. J. Virol. 75, 11720–11734 (2001).

  25. 25.

    Rixon, F. J. & Schmid, M. F. Structural similarities in DNA packaging and delivery apparatuses in Herpesvirus and dsDNA bacteriophages. Curr. Opin. Virol. 5, 105–110 (2014).

  26. 26.

    Krupovic, M. & Koonin, E. V. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nat. Rev. Microbiol. 13, 105–115 (2015).

  27. 27.

    Kazlauskas, D., Varsani, A., Koonin, E. V. & Krupovic, M. Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial and archaeal plasmids. Nat. Commun. 10, 3425 (2019).

  28. 28.

    Iranzo, J., Krupovic, M. & Koonon, E. V. The double-stranded DNA virosphere as a modular hierarchial network of gene sharing. mBio 7, 00978-16 (2016).

  29. 29.

    Allaire, M., Chernaia, M. M., Malcolm, B. A. & James, M. N. Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases. Nature 369, 72–76 (1994).

  30. 30.

    Subramanya, H. S., Bird, L. E., Brannigan, J. A. & Wigley, D. B. Crystal structure of a DExx box DNA helicase. Nature 384, 379–83 (1996).

  31. 31.

    Pan, J., Vakharia, V. N. & Tao, Y. J. The structure of a birnavirus polymerase reveals a distinct active site topology. Proc. Natl Acad. Sci. USA 104, 7385–7390 (2007).

  32. 32.

    Baltimore, D. Expression of animal virus genomes. Bacteriol. Rev. 35, 235–241 (1971).

  33. 33.

    Condit, R. C. Principles of Virology, in Fields Virology Vol. 1 (eds Knipe D. M. & Howley P.) 21–51 (Lippincott, Williams & Wilkins, 2013).

  34. 34.

    Gorbalenya, A. E. Increasing the number of available ranks in virus taxonomy from five to ten and adopting the Baltimore classes as taxa at the basal rank. Arch. Virol. 163, 2933–2936 (2018).

  35. 35.

    Van Regenmortel, M. H. Logical puzzles and scientific controversies: the nature of species, viruses and living organisms. Syst. Appl. Microbiol. 33, 1–6 (2010).

  36. 36.

    Gorbalenya, A. E., Krupovic, M., Siddell, S. G., Varsani, A & Kuhn, J. H. Proposal 2017.006G. Riboviria: a single taxon that comprises RNA viruses at the basal rank of virus taxonomy. (ICTV, 2018); https://talk.ictvonline.org/files/ictv_official_taxonomy_updates_since_the_8th_report/m/general-2008/8093.

  37. 37.

    Siddell, S. G. et al. Additional changes to taxonomy ratified in a special vote by the International Committee on Taxonomy of Viruses (October 2018). Arch. Virol. 164, 943–946 (2019).

  38. 38.

    Walker, P. J. et al. Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019). Arch. Virol. 164, 2417–2429 (2019).

  39. 39.

    Liu, J. & Mushegian, A. Displacements of prohead protease genes in the late operons of double-stranded-DNA bacteriophages. J. Bacteriol. 186, 4369–4375 (2004).

  40. 40.

    Dai, X. & Zhou, Z. H. Structure of the herpes simplex virus 1 capsid with associated tegument protein complexes. Science 360, eaao7298 (2018).

  41. 41.

    Dedeo, C. L., Cingolani, G. & Teschke, C. M. Portal protein: the orchestrator of capsid assembly for the dsDNA tailed bacteriophages and herpesviruses. Annu. Rev. Virol. 6, 141–160 (2019).

  42. 42.

    Bào, Y. et al. Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses. Viruses 9, 106 (2017).

  43. 43.

    Wolf, Y. I. et al. Origins and evolution of the global RNA Virome. mBio 9, 02329-18 (2018).

  44. 44.

    Lauber, C. & Gorbalenya, A. E. Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses. J. Virol. 86, 3890–3904 (2012).

  45. 45.

    Lauber, C. & Gorbalenya, A. E. Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses. J. Virol. 86, 3905–3915 (2012).

  46. 46.

    Gorbalenya, A. E. et al. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 5, 536–544 (2020).

  47. 47.

    ICTV Master Species List 2018b.v2 (ICTV, 2018); https://talk.ictvonline.org/files/master-species-lists/m/msl/8266.

  48. 48.

    Gorbalenya, A. E. et al. Proposal 2017.005G.A.v1. Increasing the number of ranks available in virus taxonomy. (ICTV, 2017); https://talk.ictvonline.org/files/ictv_official_taxonomy_updates_since_the_8th_report/m/general-2008/7995.

  49. 49.

    Kuhn, J. H. et al. Classify viruses — the gain is worth the pain. Nature 566, 318–320 (2019).

  50. 50.

    Koonin, E. V. et al. Global organization and proposed megataxonomy of the virus world. Microbiol. Mol. Biol. Rev. 84, e00061-19 (2020).

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Acknowledgements

A.E.G. was a Leiden University Fund (LUF) Professor. His work was supported by the EU Horizon 2020 EVAg 653316 project and the LUMC MoBiLe program. A.R.M. is a Program Director at the US National Science Foundation (NSF). His work on this project was not performed while acting in an official NSF capacity, and the statements and opinions expressed herein do not constitute the endorsement of NSF or the Government of the United States. B.E.D. was supported by the Netherlands Organisation for Scientific Research (NWO) Vidi (grant no. 864.14.004). A.J.D. is supported by the Medical Research Council (grant no. MC_UU_12014/3). B.H. was supported by National Scientific Research Fund (grant no. NN128309). S.S. is supported by the Mississippi Agricultural and Forestry Experiment Station (MAFES) and the National Institute of Food and Agriculture, US Department of Agriculture, Hatch Project 1021494. This work was supported in part through the prime contract of Laulima Government Solutions, LLC, with the US National Institute of Allergy and Infectious Diseases (NIAID) under contract no. HHSN272201800013C and Battelle Memorial Institute’s former prime contract with NIAID under contract no. HHSN272200700016I. J.H.K. performed this work as a former employee of Battelle Memorial Institute and a current employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under contract no. HHSN272201800013C. The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. USDA is an Equal Opportunity Provider and Employer. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Health and Human Services or of the institutions and companies affiliated with the authors.

Author information

Affiliations

  1. Departments of Biomedical Data Sciences and Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
    • Alexander E. Gorbalenya
  2. Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
    • Alexander E. Gorbalenya
  3. Archaeal Virology Unit, Institut Pasteur, Paris, France
    • Mart Krupovic
  4. Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA, USA
    • Arcady Mushegian
  5. Departments of Food Science and Pathobiology, University of Guelph, Guelph, Ontario, Canada
    • Andrew M. Kropinski
  6. School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
    • Stuart G. Siddell
  7. The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
    • Arvind Varsani
  8. Minehead, UK
    • Michael J. Adams
  9. MRC–University of Glasgow Centre for Virus Research, Glasgow, UK
    • Andrew J. Davison
  10. Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
    • Bas E. Dutilh
  11. Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
    • Balázs Harrach
  12. Invasive Insect Biocontrol and Behavior Laboratory, US Department of Agriculture–Agricultural Research Service, Beltsville, MD, USA
    • Robert L. Harrison
  13. Institute of Virology, Charité – Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt-University Berlin and Berlin Institute of Health, Berlin, Germany
    • Sandra Junglen
  14. The Pirbright Institute, Pirbright, UK
    • Andrew M. Q. King
    •  & Nick J. Knowles
  15. Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
    • Elliot J. Lefkowitz
  16. Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
    • Max L. Nibert
  17. Istituto per la Protezione Sostenibile delle Piante, National Research Council of Italy, Bari, Italy
    • Luisa Rubino
  18. Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
    • Sead Sabanadzovic
  19. Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
    • Hélène Sanfaçon
  20. Nuffield Department of Medicine, University of Oxford, Oxford, UK
    • Peter Simmonds
  21. School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
    • Peter J. Walker
  22. Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
    • F. Murilo Zerbini
  23. Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
    • Jens H. Kuhn

Consortia

International Committee on Taxonomy of Viruses Executive Committee

Contributions

All authors are ICTV EC members of two terms, 2014–2017 or 2017–2020, or both, and were involved in extensive deliberations about the reported taxonomic changes. The ICTV EC is chaired by A.J.D. A.E.G., M.K., A.M., A.M.K., S.G.S., A.V. and J.H.K. were members of the Additional Ranks in Taxonomy Working Group, led by A.E.G. A.E.G., M.K., A.M., A.M.K., S.G.S., A.V. and J.H.K. wrote the manuscript. A.E.G., S.G.S. and J.H.K. generated the figures. All authors reviewed the manuscript and approved its submission for publication.

Corresponding authors

Correspondence to Alexander E. Gorbalenya or Stuart G. Siddell or Jens H. Kuhn.

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Competing interests

The authors declare no competing interests.