Arch Virol (2003) 148: 1235–1246 DOI 10.1007/s00705-003-0129-2
Virus nomenclature; continuing topicality∗
L. Bos Plant Research International WUR, Wageningen, The Netherlands
Received February 6, 2003; accepted April 2, 2003 Published online June 5, 2003 c Springer-Verlag 2003
The ICTV decisions to write official virus names (a) as mere mononomials and (b) to italicize them in toto [16] (e.g., Tobacco mosaic virus and Murray River encephalitis virus) and not to use italics for the names of viruses that have not yet been recognized by ICTV (e.g., Holcus lanatus yellowing virus), have been criticized in detail in these Archives [2, 4, 5, 11]. Meanwhile one of the secretaries of ICTV has reported [15] that a ballot held during the 2002 International Congress of Virology in Paris showed an 80% in favour of (re)turning to the non-latinized binomial names (such as bean yellow mosaic potyvirus or Bean yellow mosaic potyvirus) earlier discouraged by ICTV [29]. The ICTV Study Groups and Subcommittees were requested to consider the implications of such a reversal [15]. In an earlier reaction, Van Regenmortel [25, 26], then President of the ICTV, had already aired the feasibility of a return to non-latinized binomials or their official acceptance, and this has now been presented as a proposition of ICTV [15]. Van Regenmortel and Fauquet, past-President and an ongoing Secretary of ICTV, respectively [27], have concurrently responded to the objections to the above ICTV proposal regarding the italicization. In their paper, entitled “Only italicised species names of viruses have a taxonomic mean- ing” [27], Van Regenmortel and Fauquet dwell extensively on matters beyond the subject of the paper discussed earlier by themselves and summarized by me [5]. Suffice it to say here that I would be the last to claim, as suggested by the authors, that official virus names would not be required once the species category has been formally and widely accepted for virus classification. A major point is that ICTV rules concerning viruses should not conflict with biological nomenclature and typography in general since viruses and sub-viral agents genetically behave like organisms. This paper will first (a) discuss the continuing confusion created by trying to distinguish between the abstract and concrete uses of a virus name, (b) show that, in addition to scientific names for viruses in a taxonomic sense, common names are also needed, and (c) explain that English is not the only medium of communication about viruses. It will then (d) briefly revisit the issue of italicization of virus names. Also, newly
∗The ICTV Rule for orthography of species names are not applied in this paper as the author is discussing these Rules and their use would obscure his meaning. 1236 L. Bos
emerging issues associated with the naming of viruses to be discussed are (e) the designing of common names of viruses, (f) the problem that there is more to proper naming than just linguistics and typography, and finally (g) the pros and cons of acronyms.
Confusion created by trying to distinguish between abstract and concrete uses of a virus name The confusion with respect to italicization originated in Art. 3.40 of the revised Code. Taxonomic virus entities were correctly indicated there as abstractions, but italicization (and the use of capital initials) was exclusively associated with the names of virus species recognized (accepted) by ICTV. “In other senses”, the Comments said, “such as an adjectival form (e.g. the tobacco mosaic virus polymerase), italics and capital initial letters are not needed. Equally, these are not needed when referring to physical entities such as virions (e.g. a preparation or a micrograph of tobacco mosaic virus)” [16]. Such entities were later referred to as concrete [24]. Since then, the distinction between the use of virus names in an abstract or a concrete sense continues to be used as a supportive criterion for discriminative italicization of virus names in the first sense only [27, 29]. Van Regenmortel and Fauquet [27] forget that in ‘tobacco mosaic virus polymerase’only the polymerase is concrete. What is indicated is the polymerase (concrete), in fact, the polymerase of a specific virus, an abstract entity denoted formally as Tobacco mosaic virus (sensu ICTV) or vernacularly as tobacco mosaic virus (see further below). This typography (italicization) has nothing to do with abstract or concrete but is only meant for highlighting the distinction between the scientific names already approved by the ICTV and the names of viruses not yet recognized by ICTV as species.
The need for common names as well as scientific names to designate virus species Van Regenmortel and Fauquet [27] persist in emphasizing that scientific or formal names exclusively are used for reference to viruses in an abstract, that is taxonomic, connotation, while common names should only be used in a concrete sense, as for a virus particle suspension or for virions. In other words, it is claimed that when viruses are mentioned in an abstract sense only scientific names are appropriate. The authors, and ICTV in its rules and discussions, ignore the existence of common, vernacular or trivial names for virus species, that is, in an abstract taxonomic context equal to that of the scientific names. Taxonomically, viruses do not differ from organisms. In a paper on the plant species daisy (Bellis perennis)orthe animal species rat (Rattus rattus), the Introduction or Materials and Methods section first mentioning the species will equivalently use both designations in that or their reverse order. Throughout the remainder of the paper the names daisy and rat will be used only, but still in a taxonomic connotation. Where a text deals with daisies in a lawn, or rats in the farmer’s barn, such names are used in a concrete sense. Taxonomists, when using a common name in an abstract sense, may tend to emphasize its character of proper name by using a capital initial, as of Daisy and Rat occurring in a particular biotope, or of Man (in the abstract meaning of mankind, Homo sapiens) on earth, in contrast to a man as a concrete masculine person. However, such capitalization of common names of biological species has almost, if not completely, fallen into disuse. It goes without saying that a farmer cannot grow potato or apple on his land, but potato plants and apple trees or a potato crop, and in doing so he intends Virus nomenclature; continuing topicality 1237 to produce potatoes and apples, that is, the fruits of the crops or plants concerned. Plants, trees, crops and fruits are all concrete objects. The adjectives ‘potato’and ‘apple’contained in the words ‘potato plants’ and ‘apple plants’, maintain an abstract connotation, indicating that concrete plants, characteristic of the species potato (Solanum tuberosum) and apple (Malus communis), are meant. Likewise, a phrase describing the purification of tobacco mosaic virus is editorially incorrect. It is not the species but a concrete suspension or preparation of virions (particles) characteristic of tobacco mosaic virus (i.e., characteristic of the taxonomic species tobacco mosaic virus) that is being purified. When mentioning the above tobacco mosaic virus polymerase, reference is made to the polymerase enzyme as typical of the species tobacco mosaic virus, not of a particular particle or virus preparation. Referring to the polymerase of tobacco mosaic virus (that is of the abstract species) or to the polymerase isolated from a particular suspension (concrete) of the tobacco mosaic virus (still the abstract species) would be preferable. The compound word ‘tobacco mosaic virus polymerase’ comprises two concepts of a totally different kind, that is, an abstract and a concrete one. Concatenations of more than three separate words, prevalent in much modern scientific writing, are linguistically undesirable anyhow.
Illustrative of the need of terminological and linguistic precision with respect to abstract and concrete and to the meaning of formal names of virus species and common names of viruses, is a recent paper by Drebot et al. [6] on a human virus where a formal species may contain various epidemiologically distinct members. The authors go astray when agreeing with Van Regenmortel in saying that “a virologist inoculated a tobacco plant (a member of the species Nicotiana tabacum) with a member of a virus species”. They erroneously interpret the word ‘member’in the concrete sense of ‘an individual’ (plant or virus preparation) where in both cases only ‘part’ of a species is meant. In this context, the ‘parts’ are as abstract as the two species as a whole. The only correct wording would have been that “a virologist inoculated a tobacco plant (belonging to, or characteristic of, the species Nicotiana tabacum) with an infective preparation of virions or nucleic acids typical of the species tobacco mosaic virus”. Linguistically simplified, but still fully acceptable (at least in the course of a paper) and less verbose, would be “the inoculation of a plant of tobacco (Nicotiana tabacum) with tobacco mosaic virus”. The latter name is only used in the abstract taxonomic sense, and the criterion abstract or concrete has no bearing whatsoever on typography (italicization). In this respect, at the end of the last but one paragraph of their paper, the authors get confused when saying: “We isolated dengue 2 virus (family Flaviviridae, genus Flavivirus, species Dengue virus) from the blood of a febrile human in ....” and “the name of the taxon and the name of the virus are distinct”. ‘Dengue 2 virus’ definitely has an abstract taxonomic connotation. The blood appeared to contain particles (concrete) with characters typical of the abstract species. In short, common language requires common names as equivalents of the scientific names to designate virus species. Daily communication starts with common names. Such names of organisms derive taxonomic status from their recorded association with scientific names, as of daisy (Bellis perennis). Likewise, viruses are widely designated by common names that usually preceded their scientific names. Alfalfa mosaic virus, for example, was assumed to occur as an abstract taxonomic entity long before virus taxonomy came into being. Com- parative research on its intrinsic characteristics finally revealed the virus as a taxonomically identified species within the genus later named Alfamovirus. To family doctors, veterinarians, agricultural extension officers, sick people, and farmers, common names of viruses usually are more meaningful than scientific names. 1238 L. Bos
Latin, English, and other domestic languages for the naming of viruses Cellular organisms are scientifically designated by Latin or latinized binomials. Van Regen- mortel and Fauquet [27] now advocate the use of English for scientific names of viruses because, they say, “English has replaced Latin as the language of communication used by scientists” (a claim which is not true for biological scientific naming in general). They will undoubtedly assume the same for common names of viruses. They add “all virologists are conversant with the English names of viruses”. This might hold for the citizens in English- speaking countries such as Great Britain, former Commonwealth countries, and the USA. However, inflicting names sequestrated by ICTV from English upon, for example, French and Dutch farmers and gardeners would be unrealistic. In their own countries, virologists must communicate with non-specialists in their respective languages, hence the need for domestic common names besides scientific names of whatever spelling and English common names. Otherwise, common speech is bound to become riddled by odd derivative names. An example is the Dutch name ‘chrysantenstuntvirus’, at a time used by Dutch flower growers that had been addressed by virologists thoughtlessly using the English name ‘Chrysanthemum stunt virus’ they were accustomed to. The word ‘stunten’ in Dutch has the sole meaning of ‘doing something to attract attention’, such as ‘stunt-flying’ or aerobatics. Hence the final translation into the fully comprehensible ‘chrysantendwergziektevirus’. And what to do with the English name ‘tomato spotted wilt virus’? In Dutch the word ‘spot’ exclusively denotes mockery or ridicule, and the language has no equivalent for the English ‘wilt’ which is easily mistaken for ‘wild’ when used in Dutch, suggesting something wild or ‘savage’. That is why in Dutch the bizarre name of the virus had to be replaced by the descriptive ‘tomatenbronsvlekkenvirus’, which is equivalent to the German ‘Tomatenbronzeflecken- Virus’ and refers to the highly characteristic bronze-coloured spotting of the diseased tomato fruits [17]. Obviously, large parts of the world population continue to converse in languages other than English, and each country definitely needs virus names in its own language. However, this does not imply that there is any antagonism towards English-worded sci- entific virus names within the international scientific virology community if it now decides to stick to non-latinized vernacular binomials. English-speaking virologists have taken a widely appreciated historical lead in the description of viruses, notably plant viruses, and in setting up international databases that allow classification and now assign meaning to virus names. In national publications and reports, domestic common names of viruses, when first used, must be entered alongside their international scientific equivalents to indicate and stress their abstract taxonomic connotation and link them with international documentation: e.g. tabaksmoza¨ıekvirus (Tobacco mosaic tobamovirus). Common names of viruses are thus also used in an abstract sense but always linked to scientific names. Latinized virus binomials – such as Tobravirus pisi for Pea early-browning tobravirus and Comovirus vignae for Cowpea mosaic comovirus – would be ideal for making scientific names truly international, as earlier hinted by myself [2, 5] and recently further elaborated by Agut [1]. However, there is continuing hesitation because of the frequent change to which such names are still subject due to changing taxonomic perceptions, and because of the frequent occurrence of recombination between viruses [2]. But there may be no reason to dogmatically preclude the introduction of Latin or latinized virus binomials [5]. Virus nomenclature; continuing topicality 1239
The italicization of scientific virus names revisited The title of Van Regenmortel and Fauquet’s article [27] suggested that it was to explain that italicization of English common names converts them into formal scientific names. It obviously remains a hot topic. For clarity I must briefly repeat and extend my vision on this important issue [2, 4, 5]. In biological texts, italicization of Latin or latinized scientific names of organisms is widely accepted and it is practiced in all biological journals of reputation to clearly indicate the linguistically alien nature of such names, and prevent the contamination of national languages with legion loanwords that are incomprehensible to common citizens. Virus names often include scientific names of organisms. Overall italicization of scientific virus names would unacceptably impede the recognition of the names of the organisms included in the names of viruses, and the proper distinction of these names of organisms from geographic names often also included. Van Regenmortel and Fauquet now suggest this to be an imaginary problem of my ‘own making’. They have ignored the realistic examples I have given: Aspergillus foetidus virus S totivirus and Holcus lanatus yellowing nucleorhabdovirus [5]. Admittedly, at the moment there are not many plant virus names that contain the scientific names of organisms. However, it is not frequency that counts, but principle, also with a view to future naming. Van Regenmortel and Fauquet mention the hypothetical Althea rosea enation virus, and simplistically comment that the Latin plant name within it “will be automatically italicized and one wonders why this is considered problematical” [27]. This reveals the authors’ total misappreciation of italicization of Latin or latinized words and names of organisms in biological texts. But there are more arguments strongly favouring the proper and consistent use of italics. Italicized and non-italicized words of identical spelling may refer to completely different biological species, as is the case with nasturtium and Nasturtium, and geranium and Geranium. I have also referred to the real difference between the taxonomic name Cestrum and the geographic names Epirus and Ourmia contained in the names of the viruses Cestrum yellow leaf curling caulimovirus and Epirus cherry Ourmiavirus [2, 4, 5], illustrative examples ignored by Van Regenmortel and Fauquet [27]. The converse problem is created where the ICTV insists that the names of organisms included in the names of viruses that have not yet been accepted as species by ICTV are not italicized. Like in the fully italicized names of ICTV-accepted viral species, this would unacceptably obscure the difference between the scientific names and common names of such organisms and between names of organisms and geographic names. It took quite some effort to find out that theArracacha latent virus, a tentative carlavirus (and its name thus not italicized by ICTV), is not a virus of a special geographic origin, but described from a tropical perennial herb with the Spanish name ‘arracacha’ (and thus correctly non-italicized) for Arracacia sp. Likewise, the Bajra streak virus, a tentative mastrevirus, is a virus of ‘bajra’, an Indian name for pearl millet and thus not italicized. Asystasia gangetica inAsystasia gangetica mottle virus (non-italicized according to the ICTV typography), a tentative potyvirus, is the scientific name of an acanthaceous herb or shrub, and its name must therefore be written in italics: Asystasia gangetica mottle virus, no matter whether ICTV likes it or not. In toto italicization as well as full non-italicization of virus names – depending on the taxonomic status of the virus – would thus hinder taxonomic precision, and would flagrantly conflict with nomenclature and typography widely accepted in biology at large. It would 1240 L. Bos be simpler to distinguish between the names of viruses recognized as species by ICTV and the names of viruses tentatively assigned to a genus by putting in brackets the genus name contained in the non-latinized binomials of the latter category, for example, Indian peanut clump pecluvirus and Impatiens latent (carla)virus. It seems wise to have the official (scientific) names of viruses begin with a capital initial: tobacco mosaic virus (Tobacco mosaic tobamovirus), or in another language: tabaksmoza¨ıekvirus (Tobacco mosaic tobamovirus). In all, italicization is not as simple as indicated in the one but last sentence of the paper by Drebot et al. [6]. In biological texts italicization serves another purpose than just distinction between scientific and common names.
The designing of common virus names Because of their use in a taxonomic sense, national common names of biological entities including viruses must also be meaningful and consistent [5]. That is why learned societies in several countries have established committees of experts to survey their language for common names of organisms and to select the best names and include these in compiled lists of authorized national names of viruses. I have earlier referred to the Committee on the Naming of Plant Viruses of the Nederlandse Kring voor Plantevirologie that has recently updated and authorized such a list of Dutch names of plant viruses, and has accepted rules for such naming [17] to stabilize national communication on plant viruses. I have then alluded to the possible establishment of a structure “for standardizing English names of viruses and for setting rules” [5]. Such a need is further emphasized by the fact that common names of viruses (either as mononomials sensu ICTV, or included in non-latinized binomials) have been, and will further be, accepted as official virus names for international scientific communication, and, therefore, must be short and unambiguous. Naming nearly always starts by inventing common names, and mostly at a local level and often haphazardly. Once such names have become commonly used, it is hard to change them or get rid of them. That is how several odd names or phrase-like names with redundant information have gained wide application, have entered lists of official names, and have, via ICTV, even attained scientific status. A few examples of less-than-ideal scientific names of plant viruses follow. In the name ‘Cucumber green mottle mosaic tobamovirus’ the terms ‘mottle’ and ‘mosaic’ refer to different types of variegation; so which is really meant? The name ‘Cucurbit yellow stunting disorder crinivirus’ is a real monstrosity of verbosity and terminological misinterpretation; ‘stunt’already designates a disease characterized by stunting or dwarfing, and the term ‘disorder’, according to CABI [20], refers to a “harmful deviation ...arising from causes other than pathogenic organisms or viruses, e.g. mineral deficiency”. Similarly, the term ‘syndrome’ has silently but superfluously slipped into the name of a new virus of shrimps and other Crustaceae: the ‘white spot syndrome virus’ belonging to a new group of whispoviruses [23]; ‘white spot’ already denotes a disease or syndrome, and no host name is included. Two other mutually related viruses are the ‘tomato chlorosis crinivirus’ and the ‘tomato infectious chlorosis crinivirus’. Although only one name refers to infectivity, both viruses are infectious of course. For the latter disease, the name ‘infectious chlorosis’ may have emerged to distinguish between chlorosis due to mineral deficiency and chlorosis due to virus infection, but infectivity also holds for the disease caused by the ‘tomato chlorosis virus’. The adjective ‘infectious’ must have slipped in as a totally meaningless differential code for lack of other means of nomenclatural differentiation. Redundancy in several such Virus nomenclature; continuing topicality 1241 phrase-like names also conflicts with Article 3.23 of the Code saying “a species name shall consist of as few words as practicable” [16]. Defective naming may commence indeed when, once a new disease has been detected, an ill-considered common name of a suspected virus begins circulating. Misnaming should thus be tackled at its roots. National organizations, such as theAssociation ofApplied Biologists in Britain and the American Phytopathological Society in the USA, could assume responsibility for standardizing the English common names of plant viruses within their countries, but they would be advisory and have no international authority. I have, therefore, suggested that ICTV (through its Study Groups) should accept responsibility for the worldwide English naming of viruses [5]. Such activity would logically follow ICTV’s involvement in the elevation of English common names of viruses to scientific names. Admittedly, the Code has not yet authorized the ICTV for devising common names of viruses. The same holds for acronyms of virus names, but in 1991 the ICTV has nevertheless taken initiatives for the development of a ‘standard’ list of acronyms to facilitate communication, “hoping that authors will use the acronyms ...and that editors will encourage them to do so” [13]. Involvement in setting rules for devising English common names and for standardizing such names could well be compatible with the objectives of ICTV.
There is more to proper naming than just linguistics and typography Nomenclature is intrinsic to taxonomy as a whole and cannot be viewed apart from classifi- cation and the associated issue of identification. Both, classification and nomenclature are the two basic terms in the title of the Code [16]. Nomenclatural deliberations have so far ignored the Article 3.24 of the Code. It stipulates that “a species name must provide an appropriately unambiguous identification of the species” [16]. For a name to be scientific, such identification indubitably requires inclusion of taxonomic information within the name, or indissoluble attachment of such information to the name. That is why my biology handbook said, “A species name when written alone is meaningless”. The Code itself marks the necessity of adding taxonomic qualifiers when scientifically upgrading common names of viruses. As for cellular organisms, our virus Code thus legitimates or even enforces the use of binomials, either Latin or latinized (as of Bellis perennis for daisy) or non-latinized (as of Tobacco mosaic tobamovirus for tobacco mosaic virus). But there is more to linguistically unambiguous reflection of the identity of the named virus. In their comments to Article 3.8 of the revised Code, Mayo and Horzinek [16] state that “a valid name is one that has been published, one that is associated with descriptive material, and one that is acceptable in that it conforms to the Rules of the Code”. That is why in addition to linguistics there are two more, but often neglected requisites. As for the description of new species of organisms, the first requirement is the formal publication of full data in an internationally accepted scientific journal. Incomplete descrip- tion of a virus, as of its molecular biology or part of its genome only, as was done for the ‘shallot virus X’ (genus Allexivirus) [14, 31], does not yet legitimate a new name. This is where editorial boards of journals have special responsibility when dealing with authors who submit descriptions of prospective new viruses. The middle part of the above italicized sentence mentions association of the name with descriptive material. Without specification, it prescribes the storage of type material of the 1242 L. Bos species. Article 8.1 of the International Code of Biological Nomenclature ties the name of cellular organisms to type specimens. It says “The type of a name of a species or infraspecific taxon is a single specimen ...... ”. In Article 8.2 it further specifies that “Type specimens of names of taxa must be preserved permanently and cannot be living plants or cultures.” Recommendation 7A.1 then adds that “It is strongly recommended that the material on which the name of a taxon is based ...... be deposited in a public herbarium or other public collection with a policy of giving bona fide botanists open access to deposited material, and that it be scrupulously conserved”. This is to allow (1) verification of the description of a new species by others at any time, (2) further completion of its characterization with the advent of new descriptive techniques or when apparently related new species are detected, and (3) assistance to the comparative and descriptive investigation of such new species. Unfortunately, the preservation of type material of new viruses and virus strains is often, if not mostly, left undone. That is how many viruses tentatively described during early virology by their biology (phenotype) only, are no more available for modern genotypic description and exact taxonomic placement. Molecular virologists, on the other hand, now tend to over- emphasize the value of molecular biology for taxonomy, while overlooking or neglecting ecologically important phenotypic properties. These may be extremely important because of determining the ecological niche and further evolution of the virus, even though their molecular basis is often unclear. Publication and mere administrative databank filing of the nucleotide sequence of a possibly new virus are insufficient to justify a new virus name.
An example is the description and naming in 1993 of the above ‘shallot virus X’with flexuous filamen- tous particles [30] by partial nucleotide sequencing mainly [14], and the more recent establishment of the new genus Allexivirus [31]. At the time (in 1991) a shallot mite-borne latent virus – first thought to be a rymovirus of the family Potyviridae and possibly related to the mite-borne so-called ‘onion mosaic virus’twenty years earlier reported from Russia [18] – had already been partially described in The Netherlands and biologically and serologically differentiated from the related onion mite-borne latent virus and from other Allium viruses [22]. Soon after, isolates of the Dutch shallot and onion mite-borne latent viruses were found to react strongly with an antiserum to the recombinant coat protein of ‘shallot virus X’[21]. Thereafter, Kanyuka et al. showed the Russian virus to share genome sequences with potexviruses as well as with carlaviruses [14], but this relationship is not reflected in the later invented genus name Allexivirus [31] while the name ‘shallot virus X’ erroneously suggests affiliation with potexviruses comprising all other viruses whose names end with an X. Later, other viruses of Allium species, such as the ‘garlic virus X’[19], were characterized using partial nucleotide sequences reported of shallot virus X [14]. It is of interest here that Drebot et al. [6], when recently discussing formal species names and common virus names, particularly refer to “the implication of sole reliance on molecular techniques for virus characterization”, and stress that “a viral nucleic acid sequence is not a virus”. They recognize the existence of epidemiologically distinct viruses within species sensu ICTV that are thus members (or perhaps strains, LB) of such species. However, names of such members or strains of species (perhaps infraspecies taxa) still have a taxonomic, though not yet precisely defined, meaning and refer to something abstract. Basically, each phenotype is genotypically rooted, but epidemiologically and evolutionarily important traits may be based on differences in nucleotide composition so small that they escape quantitative species demarcation. Mere databank deposition of a nucleotide sequence, particularly if only partial, therefore, is insufficient proof of novelty of a virus and insufficient justification for inventing Virus nomenclature; continuing topicality 1243 a new name. Full description and definitive naming of the ‘shallot virus X’ would require reliable type material, which I have not been able to trace other than the closely related if not similar shallot mite-borne latent virus (isolate Ac 268; [22]). The latter name may therefore well have priority, although such priority is not provided for in the virus Code [16]. It is now possible to safely preserve type material of most viruses. For plant viruses, virus-containing fresh plant tissue (preferably leaf material) can be easily desiccated and stored at 0–5 ◦C, e.g. over anhydrous calcium chloride, or freeze dried and stored in vacuum, or stored in infected fresh tissue or as a suspension in liquid nitrogen at –196 ◦C, or in purified freeze-dried form. Nucleic acids extracted from infective material can be stored in ethanol. For viruses, storage of type material should be in curated national or international type culture collections [3].
Pros and cons of acronyms The length of most virus names and their frequent use in written reports soon led to abbre- viations of such names. This is how acronyms developed: TMV for tobacco mosaic virus and RSV for Rous sarcoma virus. In 1991, plant virologists were the first to standardize such acronyms [13]. They did so under the auspices of ICTV, although this organization has no constitutional responsibility for assigning abbreviations. The regular taxonomy reports of ICTV [28] now add the acronyms in brackets to the virus names listed although they do not have any official status. Separate updated lists of acronyms have been published at regular intervals in the Virology News Division of the Archives of Virology [7, 8]. With the growing number of virus names and increasing risks of confusion (e.g. LMV for Lettuce mosaic potyvirus as well as for Leonurus mosaic begomovirus), guidelines have been developed for plant virologists as to how to create new abbreviations [8]. Major problems have arisen, through the ongoing influx of new virus names so that secondary letters have often been needed to differentiate between hosts and symptoms. The host symbol CP, for example, stands for cowpea as in CPMV (for Cowpea mosaic comovirus), and Co for cocksfoot as in CoMV (for Cocksfoot mottle sobemovirus). Several other plant hosts, including cucumber, are also designated with a C as in CMV (for Cucumber mosaic cucumovirus), but with a Cu in CuNV (or Cucumber necrosis tombusvirus) because of possible confusion with CNV (for Cacao necrosis nepovirus, a name that has priority over Cucumber necrosis tombusvirus). The symptom symbol M usually stands for mosaic, as in LMV for Lettuce mosaic potyvirus, but often also for mottle as in LiMV for Lilac mottle carlavirus. However, the latter symptom is also represented by Mo as in GMoV for Glycine mottle carmovirus because of the existence of GMV for the alphabetically neighbouring Glycine mosaic comovirus. Odd acronyms may thus result, such as TToMoV for Taino tomato mottle begomovirus. Old acronyms cannot be changed or adapted with a view to stability. Most of the guidelines for the plant viruses, have meanwhile been extended for use in vertebrate, bacterial, and fungal virology to improve harmony in the literature. Standardized lists of acronyms of these viruses have also been published [9, 10]. Complete avoidance of overlap between the different subdisciplines seems to be impossible, and it is thought reasonable to believe that in a paper on herpesviruses the use of CMV has nothing to do with cucumbers (M. Mayo, personal communication). Thus consistency is increasingly failing, and one cannot guess from visual observation what an acronym stands for, particularly when many different acronyms are used in the same text. A prominent illustration is Hull’s recent revision of Matthews’Plant Virology [12]. 1244 L. Bos
Throughout the book, a great many viruses are simply referred to by their acronyms. Those reading this virology text or devising acronyms of new viruses will be always forced to consult Hull’s guidelines, Appendix, and standard lists of acronyms. Acronyms may seem indispens- able for simplifying written texts, but their meaning must always be given in the Introduction of each paper, be listed in the Methods and Materials section or in a special appendix at the end of the book or paper, or be defined within each chapter. Prevalent exclusive reliance on acronyms further demonstrates depreciation of the biological and societal importance of viruses. Acronyms are becoming linguistically void, mere codes for reference to viruses.
Conclusions 1) With the advent of virus taxonomy, the increasing number of viruses to be named, and the need for universality in virology at large, nomenclature remains a hot but significant topic. 2) In communication on viruses, we must know exactly what we are talking about, and must therefore look for consensus, consistency, and utmost precision. 3) Wide acceptance of the species concept in virology, and the fact that viruses mutate and occupy ecological niches like organisms, have outdated theArticle 2.2 of the Code, which stipulates that virus nomenclature “is independent of other biological nomenclature” and that virus and virus taxon nomenclature should have “the status of exceptions in the proposed International Code of Bionomenclature”. Arguments in favour of virus binomials are continuously accruing and are even supported by the virus Code itself. 4) There is more to the naming of viruses than mere linguistics. For knowing what is specifically covered by a virus name, more attention must be paid to legitimate genotypic and phenotypic virus description and to publication of such descriptions, as well as to the curated preservation of type material. 5) Simplest for compliance with bionomenclature at large, and for the widest international acceptance, would be the introduction of italicized Latin or latinized binomials. But complications persist. 6) For the time being, non-latinized binomials do indeed merit preference over the monono- mials imposed by ICTV. 7) Typography of virus names should not conflict with the typography of scientific names of organisms and should not impede precision in biological nomenclature at large. Hence the unacceptability of the in toto italicization of official names (such as the ICTV mononomials) of the viruses recognized as species by ICTV, and non-italicization of names of viruses not yet recognized as species. The ICTV choice of selective typography also appears to be delusively buttressed by if the virus name is used in an abstract taxonomic sense or in a concrete sense. 8) There is a continuing need of common names for viruses (in an abstract taxonomic sense) alongside the official or scientific names authorized and standardized by ICTV, particularly for communication in languages other than English. 9) The prevalent upgrading of English common virus names into official virus names would require standardization of such names, preferably under the auspices of ICTV. 10) The popular use of virus acronyms, advocated, though not officially authorized, by ICTV, is increasingly faced with problems of complexity and inconsistency. They thus tend to hinder rather than help the recognition of the viruses so indicated. Virus nomenclature; continuing topicality 1245
11) The Van Regenmortel and Fauquet paper [27] and previous ones by the first author on similar matters do not make clear if the authors are speaking on their own authority, on behalf of ICTV, or as staff of the home institutes given as their addresses. Also, their relationships with the Virology Division of the International Union of Microbiological Societies (IUMS) – responsible for the Virology Division News section of the Archives of Virology published by IUMS and for the reports published in it – are not clear. As earlier suggested [11], many readers will assume that their comments represent the considered opinion of the ICTV.
References 1. Agut H (2002) Back to Latin and tradition: a proposal for an official nomenclature of virus species. Arch Virol 147: 1465–1470 2. Bos L (1999a) The naming of viruses: an urgent call to order. Arch Virol 144: 631–636 3. Bos L (1999b) Plant viruses, unique and intriguing pathogens–atextbook of plant virology. Backhuys Publishers, Leiden: 385 pp 4. Bos L (2000) Structure and typography of virus names. Arch Virol 145: 429–432 5. Bos L (2002) International naming of viruses – a digest of recent developments. Arch Virol 147: 1471–1477 6. Drebot MA, Henchal E, Hjelle B, LeDuc JW, Repik PM, Roehrig JT, Schmaljohn CS, Shope RE, Tesh RB, Weaver SC, Calisher CH (2002) Improved clarity of meaning from the use of both formal species names and common (vernacular) virus names in virological literature. Arch Virol 147: 2465–2471 7. Fauquet MC, Martelli GP (1995) Updated ICTV list of names and abbreviations of viruses, viroids, and satellites infecting plants. Arch Virol 140: 393–413 8. Fauquet MC, Mayo MA (1999) Abbreviations for plant virus names – 1999. Arch Virol 144: 1249–1273 9. Fauquet CM, Pringle CR (1999) Abbreviations for vertebrate virus species names. Arch Virol 144: 1865–1880 10. Fauquet CM, Pringle CR (2000) Abbreviations for bacterial and fungal virus species names. Arch Virol 145: 197–203 11. Gibbs AJ (2000) Virus nomenclature descending into chaos. Arch Virol 145: 1505–1507 12. Hull R (2002) Matthews’ plant virology. Academic Press, San Diego: 1001 pp 13. Hull R, Milne RG, Van Regenmortel MHV (1991) A list of proposed standard acronyms for plant viruses and viroids. Arch Virol 120: 151–164 14. Kanyuka KV, Vishnichenko VE, Levay KE, Kondrikov EV, Ryabov EV, Zavriev SK (1992) Nucleotide sequence of shallot virus X RNA reveals a 5 -proximal cistron closely related to those of the potexviruses and a unique arrangement of the 3 -proximal cistrons. J Gen Virol 73: 2553–2560 15. Mayo MA (2002) ICTV at the Paris ICV: Results of the Plenary Session and the Binomial Ballot. Arch Virol 147: 2254–2260 16. Mayo MA, Horzinek MC (1998) A revised version of the International Code of Virus Classification and Nomenclature. Arch Virol 143: 1645–1654 17. Nomenclatuurcommissie NKP (2000) Lijst van offici¨ele Nederlandse namen van plantenvirussen en-viro¨ıden; aangepast aan de nieuwe spellingsregels en de per eind 1998 door ICTV aangekondigde taxonomische veranderingen. Internet
22. Van Dijk P, Verbeek M, Bos L (1991) Mite-borne virus isolates from cultivated Allium species, and their classification into two new rymoviruses in the family Potyviridae. Neth J Pl Pathol 97: 381–399 23. Van Hulten MCW,Vlak JM (2002) Genetic evidence for a unique taxonomic position of white spot syndrome virus of shrimp: genus whispovirus. In: Lavilla-Pitogo CR, Cruz-Lacierda ER (eds), Diseases in Asian aquaculture IV. 23–35 24. Van Regenmortel MHV (1999) How to write the names of virus species.ArchVirol 144: 1041–1042 25. Van Regenmortel MHV (2000) On the relative merits of italics, Latin and binomial nomenclature in viral taxonomy. Arch Virol 145: 433–441 26. Van Regenmortel MHV (2001) Perspectives on binomial names of virus species. Arch Virol 146: 1637–1640 27. Van Regenmortel MHV, Fauquet CM (2002) Only italicised species names of viruses have a taxonomic meaning. Arch Virol 147: 2247–2250 28. Van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, Maniloff J, Mayo MA, McGeoch DJ, Pringle CR, Wickner RB (eds) (2000)Virus Taxonomy. Seventh Report of the International Committee on Taxonomy of Viruses. Academic Press, New York, San Diego, 1162 pp 29. Van Regenmortel MHV, Mayo MA, Fauquet CM, Maniloff J (2000) Virus Nomenclature: Consensus versus chaos. Arch Virol 145: 2227–2232 30. Vishnichenko VK, Konareva TN, Zavriev SK (1993) A new filamentous virus in shallot, Pl Pathol 42: 121–126 31. Zavriev SK, Ryabov EV, Vishnichenko VK (2000) Genus Allexivirus In: Van Regenmortel et al., Ref. nr. 27: 981–985 Author’s address: Dr. L. Bos Plant Research International WUR, P.O. Box 16, 6700 AA Wageningen, The Netherlands; e-mail: [email protected]
Verleger: Springer-Verlag KG, Sachsenplatz 4–6, A-1201 Wien. – Herausgeber: Dr. M. H. V. Van Regenmortel, Ecole´ Sup´erieure de Biotechnologie de Strasbourg (ESBS), Parc d’Innovation, Boulevard S´ebastian Brandt, F-67400 Illkirch, France. – Redaktion: Sachsenplatz 4–6, A-1201 Wien. – Satz und Umbruch: Thomson Press (India) Ltd., Chennai. – Offsetdruck: Adolf Holzhausens Nachfolger, Holzhausenplatz 1, A-1140 Wien. – Herstellungsort: Wien. – Printed in Austria.