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Archives of Virology

, Volume 163, Issue 4, pp 1125–1129 | Cite as

Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

  • Evelien M. Adriaenssens
  • Johannes Wittmann
  • Jens H. Kuhn
  • Dann Turner
  • Matthew B. Sullivan
  • Bas E. Dutilh
  • Ho Bin Jang
  • Leonardo J. van Zyl
  • Jochen Klumpp
  • Malgorzata Lobocka
  • Andrea I. Moreno Switt
  • Janis Rumnieks
  • Robert A. Edwards
  • Jumpei Uchiyama
  • Poliane Alfenas-Zerbini
  • Nicola K. Petty
  • Andrew M. Kropinski
  • Jakub Barylski
  • Annika Gillis
  • Martha R. C. Clokie
  • David Prangishvili
  • Rob Lavigne
  • Ramy Karam Aziz
  • Siobain Duffy
  • Mart Krupovic
  • Minna M. Poranen
  • Petar Knezevic
  • Francois Enault
  • Yigang Tong
  • Hanna M. Oksanen
  • J. Rodney Brister
Virology Division News

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

Name

Country

Position

Evelien Adriaenssens*

United Kingdom

Chair, Caudovirales phage study group

Dann Turner

United Kingdom

Chair, Acinetobacter phage study group

Jakub Barylski*

Poland

Chair, Bacillus phage study group

Jochen Klumpp*

Switzerland

Chair, Listeria phage study group

Małgorzata Łobocka

Poland

Chair, Staphylococcus phage study group

Poliane Alfenas-Zerbini

Brazil

Member

Ramy Aziz

Egypt

Member

Andrea Moreno Switt

Chile

Member

Yigang Tong

People’s Republic of China

Member

Leonardo van Zyl

South Africa

Member

Jumpei Uchiyama

Japan

Member

Nicola K. Petty

Australia

Member

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]. 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

Family

Subfamily

Genus

Type species

No. of species in genus***

Ackermannviridae

Aglimvirinae

Ag3virus

Shigella virus AG3

1 (2)

Ackermannviridae

Aglimvirinae

Limestonevirus

Dickeya virus Limestone

1 (2)

Ackermannviridae

Cvivirinae

Cba120virus

Escherichia virus CBA120

4 (9)

Ackermannviridae

Cvivirinae

Vi1virus*

Salmonella virus ViI

(5)

Ackermannviridae

unassigned

unassigned

Erwinia virus Ea2809, Serratia virus MAM1, Serratia virus IME250, Klebsiella virus 0507KN21

4

Myoviridae*

 

Arvunavirus

Arthrobacter virus ArV1

2

Myoviridae*

 

Eah2virus

Erwinia virus EaH2

2

Myoviridae*

 

Machinavirus

Erwinia virus Machina

1

Myoviridae*

 

Ntreusvirus

Salmonella virus SPN3US

1

Myoviridae*

 

Svunavirus

Geobacillus virus GBSV1

2

Myoviridae*

Ampvirinae

Chippewavirus

Arthrobacter virus BarretLemon

1

Myoviridae*

Ampvirinae

Jawnskivirus

Arthrobacter virus Jawnski

2

Myoviridae*

Ampvirinae

Sonnyvirus

Arthrobacter virus Sonny

3

Podoviridae*

 

Dfl12virus

Dinoroseobacter virus DFL12phi1

1

Podoviridae*

 

Jwalphavirus

Achromobacter virus JWAlpha

2

Podoviridae*

 

P22virus*

Salmonella virus P22

1 (5)

Podoviridae*

 

Sp58virus

Salmonella virus SP058

3

Portogloboviridae

 

Alphaportoglobovirus

Sulfolobus alphaportoglobovirus 1

1

Siphoviridae*

 

Anatolevirus

Propionibacterium virus Anatole

2

Siphoviridae*

 

Attisvirus

Gordonia virus Attis

1

Siphoviridae*

 

Doucettevirus

Propionibacterium virus Doucette

4

Siphoviridae*

 

Hk97virus

Escherichia virus HK97*

9 (11)

Siphoviridae*

 

Lambdavirus*

Escherichia virus Lambda

3 (4)

Siphoviridae*

 

Pfr1virus

Propionibacterium virus PFR1

1

Siphoviridae*

 

Tp84virus

Geobacillus virus TP84

1

Siphoviridae*

 

Trigintaduovirus

Mycobacterium virus 32HC

1

Siphoviridae*

 

Wizardvirus

Gordonia virus Wizard

2

Siphoviridae*

Chebruvirinae

Brujitavirus

Mycobacterium virus Brujita

(2)

Siphoviridae*

Chebruvirinae

Che9cvirus*

Mycobacterium virus Che9c

1 (2)

Siphoviridae*

Dclasvirinae

Hawkeyevirus

Mycobacterium virus Hawkeye

1

Siphoviridae*

Dclasvirinae

Plotvirus

Mycobacterium virus PLot

1

Siphoviridae*

Mccleskeyvirinae

Lmd1virus

Leuconostoc virus Lmd1

6

Siphoviridae*

Mccleskeyvirinae

Una4virus

Leuconostoc virus 1A4

6

Siphoviridae*

Nclasvirinae

Buttersvirus

Mycobacterium virus Butters

2

Siphoviridae*

Nclasvirinae

Charlievirus

Mycobacterium virus Charlie

2 (3)

Siphoviridae*

Nclasvirinae

Redivirus

Mycobacterium virus Redi

3 (4)

Siphoviridae*

Nymbaxtervirinae

Baxtervirus

Gordonia virus BaxterFox

2

Siphoviridae*

Nymbaxtervirinae

Nymphadoravirus

Gordonia virus Nymphadora

3

Cystoviridae*

 

Cystovirus*

Pseudomonas virus phi6

6 (7)

Tectiviridae*

 

Alphatectivirus**

Pseudomonas virus PRD1

1 (2)

Tectiviridae*

 

Betatectivirus

Bacillus virus Bam35

2 (4)

*taxon established, **previously known as Tectivirus, ***Number in parenthesis indicates the total number of viral species in this genus

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, 11, 12].

Notes

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.

Compliance with ethical standards

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.

Conflict of interest

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.

Supplementary material

705_2018_3723_MOESM1_ESM.docx (29 kb)
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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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUnited Kingdom
  2. 2.Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHBraunschweigGermany
  3. 3.Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthFrederickUSA
  4. 4.Faculty of Health and Applied SciencesUWE BristolBristolUnited Kingdom
  5. 5.Department of MicrobiologyThe Ohio State UniversityColumbusUSA
  6. 6.Theoretical Biology and BioinformaticsUtrecht UniversityUtrechtThe Netherlands
  7. 7.Centre for Molecular and Biomolecular InformaticsRadboud University Medical CentreNijmegenThe Netherlands
  8. 8.Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics (IMBM)University of the Western CapeBellvilleSouth Africa
  9. 9.Institute of Food, Nutrition and HealthETH ZurichZurichSwitzerland
  10. 10.Department of Microbial BiochemistryInstitute of Biochemistry and Biophysics of the Polish Academy of SciencesWarsawPoland
  11. 11.Faculty of Ecology and Natural Resources SchoolUniversidad Andres BelloSantiagoChile
  12. 12.Latvian Biomedical Research and Study CenterRigaLatvia
  13. 13.Departments of Computer Science and BiologySan Diego State UniversitySan DiegoUSA
  14. 14.School of Veterinary MedicineAzabu UniversityKanagawaJapan
  15. 15.Laboratory of Industrial Microbiology,Instituto de Biotecnologia Aplicada à AgropecuáriaUniversidade Federal de ViçosaViçosaBrazil
  16. 16.The ithree instituteUniversity of Technology SydneySydneyAustralia
  17. 17.Departments of Food Science, and PathobiologyUniversity of GuelphGuelphCanada
  18. 18.Department of Molecular Virology, Institute of Experimental BiologyAdam Mickiewicz UniversityPoznanPoland
  19. 19.Laboratory of Food and Environmental MicrobiologyUniversité Catholique de LouvainLouvain-la-NeuveBelgium
  20. 20.Department of Infection, Immunity and InflammationUniversity of LeicesterLeicesterUnited Kingdom
  21. 21.Unit of Molecular Biology of the Gene in Extremophiles, Department of MicrobiologyInstitut PasteurParisFrance
  22. 22.Laboratory of Gene TechnologyKU LeuvenLeuvenBelgium
  23. 23.Department of Microbiology and Immunology, Faculty of PharmacyCairo UniversityCairoEgypt
  24. 24.Department of Ecology, Evolution and Natural ResourcesRutgers UniversityNew BrunswickUSA
  25. 25.Department of BiosciencesUniversity of HelsinkiHelsinkiFinland
  26. 26.Department of Biology and Ecology, Faculty of SciencesUniversity of Novi SadNovi SadSerbia
  27. 27.Université Clermont Auvergne, CNRS, LMGEClermont-FerrandFrance
  28. 28.Beijing Institute of Microbiology and EpidemiologyState Key Laboratory of Pathogen and BiosecurityBeijingPeople’s Republic of China
  29. 29.National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUSA

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