Position paper: The creation of a rational scheme for the nomenclature of viruses of Bacteria and Archaea

Authors

  • Andrew M. Kropinski,

    1. Laboratory for Foodborne Zoonoses, Public Health Agency of Canada,110 Stone Road West, Guelph, ON, N1G 3W4, Canada.
    2. Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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  • David Prangishvili,

    1. Institut Pasteur, Department of Microbiology, 25 rue du Doctuer Roux, 75724 Paris cedex 15, France.
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  • Rob Lavigne

    Corresponding author
    1. Biosystems Department, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, Leuven, B-3001, Belgium.
      *E-mail rob.lavigne@biw.kuleuven.be; Tel. (+32) 16 32 96 70; Fax (+32) 16 32 19 65.
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*E-mail rob.lavigne@biw.kuleuven.be; Tel. (+32) 16 32 96 70; Fax (+32) 16 32 19 65.

The taxonomy of prokaryotes involves classification (systematics) of cells into related groups, their nomenclature and the development of identification procedures (Cowan, 1971). It is not our purpose here to discuss whether the species concept applies to the viruses of archael and bacterial cells (Morgan and Pitts, 2008) but rather, the current lamentable status of bacteriophage nomenclature, and a possible solution. Apart from viruses such as ϕX174, M13, λ, T1-T7, P22 and a few others, most phage names do not result in immediate recognition, even among phage researchers. Bacteriophages have been named based on different strategies ranging from meaningless assemblies of letters (Greek and Roman) or simple numeric codes (phage 68, phage 25), morphological peculiarities (Rosebush, Corncob) (Pedulla et al., 2003; Hatfull et al., 2006), references to persons or sources (Twort, φKMV, Berlin, EL) (Lavigne et al., 2003; Kwan et al., 2005) or even to fictional creatures like Tweety or BcepNazgul. Often, the origin of the names is difficult to trace, or is entirely lacking in the scientific literature. For example, Delftia phage ϕW-14 was named after Westbrook building room 14 where it was isolated at the University of British Columbia (Kropinski and Warren, 1970). Pseudomonas phage LKA1 is named after the research institute (K.U.Leuven), the area from which the phage was isolated (Kasteelpark Arenberg) and the isolate number (1) (Ceyssens et al., 2006). Bcep is the epithet used to describe Burkholderiacepacia phages (Summer et al., 2004; 2006).

Although this nomenclature reflects the dedication and creativity of phage researchers, some phages change names when used in different labs. For example, Salmonella phage Felix O1 is also referred to as bacteriophage Felix 01, O1 or 0-1 in the scientific literature. In addition, numerous examples of redundancy in phage names exist (Table 1; http://www.phage.org/names.htm). This can lead to confusion or errors in scientific publications or difficulties in bioinformatic database mining. In many cases these identically named viruses are obscure phages that do not affect most individuals. P1 to most bacteriophage workers and microbial geneticists is an important generalized transducing coliphage (Lehnherr, 2006). Unfortunately, the same name applies to five other viruses.

Table 1.  Phages with identical names and their redundancy in occurrence (between brackets).
A (4)C (4)C1 (5)C2 (5)F1 (8)G4 (4)HP1 (4)III (4)J (4)K (11)
L (4)M (5)M1 (6)N3 (4)N4 (4)P (5)P1 (6)P2 (4)P6 (4)P8 (4)
P9 (4)R (4)S (5)S1 (4)S2 (5)VI (4)X (6)ϕ1 (4)ϕ2 (4) 

To bring prokaryotic virus nomenclature into the 21st century, more systemized rules and guidelines are needed. Ideally, such a scheme must provide consistent identifiers for database/search applications. We therefore propose a nomenclature based roughly on a first name-last name basis. From this perspective, a proposed name has two components: the first part contains a preface, identifying what follows as a bacterial virus: the isolation host and virus familial relationship. The second part provides the specific laboratory designation (freely chosen but with proposed guidelines).

  • (a) The name is preceded by the prefix vB (bacterial virus) or vA (archaeal virus). This will provide, like the small ‘p’ preceding the name of a plasmid, instant recognition of what is being described (Novick et al., 1976).
  • (b) The host abbreviation system used for restriction enzymes based upon the genus and species (see: REBASE (http://rebase.neb.com/rebase/rebase.html) (Roberts et al., 2003), e.g. Eco (Escherichia coli), Pae (Pseudomonas aeruginosa) and Sau (Staphylococcus aureus). Where there is no organismal three-letter abbreviation in REBASE, the authors may propose their own mnemonic.
  • (c) The name ends with the single letter virus family designation as outlined in Table 2. This will encourage investigators to study the morphology of their viruses before submission to GenBank.
  • (d) The specific laboratory designation or common name remains the responsibility of the researchers. Databases, editors and authors publishing the data must verify that the letter/number combination is unique. Although we do not wish to restrict the use of laboratory-specific names, we urge researchers to bear in mind specific difficulties associated with phage nomenclature (Table 1). Our recommendations are that:
    • (i) The letter/number combination should be at least three characters in length.
    • (ii) Greek letters should be avoided as the databases will translate all ϕ (φ) as phi.
    • (iii) Avoid all Roman numerals – please note that ϕX-174 should be referred to as ‘phi-10-174’, not ‘phi-X-174’.
    • (iv) Avoid confusions involving O (capital letter O) and 0 (zero); and, I (capital letter I) and the numeral 1.
    • (v) Avoid superscripts and superscripts.
    • (vi) It should be noted that the naming of genera, etc. depends upon the first identified isolate. International Committee on Taxonomy of Viruses (ICTV) genus names will always take into account elements like legibility and name recognition.
Table 2.  Viral family single-letter identification code.
Ampullaviridae– AGuttavirudae– UPodoviridae– P
Bicaudaviridae– BInoviridae– IPlasmaviridae– E
Corticoviridae– CLeviviridae– LRudiviridae– R
Cystoviridae– YLipothrixviridae– XSiphoviridae– S
Fuselloviridae– FMyoviridae– MTectiviridae– T
Globuloviridae– GMicroviridae– OProvirus – Z

As shown in Table 1, six bacteriophages bear the name P1. Using the proposed nomenclature one can easily differentiate transducing coliphage ‘vB_EcoM-P1’ from the other phages named P1: ‘vB_CboM-P1’ (Clostridium botulinum, Myoviridae), ‘vB_SauM_P1’ (Staphylococcus aureus, Myoviridae), ‘vB_CjeM-P1’ (Campylobacter jejuni, Myoviridae), ‘vB_PciS-P1’ (Promicromonospora citrea, Siphoviridae), ‘vB_SagS-P1’ (Streptococcus agalactiae, Siphoviridae).

Within the manuscript describing a new virus, bacterial or archaeal, the full name should be present in the title and/or abstract; and, after its first introduction in the text of the paper it can be subsequently referred to by its shorter common laboratory name. It is not our intention that this system be used to rename existing phages but to present a workable system for naming newly identified bacteriophages and prophages, and furthermore, to encourage the researcher to examine the viruses by electron microscopy.

The bacterial and archaeal virus nomenclature being proposed here are currently being discussed by a work group of the ICTV subcommittee for prokaryotic viruses. As such, your constructive feedback on these proposals are welcome and will aid in establishing a consensus proposal which can be submitted to the official Executive Committee of the ICTV for evaluation/ratification.

Acknowledgements

R.L. is Chair of the Viruses of Prokaryotes Subcommittee of the ICTV. A.K. is Deputy Chair of this committee and is supported by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada. D.P. is an elected member of the Executive Committee of the ICTV.

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