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Home , Avsunviroidae, Guttaviridae, Polerovirus, Tymoviridae

Family Genera Hosts Genome size (kb)

dsDNA 6 Pro 169 –ssRNA 1 V 9 8 Pro 43 6 V,Pl,I 12 4 Pro 40 2 V 19 Tectiviridae 1 Pro 15 7 V 15 Corticoviridae 1 Pro 10 5 V,I 10 1 Pro 12 Bunyaviridae 5 V,Pl,I 12 3 Pro 16 Arenaviridae 1 V 11 Rudiviridae 1 Pro 33 Unassigned genera 4 1 Pro 15 1 Pro 20 11 V 170 +ssRNA Leviviridae 2 Pro 4 Asfarviridae 1 V,I 180 Narnaviridae 1 F 3 systematics: 5 I 150 Picornaviridae 9 V 7 6 Algae 335 1 I 9 2 I 134 1 F 9 Nimaviridae 1 I 293 Sequiviridae 2 Pl 10 10 V 130 Comoviridae 3 Pl 10 4 V 31 6 Pl 10 1 V 5 4 V 8 16 V 7 Astroviridae 2 V 7 taxonomy for Polydnaviridae 2 I 245 2 I 4 1 I 120 Unassigned genera 3 Tetraviridae 2 I 8 Luteoviridae 3 Pl 6 ssDNA Inoviridae 2 Pro 6 8 Pl 4 4 Pro 6 2 V 28 4 Pl 6 1 V 13 2 V 2 Roniviridae 1 I 26 the tiny 1 Pl 6 3 V,I 11 9 V 5 Togaviridae 2 V,I 10 Unassigned genera 1 5 Pl 8 3 Pl,I 6 RT 2 V 3 3 Pl 16 6 Pl 8 3 I,Pl,F 6 Flexiviridae 8 Pl 6 3 I,Pl,F 5 1 F 4 Retroviridae 7 V 7 Unassigned genera 14 5 Pl 0.4 The classification of poses different problems dsRNA Cystoviridae 1 Pro 13 2 Pl 0.3 12 V,I,Pl,F 24 3 V 6 Table 1. Virus families and some representative properties 3 F 5 from those of classifying more elaborate forms as 3 F,Pl 4 1 F 13 Abbreviations: Pro, prokaryotes; V, vertebrates; I, invertebrates; Hypoviridae 1 F 10 Pl, ; F, fungi. Colours indicate main hosts, gradients signify more Anne-Lise Haenni and Mike Mayo describe. Unassigned genera 1 than one type of host. Genome sizes are for a representative species.

question frequently asked of virologists any number of , that allows easier reference to its of that are described every are as yet unassigned to taxa above Complicating factors – by non-virologists is – are viruses living? components, nomenclature – the construction of a system year, the virus world consists of a mere the level of genus. This reflects some properties of viruses Perhaps one answer to this chestnut is in of names and a formal guide to their use in taxonomy, and 1,950 species. As parasite diversity of the uncertainties in current virus As for many microbes, morphological the nature of virus systematics. Although taxonomy – the process of naming organisms and classifying surely parallels host diversity, this taxonomy. characters are of limited use (although molecular in scale ( have ~20 nm them hierarchically to express their mutual relationship in number is clearly a massive under- The nomenclature of virus taxa, in the advent of electron microscopy did diameter virions and ~2 kb ssDNA ; a simplified way and according to internationally agreed representation, but is probably held in particular species, differs fundamentally lead to significant taxonomic advances) viroidA genomes consist of ssRNA of only ~0.3 kb), viruses codes of practice. In virology, these activities are undertaken check because to establish a new virus from that of the rest of biology. It is and small genetic changes can result and viroids are replicated by error-prone mechanisms that by the International Committee on the Taxonomy of Viruses species is a laborious research exercise regulated by the International Code of in substantial changes in pathological result in variations from which natural selection yields (ICTV). ICTV consists of a network of some 500 virologists and only ‘important’ hosts such as man Virus Classification and Nomenclature, impact. Virus genomes are small (see distinctive forms fitted to particular niches. Thus one can organized into Study Groups for particular groups of viruses are studied intensively. which is published on the ICTV Table 1) and can often vary rapidly. study and describe virus variation, investigate the causes and (e.g. a family) that report to a subcommittee for each of the Viruses are diverse in genome type website (www.danforthcenter.org/iltab/ However, it is now possible to obtain consequences of this variation and manipulate the data to major groups of hosts (vertebrates, invertebrates, plants, and size and infect hosts in all major ICTVnet/asp/_MainPage.asp) and in nucleotide sequences very quickly, produce a system of classification. This constitutes a classic prokaryotes, or fungi, protozoa and algae). The Chairs of types of organisms. The table shows reports such as the current 8th ICTV sometimes without isolating the virus definition of systematics and can be said to describe much of these subcommittees form the backbone of the Executive the currently recognized virus families Report. This article is concerned only from its host. By using appropriate current virological research activity. Committee of ICTV. clustered according to genome type. with the classification aspects of ICTV’s software, evolutionary distances be- It is feasible to administer virus taxonomy (including Taxonomy above the level of families is work, in particular the factors that tween sequences can be deduced and Background nomenclature) through such an organization because of at present limited to the recognition of complicate virus classification: the in- phylogenetic trees obtained. This Intrinsic to any biological research are classification – the the relatively small number of virus species currently recog- three orders; most families are not trinsic properties of viruses and the prob- assumes that the sequences are derived production of a logical system of categories, each containing nized. In contrast to the approximately 17,000 new species clustered into orders and some genera able evolutionary origins of viruses. from a single ancestral sequence and

156 microbiology today nov 06 microbiology today nov 06 157 that differences have arisen by mutation bination between blocks has been formed by recombination different from those applying to independently replicating acute respiratory syndrome coronavirus; SARS-CoV), making of single bases. Such a model seems happened during the evolution of these (joining of parts of separate genomes genomes. it possible to predict their properties, and others are unlike most reasonable when sequences are viruses (Fig. 1). Expecting sequence to produce a new genome) and/or 5. Some viruses infect more than one type of host (one often anything seen previously (e.g. Acanthamoeba polyphaga clearly similar, such as when viruses in a comparisons and the resulting trees reassortment (making new com- serving as vector for transmission between other hosts) ). Thus, virus taxonomy must have both an genus are compared. When other sorts to produce a durable classification binations among separate parts and therefore will have evolved in response to complex internal logical justification and a capability of expansion to of sequence variation have happened, is thus, at least in some instances, a of the genomes of viruses with selection pressures. accommodate novelty. Whatever the virological endeavour, such as recombination, these simple naïve approach to virus classification. multipartite genomes, such as Any or all of these factors greatly complicate, if not vitiate, virus taxonomy should provide a provocative framework to comparison techniques are likely to Whereas it works for some virus taxa, influenza viruses), resulting in attempts to deduce phylogeny from studies of current genome which all virologists can contribute. Current ICTV practice lead to erroneous conclusions. This is for others a more arbitrary and broadly chimeric viruses with polyphyletic sequences and thus, whatever the taxonomic arrangement, aims to achieve this. vividly illustrated by the genomes of based approach that uses multiple (i.e. hybrid) genomes whose ori- some viruses and/or taxa will always seem to be misfits. viruses that are classified in the family criteria is clearly necessary. gins cannot be represented in a Luteoviridae. There is no dispute that monophyletic scheme. Anne-Lise Haenni viruses in this family are related both Complicating factors – 2. Genomes of some viruses seem to Conclusion Current ICTV Secretary in sequence details and in their biology evolutionary history contain acquired from their Notwithstanding the complications, some sort of classification Institut Jacques Monod, CNRS and Universities VI (all are transmitted by aphids in a Biological taxonomy is well suited to hosts. is fundamental to most virological research, whether it be and VII, 2 Place Jussieu – Tour 43, 75251 Paris circulative fashion that involves virions classifying organisms that are related 3. Viruses are unlikely to be descended deducing the nature of a new disease agent by working out Cedex 05, France crossing several barriers inside aphid to one another via simple branched from one original ‘protovirus’; they which of the known taxa it most resembles or developing a (e [email protected]) bodies). The RNA genomes of luteo- and diverging descent, with relatively probably arose more than once, better understanding of the nature of a virus by predicting virids consist largely of two gene blocks, long evolutionary distances between but when and how many times is properties based on its assumed classification. Mike Mayo one of structural genes and the other successive branch points. However, unclear. To develop and maintain such a classification, ICTV com- ICTV Secretary, 1999–2005 of replication-related (pol) genes (Fig. virus evolution differs from this simple 4. Genomes of some viruses (e.g. municates with virologists in several ways. Via its website, Scottish Crop Research Institute, Invergowrie, ICTV provides many of the details of its organization as well 1). The phylogenetic trees obtained by paradigm in several ways. ) integrate into the Dundee DD2 5DA, UK as current issues in virus taxonomy. ICTV also publishes comparing luteovirid structural genes 1. Genomes of some viruses, such as genomes of the hosts, where they (e [email protected]) confirm the family cluster and show a luteovirids (see above; Fig. 1), have are subject to selection pressures regular formal reports (such as the recent 8th ICTV Report) separation of species into the constit- and occasional notes in the Virology Division News section uent genera. But when pol genes are of Archives of Virology. Also, workshops, such as the recent Further reading compared with those of other viruses, meeting on virus evolution and taxonomy which has been Fauquet, C.M., Mayo, M.A., Malinoff, J., Desselberger, U. the genera and  Fig. 1. Diagram of possible origins of the genomes of viruses in different genera in the family summarized by U. Desselberger, are held and, as work pro- & Ball, L.A. (editors) (2005). Virus taxonomy, VIIIth Report differ greatly and each seems more Luteoviridae. The upper boxes contain hypothetical genomes and assume that the ancestors of gresses, ICTV expects to organize further such workshops. of the ICTV. London: Elsevier/Academic Press. and sobemoviruses had genomes like those of their current-day counterparts. closely related to one or the other non- Red boxes represent blocks of structural protein genes. pol signifies replication-related genes. New viruses are being discovered all the time. Some can Desselberger, U. (2005). Report on an ICTV-sponsored luteovirid genus. It seems that recom- ? signifies a gene block of unknown type. Further details can be found in the 8th ICTV Report. be fitted into existing taxonomic structures (e.g. Severe symposium on virus evolution. Arch Virol 150, 629–635.

Ancestor of Ancestor of Ancestor of Virus taxonomy must have both an internal genus family Luteoviridae genus Sobemovirus logical justification and a capability of expansion pol pol ? to accommodate novelty. Whatever the virological endeavour, virus taxonomy should provide a provocative framework to which all virologists can contribute.

pol Present-day pol Present-day genus genus Genus Luteovirus Genus Polerovirus Tombusvirus Sobemovirus Present-day family Luteoviridae

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