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Taxonomy of Prokaryotic Viruses: Update from the ICTV Bacterial and Archaeal Viruses Subcommittee

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Taxonomy of Prokaryotic Viruses: Update from the ICTV Bacterial and Archaeal Viruses Subcommittee Arch Virol (2016) 161:1095–1099 DOI 10.1007/s00705-015-2728-0 VIROLOGY DIVISION NEWS Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee 1 2,3,4 5 Mart Krupovic • Bas E. Dutilh • Evelien M. Adriaenssens • 6 7 8,9 Johannes Wittmann • Finn K. Vogensen • Mathew B. Sullivan • 10 1 11 22 Janis Rumnieks • David Prangishvili • Rob Lavigne • Andrew M. Kropinski • 12 13 14,15 16 Jochen Klumpp • Annika Gillis • Francois Enault • Rob A. Edwards • 17 18 19 20 Siobain Duffy • Martha R. C. Clokie • Jakub Barylski • Hans-Wolfgang Ackermann • Jens H. Kuhn21 Received: 10 December 2015 / Accepted: 12 December 2015 / Published online: 5 January 2016 Ó Springer-Verlag Wien (Outside the USA) 2016 The prokaryotic virus community is represented on the genome-based relationships between phages. Today, the International Committee on Taxonomy of Viruses (ICTV) order includes six subfamilies, 80 genera, and 441 species. by the Bacterial and Archaeal Viruses Subcommittee. In This year, additional changes in prokaryotic virus taxon- 2008, the three caudoviral families Myoviridae, Podoviri- omy have been brought forward under the new subcom- dae, and Siphoviridae included only 18 genera and 36 mittee chair, Andrew M. Kropinski (University of Guelph, species. Under the able chairmanship of Rob Lavigne (KU Canada). These changes are: Leuven, Belgium), major advances were made in the 1. replacement of ‘‘phage’’ with ‘‘virus’’ in prokaryotic classification of prokaryotic viruses and the order Cau- virus taxon names. In recognition of the fact that dovirales was expanded dramatically, to reflect the phages are first and foremost genuine viruses, and to adhere to ICTV’s International Code of Virus Classi- The content of this publication does not necessarily reflect the views fication and Nomenclature (ICVCN), the word or policies of the US Department of Health and Human Services, or ‘‘phage’’ will disappear from taxon names, but not the institutions and companies affiliated with the authors. The from phage names. For instance, the current taxon taxonomic changes summarized here have been submitted as official taxonomic proposals to the International Committee on Taxonomy of Escherichia phage T4 will be renamed Escherichia Viruses (ICTV) (www.ictvonline.org) and are by now accepted, but virus T4, while the name of this taxon’s member will not yet ratified. These changes therefore may differ from any new remain unchanged (Escherichia phage T4). It is taxonomy that is ultimately approved by the ICTV. 6 & Andrew M. Kropinski Leibniz-Institut DSMZ-Deutsche Sammlung von [email protected] Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany Jens H. Kuhn 7 [email protected] Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark 1 Unit of Molecular Biology of the Gene in Extremophiles, 8 Department of Microbiology, Ohio State University, Department of Microbiology, Institut Pasteur, 25 rue du Dr 496 W 12th Ave, Columbus, OH 43210, USA Roux, 75015 Paris, France 9 Department of Civil, Environmental, and Geodetic 2 Theoretical Biology and Bioinformatics, Utrecht University, Engineering, Ohio State University, 470 Hitchcock Hall, Utrecht, The Netherlands 2070 Neil Avenue, Columbus, OH 43210, USA 3 Centre for Molecular and Biomolecular Informatics, 10 Latvian Biomedical Research and Study Center, Ra¯tsupı¯tes 1, Radboud University, Medical Centre, Nijmegen, Riga, LV 1067, Latvia The Netherlands 11 Laboratory of Gene Technology, KU Leuven, Kasteelpark 4 Instituto de Biologia, Universidade Federal do Rio de Janeiro, Arenberg 21-box 2462, 3001 Leuven, Belgium Rio de Janeiro, Brazil 12 Institute of Food, Nutrition and Health, ETH Zurich, 5 Department of Genetics, Centre for Microbial Ecology and Schmelzbergstrasse 7, 8092 Zurich, Switzerland Genomics, University of Pretoria, Private Bag X20, Hatfield, Pretoria 0028, South Africa 123 1096 M. Krupovic et al. important that the community remembers the ICVCN founding member of the genus was retained as a root distinction between viral taxa (such as species, genera, of the taxon name; families, or orders) and their members, the actual 3. discontinuation of the use of ‘‘Phi’’ and other viruses/phages: ‘‘viruses are real physical entities transliterated Greek letters in the naming of new produced by biological evolution and genetics, prokaryotic virus genera. Since some scientists are whereas virus species and higher taxa are abstract under the impression that ‘‘Phi’’ in its various forms concepts produced by rational thought and logic’’; (phi, u, U) indicates a phage, over the years, many 2. elimination of the infix ‘‘like’’ from prokaryotic phages were given names containing the prefix ‘‘Phi’’. virus genus names. The naming of phage taxa has However, the prefix ‘‘Phi’’ adds no informational value been an evolving process with genus names in the when naming phage genera. Consequently, the Sub- form ‘‘P22-like virus’’, which was always considered committee decided that, unless there was sufficient to be a stop-gap measure, being replaced by P22like- historical precedent (e.g., U29 or UX174), Phi would virus. However, the latter convention is also prob- no longer be added to genus names. In addition, Greek lematic since it was only applied to genera included letters can create problems in electronic databases, as in the order Caudovirales, and the infix ‘‘like’’ was exemplified by a PubMed search for references on unnecessary since the grouping of viruses in genera Bacillus phage U29 [1], which retrieved articles on phi implies per se that their constituent members are 29, phi29, Phi 29, Phi29, 29 phi, {phi}29, u29, and alike. Consequently, the infix ‘‘like’’ will be removed u29 phages. Therefore, the Subcommittee strongly from the names of phage genera and genus names discourages phage scientists from using Phi or any such as Lambdalikevirus and T4likevirus will become other Greek letter in virus and virus taxon names in the Lambdavirus and T4virus, respectively. It will of future; course remain correct to refer to ‘‘lambda-like 4. elimination of hyphens from taxon names. The viruses’’ and ‘‘T4-like phages’’ during discussions ICVCN discourages hyphens in virus taxon names. regarding specific groups of phages classified in these Accordingly, taxon names such as Yersinia phage taxa. There have also been discussions in the L-413C have been renamed (in this instance to Yersinia Subcommittee whether all prokaryotic virus genera virus L413C). However, hyphens are retained when should adopt the system used for some archaeal and appearing in a number string: Thermus phage P2345 eukaryotic viruses, in which names of genera are becomes Thermus virus P23-45 (its correct name) [2]. created from the root of the corresponding family 5. inclusion of the isolation host name in the taxon name with sequentially appended transliterated Greek name. On several occasions, terms such as ‘‘Enter- letters (e.g., Alphabaculovirus, Betabaculovirus, etc.). obacteria’’ or ‘‘Pseudomonad’’ have been used in However, it was decided that recognition of new phage taxon names. However, such terms do not refer genus names is of paramount importance and that to a specific bacterial host; nor do they indicate further drastic changes in one setting might overly whether the phage in question was tested upon a confuse the community. Thus, in most cases, the infix variety of members of the particular host group. To ‘‘like’’ was merely removed and the name of the improve the situation, terms such as ‘‘Enterobacteria’’ 13 Laboratory of Food and Environmental Microbiology, 19 Department of Molecular Virology, Institute of Experimental Universite´ catholique de Louvain, Croix du Sud 2, L7.05.12, Biology, Adam Mickiewicz University, Umultowska 89, 1348 Louvain-la-Neuve, Belgium 61-614 Poznan, Poland 14 Clermont Universite´, Universite´ Blaise Pascal, 20 L’Institut de biologie inte´grative et des systems, Universite´ Laboratoire ‘‘Microorganismes: Ge´nome et Environnement’’, Laval, Pavillon Charles-Euge`ne-Marchand, 1030, avenue de Clermont-Ferrand, France la Me´decine, Quebec, QC G1V 0A6, Canada 15 CNRS UMR 6023, LMGE, Aubie`re, France 21 Integrated Research Facility at Fort Detrick, National 16 Bioinformatics Lab, Department of Computer Science, San Institute of Allergy and Infectious Diseases, National Diego State University, 5500 Campanile Drive, San Diego, Institutes of Health, Fort Detrick, Frederick, MD 21702, USA CA 92182-7720, USA 22 Departments of Food Science, Molecular and Cellular 17 Department of Ecology, Evolution and Natural Resources, Biology, and Pathobiology, University of Guelph, 50 Stone Rutgers University, 14 College Farm Rd, New Brunswick, Rd E, Guelph, ON N1G 2W1, Canada NJ 08901, USA 18 Department of Infection, Immunity and Inflammation, University of Leicester, University Road, Leicester LE1 9HN, UK 123 Prokaryotic virus taxonomy 1097 Table 1 Taxonomy proposals describing new taxa (genera, subfamilies, families) submitted to the ICTV in 2015 New genus Family Subfamily Type species Number of genus-included species Ap22virus Myoviridae Acinetobacter virus AP22 4 Secunda5virus Myoviridae Aeromonas virus 25 5 Biquartavirus Myoviridae Aeromonas virus 44RR2 1 Agatevirus Myoviridae Bacillus virus Agate 3 B4virus Myoviridae Bacillus virus B4 5 Bastillevirus Myoviridae Bacillus virus Bastille 2 Bv431virus Myoviridae Bacillus virus Bc431 4 Cp51virus Myoviridae Bacillus virus CP51 3 Nit1virus Myoviridae Bacillus virus NIT1 3 Wphvirus Myoviridae Bacillus
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