Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee (original) (raw)

The prokaryotic virus community is represented at the International Committee on Taxonomy of Viruses (ICTV) by the Bacterial and Archaeal Viruses Subcommittee. Since our last report [5], the committee composition has changed, and a large number of taxonomic proposals (TaxoProps) were submitted to the ICTV Executive Committee (EC) for approval.

1. Changes in subcommittee membership. During the past year we have lost two members. Dr. Hans-Wolfgang Ackermann, a life member of the ICTV, the father of caudovirus taxonomy [1] and an electron microscopist extraordinaire [2,3,4], lamentably died and will be gravely missed. In addition, Dr. Jens H. Kuhn, who, in spite of protestations about not being a genuine phage biologist, proved invaluable to our discussions and preparation of TaxoProps and manuscripts, resigned from the Subcommittee. Both Hans and Jens are acknowledged for their significant contributions to prokaryotic virus taxonomy. Furthermore, a number of current members have new responsibilities; and, in an effort to increase the geographical diversity of members, we appointed representatives from South America, Africa, and Asia (Table 1).

Table 1 List of current subcommittee members who have new responsibilities (*), along with new members of the subcommittee

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2. Changing the names of prokaryotic virus genera. A significant number of prokaryotic virus genera have either unpronounceable names (e.g., Pocjvirus, Rdjlvirus) or incorporated numerals (e.g., T4virus, D3112virus). In the first case, these names contravene The International Code of Virus Classification and Nomenclature (ICVCN, April 2017) Rule 3.12, which states “Names for taxa shall be easy to use and easy to remember. Euphonious names are preferred.” In the latter case, pronunciation is a problem. For example, is D3112virus pronounced “Dee+three thousand one hundred and twelve+virus” or “Dee+thirty one+twelve+virus” or “Dee+three+one+one+two+virus”? In addition, this nomenclature differs drastically from that for other virus taxa; and, would be incompatible with a Linnaean system of nomenclature [13]. We identified all prokaryotic taxon names that are problematic in the ICTV Master Species List (https://talk.ictvonline.org/files/master-species-lists/m/msl/6776) and suggested alternative names (Supplementary data file S1). These changes will be proposed officially at the next meeting of the ICTV EC in 2018.

3. Re-evaluation of the SPO1-like virus taxonomy. Over the past two years, members of the subcommittee have re-evaluated the taxonomy of a subset of myoviruses related to Bacillus phage SPO1. This group, made up of members of the subfamily Spounavirinae [10] and several genera of _Bacillus_-infecting viruses, was represented as a distinct module in various network analyses published recently [8, 9]. Using a combination of genomic, proteomics, and phylogenetic approaches, we have shown that this group of phages represents a new family, comprising five subfamilies and 13 genera [[7](/article/10.1007/s00705-018-3723-z#ref-CR7 "Barylski J, Enault F, Dutilh BE, Schuller MBP, Edwards RA, Gillis A, Klumpp J, Knezevic P, Krupovic M, Kuhn JH, Lavigne R, Oksanen HM, Sullivan MB, Wittmann J, Tolstoy I, Brister JR, Kropinski AM, Adriaenssens EM (2017) Genomic, proteomic, and phylogenetic analysis of spounaviruses indicates paraphyly of the order Caudovirales. bioRxiv preprint: http://biorxiv.org/content/early/2017/11/16/220434.abstract

")]. We therefore suggest that these viruses be moved from their current taxonomic position in the family Myoviridae to a new family included in the order Caudovirales.

4. New taxa. Table 2 lists of all new taxa proposed at the ICTV EC49 meeting in Singapore in 2017. In total, two new families, eight new subfamilies, 34 new genera, and 91 new species were proposed. Two significant items are on this list. The first item is the introduction of two new families of prokaryotic viruses: Ackermannviridae and Portogloboviridae. With the acceptance of changes to ICVCN Rule 3.11, the second item is the application of the names of eminent phage scientists, specifically Hans-Wolfgang Ackermann (Université Laval) and Charles Shelton McCleskey (Louisiana State University) as prefixes for taxon name stems.

Table 2 Taxonomy proposals (TaxoProps) proposing new taxa (families, subfamilies, genera, species) submitted to the ICTV Executive Committee in 2017

Full size table

5. Updates to taxonomy. As the readership may be aware, “Virus Taxonomy: The Classification and Nomenclature of Viruses - The Online (10th) Report of the ICTV” is freely accessible at http://ictv.global/report. We would like to acknowledge the hard work of Hanna M. Oksanen (Corticoviridae), Dennis H. Bamford (Pleolipoviridae), and Minna M. Poranen (Cystoviridae) for completing updates to their sections. The family Pleolipoviridae is now recognized as the first virus taxon in the newly established ICTV category for ssDNA/dsDNA Viruses. The summaries of the ICTV Report chapters are published in The Journal of General Virology [[6](/article/10.1007/s00705-018-3723-z#ref-CR6 "Bamford DH, Pietila MK, Roine E, Atanasova NS, Dienstbier A, Oksanen HM, Ictv Report C (2017) ICTV Virus Taxonomy Profile: Pleolipoviridae. J Gen Virol. https://doi.org/10.1099/jgv.0.000972

(Epub ahead of print) "), 11, 12].

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Acknowledgements

The committee would like to thank Dr. Graham Hatfull (University of Pittsburgh) for permitting us to use Actinobacteriophage Database electron micrographs in 2017’s taxonomy proposals. The authors thank Laura Bollinger (National Institutes of Health/National Institute of Allergy and Infectious Diseases, Integrated Research Facility at Fort Detrick, Frederick, MD, USA) for editing this paper.

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Authors and Affiliations

  1. Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, United Kingdom
    Evelien M. Adriaenssens
  2. Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124, Braunschweig, Germany
    Johannes Wittmann
  3. Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, 21702, USA
    Jens H. Kuhn
  4. Faculty of Health and Applied Sciences, UWE Bristol, Frenchay Campus, Bristol, BS16 1QY, United Kingdom
    Dann Turner
  5. Department of Microbiology, The Ohio State University, Columbus, OH, 43210, USA
    Matthew B. Sullivan & Ho Bin Jang
  6. Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
    Bas E. Dutilh
  7. Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
    Bas E. Dutilh
  8. Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville, Cape Town, 7535, South Africa
    Leonardo J. van Zyl
  9. Institute of Food, Nutrition and Health, ETH Zurich, 8092, Zurich, Switzerland
    Jochen Klumpp
  10. Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
    Malgorzata Lobocka
  11. Faculty of Ecology and Natural Resources School, Universidad Andres Bello, 8370146, Santiago, Chile
    Andrea I. Moreno Switt
  12. Latvian Biomedical Research and Study Center, Riga, LV-1067, Latvia
    Janis Rumnieks
  13. Departments of Computer Science and Biology, San Diego State University, San Diego, CA, 92182, USA
    Robert A. Edwards
  14. School of Veterinary Medicine, Azabu University, Fuchinobe 1-7-71, Chuo-ku Sagamihara-shi, Kanagawa, 252-0206, Japan
    Jumpei Uchiyama
  15. Laboratory of Industrial Microbiology,Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
    Poliane Alfenas-Zerbini
  16. The ithree institute, University of Technology Sydney, Sydney, NSW, 2007, Australia
    Nicola K. Petty
  17. Departments of Food Science, and Pathobiology, University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada
    Andrew M. Kropinski
  18. Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznan, Poland
    Jakub Barylski
  19. Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, 1348, Louvain-la-Neuve, Belgium
    Annika Gillis
  20. Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, LE1 9HN, United Kingdom
    Martha R. C. Clokie
  21. Unit of Molecular Biology of the Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015, Paris, France
    David Prangishvili & Mart Krupovic
  22. Laboratory of Gene Technology, KU Leuven, 3001, Leuven, Belgium
    Rob Lavigne
  23. Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy St, 11562, Cairo, Egypt
    Ramy Karam Aziz
  24. Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
    Siobain Duffy
  25. Department of Biosciences, University of Helsinki, Helsinki, Finland
    Minna M. Poranen & Hanna M. Oksanen
  26. Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
    Petar Knezevic
  27. Université Clermont Auvergne, CNRS, LMGE, 63000, Clermont-Ferrand, France
    Francois Enault
  28. Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing, People’s Republic of China
    Yigang Tong
  29. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    J. Rodney Brister

Authors

  1. Evelien M. Adriaenssens
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  2. Johannes Wittmann
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  3. Jens H. Kuhn
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  4. Dann Turner
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  5. Matthew B. Sullivan
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  6. Bas E. Dutilh
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  7. Ho Bin Jang
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  8. Leonardo J. van Zyl
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  9. Jochen Klumpp
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  10. Malgorzata Lobocka
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  11. Andrea I. Moreno Switt
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  12. Janis Rumnieks
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  13. Robert A. Edwards
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  14. Jumpei Uchiyama
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  15. Poliane Alfenas-Zerbini
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  16. Nicola K. Petty
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  17. Andrew M. Kropinski
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  18. Jakub Barylski
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  19. Annika Gillis
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  20. Martha R. C. Clokie
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  21. David Prangishvili
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  22. Rob Lavigne
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  23. Ramy Karam Aziz
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  24. Siobain Duffy
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  25. Mart Krupovic
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  26. Minna M. Poranen
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  27. Petar Knezevic
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  28. Francois Enault
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  29. Yigang Tong
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  30. Hanna M. Oksanen
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  31. J. Rodney Brister
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Corresponding author

Correspondence toAndrew M. Kropinski.

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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.

Funding

This work was funded in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I (J.H.K.). B.E.D. was supported by the Netherlands Organization for Scientific Research (NWO), Vidi Grant 864.14.004. R.A.E was supported by grant MCB-1330800 from the National Science Foundation. J.R.B. was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine. R.L. is a member of the phagebiotics research community, supported by FWO Vlaanderen. M.M.P. was supported by the Academy of Finland (272507). A.G. was supported by the National Fund for Scientific Research (FNRS). H.M.O. was supported by University of Helsinki funding for Instruct-F1 research infrastructure.

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The authors declare that they have no conflict of interest.

Ethical approval

The authors did not perform any studies with human participants or animals in this article.

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Handling Editor: Sead Sabanadzovic.

Electronic supplementary material

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Supplementary Table S1.

Proposed new names for bacteriophage taxa which contravene ICVCN Rule 3.12 or contain numerals. (DOCX 28 kb)

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Adriaenssens, E.M., Wittmann, J., Kuhn, J.H. et al. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.Arch Virol 163, 1125–1129 (2018). https://doi.org/10.1007/s00705-018-3723-z

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