genome sequence relatedness,
natural host range,
cell and tissue tropism,
pathogenicity and cytopathology,
mode of transmission,
physico-chemical properties of virions,
antigenic properties of viral proteins.
The question of what is a virus species is related to the general problem of how the world of viruses should be partitioned in a coherent scheme of distinct and easily recognizable viral entities. In view of the variability of viruses, it is often difficult to decide if one virus is the same as another, since this requires that an answer be given to the vexed problem of identity: how different is different enough to be something else? Although viral mutants or pathogenic variants may be clearly distinguishable from the wild type virus, virologists will usually recognize them as being the same kind of virus. Even without realizing it we constantly pass judgement on the significance of the extent of difference we observe between individual virus isolates. If the degree of difference appears to be small enough for the variants to be considered the same virus, they will, taxonomically speaking, be considered as the same virus species.
Species is the universally accepted term for the lowest taxonomic clustering of living organisms. Although the species is the most fundamental unit in all biological classifications, it took many years before an internationally agreed definition of virus species applicable to all viruses became generally accepted and was ratified by the International Committee on Taxonomy of Viruses (ICTV). The virologists who study viruses that infect plants were particularly reluctant to accept that the species concept could be used in virology ( Harrison, 1985; Milne, 1985). Some of them argued that the only legitimate definition of species was that of biological species, used for sexually reproducing organisms (Mayr, 1982). This concept which is based upon gene pools and reproductive isolation is obviously not applicable to entities such as viruses that replicate by clonal means. However, a great variety of species concepts exists and some of them which have been used for asexual organisms may be applied to viruses ( Bishop, 1985; Kingsbury, 1988). Unfortunately, there is no general agreement among biologists on what counts as a good species concept. Before outlining the concept of virus species, it will be helpful to define a few terms and to analyze some of the key concepts used in biological classification.a
A virus is an elementary biosystem that possesses some of the properties of living systems such as having a genome and being able to adapt to changing environments. However, viruses cannot capture and store free energy and they are not functionally active outside their host cells. Although viruses are pathogens, they are not genuine pathogenic microorganisms.
A virus has both intrinsic properties (e.g., its size) and relational properties (e.g., its host), the second type of property existing only by virtue of a relation with other objects. These properties are either resultant properties already possessed by the components of the virus (the mass of the virion equals the sum of the mass of its parts) or emergent properties that are only possessed by the system as a whole and are not present in its constituent parts (e.g., the viral replication cycle or the viral ecological niche). It should be stressed that only cells and multicellular systems possess the emergent property of being alive and that this property is not present in subcellular organelles or individual molecules. A virus becomes part of a living system only after its genome has been integrated in the host cell and viral replication is made possible through the metabolic activity of the cell. Viruses are not living organisms and they occupy a unique position in biology. Since they are not functionally active outside of their host cells, they lead only a kind of borrowed life.
It is also important to distinguish clearly between the entity called a virus and a single, discrete virus particle or virion. A virion possesses intrinsic biochemical and structural properties which include as one of the phenotypic characters the composition and sequence of the viral genome (although this is generally called the genotype). A virus, on the other hand, possesses in addition a number of relational and emergent properties that become actualized when it infects a host and becomes integrated in the host cell during the viral replication cycle. A virus can thus not be reduced to the physical constituents or chemical composition of a virion and it is necessary to include in its definition the various biotic interactions and functional activities that make it a biological system. Another important point is that the hereditary material of a particular virus cannot be described in terms of the unique genomic sequence present in a single virion. The genome of a virus is not a single molecular species but must be viewed as a dynamic population consisting of thousands of viral mutants that are always present in any viral clone. This population which is the target of selection is referred to as a viral quasi-species (see below).
Species, Classes and Fuzzy Sets
One of the difficulties in defining species is that the term is used in many different ways which unfortunately are not always clearly distinguished. For instance, the term species is often used to designate groups of real organisms studied by taxonomists, in which case it refers to concrete objects, i.e., material things that are located in time and space. One influential taxonomic theory states that species are concrete individuals in the sense that they correspond to historical entities related by common descent. The thesis that species should be regarded as individuals instead of classes has led to vigorous debate, although this has not solved the species problem in biology (Ghiselin, 1997; Hull, 1976).
A second meaning of the term species is that of a class, i.e., a conceptual construct or abstraction that does not exist on its own in the absence of someone conceiving of the idea. Properties and classes are related abstract entities. Whatever is said about a thing is seen as ascribing a property to it, and the thing thereby becomes a member of a particular class (Quine, 1987). If a virus has a positive strand RNA genome, it becomes automatically a member of the class of positive strand RNA viruses. Such a class is called a universal class because it is defined by a single property or a combination of properties necessarily present in every member of the class.
A biological classification is a conceptual construction made up of classes with a hierarchical structure, the ranks being the species, genus, family, order and phylum. It must be emphasized that the classes or taxonomic categories used for building up a classification are conceptual constructions that do not correspond to groups of real organisms with a location in space and time. This is why it is impossible for a biologist ever to encounter an abstract genus or species during his handling of organisms. It is odd that many biologists who readily accept that genera, families or orders are conceptual constructions of the mind, i.e., abstractions, insist that species have a real existence in space and time and are not abstract classes. It seems that species are more readily perceived as populations of real organisms rather than as abstractions. On the other hand, higher ranks such as genera and families are more easily accepted as universal classes defined by one or more properties present in every member of the class.
Another difference arises from the fact that part-whole relationships are found only among concrete, spatiotemporally localized entities. When a species is viewed as an abstract class, it is impossible for individual organisms to be part of that species. The organisms belonging to a species can only take part in a relation known as class-inclusion or class membership. An organism can only be a member of the species and not a part of it because it is logically impossible for a concrete object to be part of an abstract entity, i.e., of an entity of different logical type. One problem with the species class is that its members, i.e., living organisms, undergo continuous developmental and evolutionary changes in time and, therefore, are always endowed with intrinsic variability. This seems to contradict the notion that organisms could belong to a universal class, seen as immutable and timeless. It also seems problematic to speak of the origin of species if one conceives of them as abstract concepts with neither beginning nor end in time (Hull, 1976). However, these difficulties disappear when species are viewed, not as classical, universal classes, but as polythetic and historical classes, the members of which appear at a certain time in history and share only a certain number of characteristic attributes which can change with time. Classes of paintings belonging to the French impressionist or German expressionist schools are examples of classes with a clear historical dimension.
Whereas a traditional class is defined by the necessary presence of at least one property in all its members, the members of a polythetic class need not have a single defining property in common (Fig. 1). When species are viewed as polythetic classes, it is possible to accommodate individuals that lack one or other character normally considered typical for the species. The concept of polythetic species is thus particularly suited for dealing with replicating biological entities endowed with intrinsic variability and undergoing continual evolutionary changes. When viewed in this way, species correspond to fuzzy sets with hazy boundaries, and it is not possible to draw sharp boundaries between them as is done with classical sets and universal classes.
The use of vagueness or fuzziness as a descriptor of reality has a long history in western philosophy. Vagueness stems from a continuum with innumerable steps and is exemplified in the well-known sorites paradox of the heap described by Greek philosophers. This paradox arises because it is impossible to say how many grains of sand can be removed from a heap before it stops being a heap. This implies that the concept of heap cannot be defined in a precise manner. In a similar way, fuzzy sets have no sharp boundaries and since the set is defined by a vague predicate, membership of a fuzzy set is not an all-or-nothing matter. This means that the two pillars of classical logic, the law of excluded middle (a swan is either white or non-white) and the law of contradiction (a swan cannot be both white and non-white) do not apply since in some cases it may not be possible to ascertain if an object is a member of the set or not. Handling fuzzy sets, therefore, falls outside the scope of classical, bivalent logic (McNeill and Freiberger, 1993). In a biological classification, it may sometimes be necessary to allocate an organism to a particular species purely as a matter of convention or convenience rather than logical necessity.
Science is based on empirical observations, the precision of which is always limited. Scientific evidence, therefore can never be assigned the absolute truth value possessed by certain types of statement in formal logic which lack factual reference. Scientific knowledge always remains approximate and incomplete and it is counterproductive in science to look for certainty and for absolutely precise boundaries where none exist.
Fuzzy logic as a method for handling fuzzy sets admits of the inherent imprecision of terms and categories used both in ordinary language and in science (McNeill and Freiberger, 1993). When fuzziness is accepted as an unavoidable ingredient of species taxa, spurious problems of definition disappear and it becomes possible to describe species in terms of continuums devoid of artificial sharp edges (Van Regenmortel, 1998). In a similar way, colors can be distinguished conceptually in spite of the continuous nature of the spectrum of electromagnetic waves, and mountain peaks are given names although there are no sharp boundaries in geological rock formations.
It is remarkable that a century and a half after Darwin, there is still no agreement about what a species is. In spite of the enormous development of biological science and molecular biology, there is at present no general agreement about what constitutes a plant, animal or microbial species. At a recent meeting devoted to the species problem in biology, as many as 22 different species concepts were compared (Mayden, 1997) and one contribution was entitled: “The ideal species concept and why we can’t get it” (Hull, 1997).
The traditional view of species is that they correspond to groups of similar organisms that can breed among themselves and produce fertile offspring. Mayr’s classical definition of biological species states that “species are groups of interbreeding natural populations that are reproductively isolated from other such species” (Mayr, 1963). This definition has been criticized because it defines species as a population instead of a class and can be applied only to organisms that reproduce sexually; for instance it fails to take into account the phenomenon of interspecies hybridization which is prevalent in the plant kingdom. Since groups of plants lie on a continuum from completely interfertile to completely reproductively isolated, the criterion of infertility for demarcating species is very often inapplicable and the choice of what constitutes a significant breeding discontinuity is rather arbitrary ( Levin, 1979; Mishler and Donoghue, 1982). In order to make it applicable to asexual organisms, Mayr subsequently modified his definition and stated that “a species is a reproductive community of populations, reproductively isolated from others, that occupies a specific niche in nature” (Mayr, 1982).
As biologists became increasingly committed to evolutionary theory, several authors introduced the notion of evolutionary species defined as a time-slice in an evolving lineage (Wiley, 1981). By including in the definition the idea of ancestry and descent, the concept of species acquired an internal cohesion which was absent when species were defined purely on a morphological or phenetic basis, i.e., only in terms of similarity. However, the evolutionary species concept remains a highly theoretical one since it gives no indication of how and when individual time-slices of evolving lineages segregate into separate species. Transition from one species to another during evolution occurs within an uninterrupted chain of replicating nucleic acid molecules and of ancestral-descendant organisms and there are no criteria for deciding how far back in time a species can be traced. It is thus equally difficult to demarcate boundaries in time in order to identify evolutionary species as it is to define clear-cut breeding discontinuities for identifying biological species.
For most practical purposes, biologists today still tend to distinguish between different species on a phenetic or morphological basis. As noted before, the genomic sequence of an organism may also be considered a phenotypic trait and it is generally found that the overall degree of phenotypic difference observed between organisms, which also includes genomic divergence, is roughly proportional to the amount of evolutionary distance from a common ancestor. This is the reason why phenetic species defined in terms of overall similarity are often very similar to the species defined as lineages of ancestral-descendant populations.
The rationale for using the species concept in viral taxonomy is that viruses are biological entities and not simply chemicals. Viruses possess genes, replicate, evolve and are adapted to particular biotic habitats and ecological niches. Like all biological entities that possess the ability to replicate and reproduce themselves, viruses are endowed with an intrinsic variability derived from the error-prone process of nucleic acid replication. Whereas the molecules of a compound studied by a chemist are all identical, the virus particles in a clone always include thousands of mutants which constitute a so-called quasi-species population. This built-in variability allows biological systems to become adapted through selection and in the end guarantees their survival.
In 1981, the ICTV proposed the following definition of virus species: “A virus species is a concept that will normally be represented by a cluster of strains from a variety of sources, or a population of strains from a particular source, which have in common a set of correlating stable properties that separate the cluster from other clusters of strains“. This definition does not explain what is a strain and it proposes to group viruses purely on a phenetic basis without considering the cohesive forces present in ancestral-descendant populations. In 1989, another definition of virus species was proposed which took into account that a species is a polythetic class, the members of which are united by relational properties of descent and by occupation of a particular biotic niche ( Van Regenmortel, 1989; Van Regenmortel, 1990). In 1991, the ICTV endorsed this definition which states that: “A virus species is a polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche”.
Virus Species as Polythetic Classes
A polythetic class is defined as a class whose members always have several properties in common although no single common attribute is present in all of its members (Fig. 1). As a result no single property can be used as a defining property of polythetic species on the basis that it is universally present in all the members of the species and absent in the members of other species. A single discriminating character, for instance a particular host reaction or a certain degree of genome sequence dissimilarity cannot be used as an absolute criterion for differentiating two virus species within the same genus. Attempts to use a single discriminating character for distinguishing species fail because of the inherent variability of members of the species.
Species are not universal classes definable by a single property, and they are therefore different from higher taxa such as genera and families which are universal classes and include members which share one or more defining properties that are both necessary and sufficient for class membership. As far as virus species are concerned, it is always a combination of statistically covariant properties that provides the rationale for deciding that a particular virus should be considered a member of a species. ICTV Study Groups, with their in depth knowledge of particular virus genera and families, serve as judges of such issues for the international virology community. Only specialists are aware of the facts, issues and nuances about viruses and their biotic interactions and of the importance of making certain distinctions, that may not be the same in all virus genera, for achieving a convenient and practical classification (Van Regenmortel, Bishop, Fauquet, Mayo, Maniloff and Calisher, 1999).
Virus Species as a Replicating Lineage
This part of the definition acknowledges that a virus species, in addition to being a polythetic class, is made up of members that represent an evolving lineage. The membership of a virus species varies over time but all its members share descent from a common ancestor. It should be noted that shared descent is a property that also links different species and different genera and phylogeny is thus not a sufficient criterion for species demarcation. Species undergo continuous variation in time and transition from one species to another during evolution occurs within the continuity of gene replication. As variations accumulate, a point will be reached where the importance of genotypic and phenotypic differences will lead an observer to conclude that he is dealing with a separate entity. In general no particular degree of genome sequence dissimilarity can be used as a cut-off point to differentiate between two species. Within a single genus, sequence data do provide some guidance, as they indicate the extent to which the viruses in question have diverged over time.
The genomic plasticity inherent in any viral replicating lineage leads to continual phenotypic variation that makes the virus species a polythetic rather than a universal class. For this reason a single criterion such as the degree of genome sequence divergence or the potential for genetic reassortment cannot serve as a criterion for species demarcation. The need to record phylogeny should not overshadow the importance of phenotypic and biotic distinctions which are the ultimate reason why virologists engage in species demarcation and want to classify viruses. Classifying viral genomes should not be confused with classifying viruses. Genome comparisons cannot by themselves justify taxonomic placements that would disregard the biotic and phenotypic properties of viruses.
The ecological niche refers to biotic properties of members of a virus species such as host range, tissue tropism, virulence, pathogenesis, host responses, vectors and habitat. The ecological niche does not simply refer to a location in three dimensional space but is a functional concept based on relational properties of the virus. The niche is not a property of the environment but a property of the virus related to its biotic habitat. There are therefore no vacant or empty niches but only unoccupied habitats or geographical spaces. In the absence of the virus, its ecological niche property is also absent and the notion of a vacant niche is thus meaningless. A niche provides the needs that must be met for the virus to replicate and to survive and it is restricted to the relations that are beneficial to the virus.
Taxonomic Polythetic Species Versus Molecular Quasi-species
As mentioned above, the genome of a virus cannot be defined by a unique sequence corresponding to a so-called wild type but consists of a distribution of mutant sequences, each one differing in one or a few nucleotide positions from the consensus sequence of the clone. This consensus sequence identified by sequencing a clone may give the impression of a stable, unique structure although it corresponds in fact to the average of a large number of different individual sequences. Since RNA viruses have genomes that replicate in the absence of repair mechanisms, they evolve very rapidly with a mutation frequency per nucleotide site in the genome of 10-3 to 10-5. The genome of an RNA virus, therefore, consists of a master sequence corresponding to the most fit genome sequence under a given environment, together with a large number of competing mutants. Such a population is usually referred to as a quasi-species, a somewhat unfortunate term since it may seem to imply that the virus corresponds to some sort of imperfect species as opposed to a “true” or genuine species that would possess a single, invariant genome sequence ( Domingo, Holland, Biebricher and Eigen, 1995; Holland, De La Torre and Steinhauer, 1992). Such idealized species, of course, do not exist. The term quasi-species was introduced by Manfred Eigen and his colleagues to describe self-replicating RNA molecules which because of mutation do not consist of a unique molecular species (Eigen, 1993). In this context, the term species refers to a purely chemical entity, i.e., a species of molecule, and not to the taxonomic concept of virus species as a variable biological entity. Whereas all the members of a chemical species are identical molecules, the members of a virus species are not. Taxonomic species are thus inevitably quasi-species in the molecular sense (Smith, McAllister, Casino and Simmonds, 1997). It has been proposed that virus species could be considered as “an ensemble that occupies a coherent part of the sequence space which is continuously populated for prolonged periods of time and under a wide variety of environmental conditions” (Domingo, Holland, Biebricher and Eigen, 1995). However, such a definition reduces viruses to genome sequences and ignores the phenotypic characteristics which are the reason why viruses are being classified as species in the first instance. Furthermore, focusing on sequences that correspond to heterogeneous chemical populations does not help to resolve the inherent fuzziness of all species boundaries.
Although the acceptance of a definition of virus species by the international virological community was an important step for establishing a unified virus classification system based on traditional taxonomic categories, it should be stressed that such a definition is of little use for deciding if a particular virus isolate is a member of a certain species or not. The reason for this is that definitions apply only to abstract concepts such as the notion of species taken as a class. Individual viruses located in time and space cannot be “defined” but can only be identified by means of so-called diagnostic properties (Ghiselin, 1984). The difference between definition and identification can be clarified by the following analogy. It is possible to define the concept of a human family in terms of an ancestral-descendant population comprising parents, grandparents, children siblings, etc. However, such a definition of the family concept would be of no help whatsoever if one wanted to identity the members of the Smith family present at the annual school concert and distinguish them from members of the Brown family. What is required is a set of characters and diagnostic properties that can be used for identifying individual members of a particular class. It is thus necessary to reach an agreement about which diagnostic properties are most useful for identifying the members of a virus species. For different virus species, different types of properties may have to be used.
The identification of a virus isolate is a comparative process based on a number of different characters that will indicate the extent of relationship of the isolate with members of an established species. Since species are polythetic, the comparison must involve several characters rather than the presence or absence of a single key feature. For species diagnosis it is of course essential not to use characters that are present in all the members of a genus or family, since these obviously will not permit species demarcation within the group. Characters such as virion morphology, genome organization, method of replication and the number and size of structural and non-structural viral proteins are family- or genus- defining properties that are of little value for identifying individual species. The following characters are useful for discriminating between virus species within the same genus:
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genome sequence relatedness, |
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natural host range, |
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cell and tissue tropism, |
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pathogenicity and cytopathology, |
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mode of transmission, |
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physico-chemical properties of virions, |
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antigenic properties of viral proteins. |
The relative importance of these characters for species demarcation vary in different genera. A list of characters that have been used to decide if two virus isolates belonging to the plant virus families, Potyviridae or Geminiviridae, are different species or not are listed in Table 1. Some criteria are the same for the two families, others are qualitatively the same but quantitatively different and some criteria do not apply to viruses in both families. No one criterion has an absolute supremacy over others; some are more informative and discriminatory than others, but it is the sum total of the information that is gathered which allows reliable species demarcation. Once different species have been established on this basis in the classification scheme, it may be sufficient to check for the presence of a few characters in a particular isolate to be able to allocate it to a particular species.
In each genus, one species for which considerable knowledge is available is designated as the type species. However, this designation does not imply that the properties of the type species are most typical and representative of the properties of all species in the genus.
Two examples of how species demarcation criteria have been used in practice will be illustrated with the families Potyviridae and Picornaviridae.
Species of the Family Potyviridae
For a number of years, and for many plant viruses, the main characters used to distinguish between different viruses have been combinations of biological features such as transmission characteristics and host range, physico-chemical features of virus particles, such as shape, and the serological cross-reactivity of antibody preparations made against purified virus particles. As the concept of clustering viruses in groups, and then higher taxa, has been developed and applied to plant viruses, discrimination of viruses by criteria such as particle morphology ( Brandes and Bercks, 1965; Brandes and Wetter, 1959) led to the formation of distinct groups later called, genera or families. Other criteria, for example serological relatedness, have been used to discriminate between individual viruses ; normally a serological differentiation index of about 2 or less was deemed strongly suggestive that two virus isolates were related as strains of a single virus (Van Regenmortel, 1985). However, not all groups of viruses have been amenable to non-controversial clustering into species or strains of particular species.
The family Potyviridae, which is the largest family of plant viruses, is a good example of how an initially confusing situation has been resolved into coherent grouping of species and genera. Potyviruses are characterized by having filamentous particles of a length of 650-900 nm containing genomic positive-sense linear ssRNA which is expressed as a polyprotein. The family contains six genera which are distinguished on the basis of genome organization, the type of vector responsible for transmission and susceptible hosts. The genus Bymovirus contains 6 virus species with bipartite genomes which are transmitted by soil-inhabiting plasmodiophoromycete fungi. The genera Rymovirus and Tritimovirus contain viruses with monopartite genomes which are transmitted by mites while the genus Potyvirus contains 91 virus species also with monopartite genomes but which are transmitted by aphids. The genus Ipomovirus contains one species transmitted by whiteflies.
Species demarcation among the Potyviridae has always been somewhat problematic. Traditionally, biological criteria like seed transmission, cross-protection, aphid vector specificity, host range and symptomatology were used to classify potyviruses ( Brunt, 1992; Shukla, Ward and Brunt, 1994). Particular criteria, such as the morphology of the cytoplasmic inclusion bodies formed in infected cells, can be applied to species clustering within a genus (Edwardson, 1992). The most frequently used criterion for discrimination among similar plant viruses, namely serological relatedness, proved to be of only limited use ( Bos, 1992; Shukla, Lauricella and Ward, 1992). Sequence analysis has revealed why serological data were often confusing. Potyvirus coat proteins were found to consist of a conserved core sequence, which elicits highly cross-reactive antibodies (Joisson, Dubs and Van Regenmortel, 1992) and a strongly immunogenic N-terminal region which tends to vary among most viruses and which elicits potentially discriminatory antibodies. A complication is that the N-terminal sequence of the coat protein is readily lost by proteolysis when sap extracts are prepared although the virus particles remain intact. Nevertheless, when antibodies are appropriately raised, and when serological tests are well conducted, the results do help to differentiate between species of potyviruses.
It was only when genome organization and sequences were elucidated that demarcation of potyvirus species and the definition of the family structure produced a coherent classification (Ward, Mc Kern, Frenkel and Shukla, 1992; Ward, Weiller, Shukla and Gibbs, 1995). Complete sequences of the genomes of many potyviruses are now available and there are more than 220 potyvirus coat protein sequences available in the database. Extensive sequence comparisons among these sequences have shown that the application of such quantitative taxonomy to all members of the family Potyviridae results in a clear cut distinction between each of the different taxonomic levels ; strains, species, and genera (Shukla, Ward and Brunt, 1994). Fig. 2 shows the discontinuous distribution of pairwise similarities between coat protein sequences of different potyviruses. The “minima”, or gaps between the peaks, provide the necessary “cut-off” values that allow the criterion to be used. It should be stressed, however, that such a clear-cut distinction between strains, species and genera need not necessarily be present in other virus families.
The current discriminatory characters, summarized as those characters which would be taken to indicate that two species are distinct are listed in Table 1. It is clear that no one criterion has an absolute supremacy over others, some are more informative and discriminate better or they are easier to acquire, but it is the sum of the information accumulated that has built up a clear and generally accepted taxonomy for potyviruses.
Species of the Family Picornaviridae
The virions of picornaviruses are small isometric particles, 30 nm in diameter, containing a single molecule of single-stranded RNA. The capsid of most picornaviruses is composed of 60 identical protomers, each consisting of three surface proteins, 1B, 1C and 1D, and of an internal protein, 1A. Proteins 1A, 1B, 1C and 1D are also named VP4, VP2, VP3 and VP1 respectively. The fine structure of these proteins varies in the six genera of the family. The genus Enterovirus contains eight species: Bovine enterovirus (2 serotypes), Human enterovirus A (10 serotypes), Human enterovirus B (36 serotypes), Human enterovirus C (11 serotypes), Human enterovirus D (2 serotypes), Poliovirus (3 serotypes), Porcine enterovirus A (1 serotype) and Porcine enterovirus B (2 serotypes). Members of an enterovirus species share greater than 70% amino acid identity in the structural proteins and non-structural proteins 2C+ 3CD; they also share a limited range of natural hosts and host cell receptors and multiply primarily in the gastrointestinal tract.
The genus Rhinovirus is closely related to the genus Enterovirus and contains two species: Human rhinovirus A (18 serotypes) and Human rhinovirus B (3 serotypes). In addition, 82 rhinovirus serotypes have not yet been assigned to a species. Members of a rhinovirus species share greater than 70% amino acid identity in the structural proteins and the non-structural proteins 2C+3CD and have a similar susceptibility of receptor attachment to inhibition by pocket-binding antiviral agents. Human rhinoviruses cause the common cold and upper and lower respiratory tract illness in human.
The genus Cardiovirus contains two species: Encephalomyocarditis virus and Theilovirus, the members of which cause encephalitis and myocarditis in different host species and share greater than 70% amino acid identity in structural and non-structural proteins 2C+3CD.
The genus Aphthovirus contains two species: Equine rhinitis A virus (1 serotype) and Foot-and-mouth disease virus (7 serotypes). Members of an aphthovirus species share greater than 50% amino acid identity in the structural and non-structural proteins and greater than 70% amino acid identity in the non-structural proteins 2C+3CD; they also share a natural host range and a common genome layout.
The genus Hepatovirus has only one species: Hepatitis virus A which differs from other picornaviruses by the small size of its protein 1A and by unique genome characteristics. The virus infects hepatocytes of primates and causes fever and jaundice but not chronic hepatitis.
The genus Parechovirus contains a single species: Human Parechovirus (2 serotypes) which differs from other picornaviruses by having less than 30% amino acid identity in the viral proteins. Throughout the six genera, the members of a picornavirus species are usually antigenically related and share a limited range of hosts and cellular receptors, an essentially identical genome map and a significant degree of compatibility in genetic recombination.
In formal virus taxonomy, the names of orders, families, subfamilies and genera are always printed in italics and the first letters of the names are capitalized. At its meeting in San Diego in March 1998, The Executive Committee of the ICTV extended this practice to the names of species taxa to give a clear indication that the species name has been approved as the official name (Pringle, 1998).
The new rule 3.40 of the International Code of Virus Classification and Nomenclature is as follows: “Species names are printed in italics and have the first letter of the first word capitalized. Other words are not capitalized unless they are proper nouns, or parts of proper nouns.”
This rule applies when the species name is used to refer to a taxonomic entity, i.e., an abstraction corresponding to a taxon in the classification. Examples of correct spelling and typographical style for the corresponding taxonomic entities are Tobacco mosaic virus, Poliovirus and Murray River encephalitis virus (River is a proper noun).
It should be stressed that italics and capital letters need to be used only if the species name refers to a taxonomic category, this is the case, for instance, when the virus used in a study is described in the Materials and Methods section of a paper as a member of a particular species, e.g., Poliovirus, genus Enterovirus, family Picornaviridae. Such taxonomic names do not refer to physical entities like the virions in a preparation or the particles in an electron micrograph. It is not possible to centrifuge the family Picornaviridae, the genus Enterovirus or the species Poliovirus for abstractions cannot be centrifuged. When referring to concrete viral objects such as virions, italics and capital initial letters are not needed and the names are written in lower case Roman script. This corresponds to informal vernacular usage and is appropriate for instance when picornaviruses (not italicized) or poliovirus particles are being centrifuged or are visualized in a microscope. This also applied when the names are used in adjectival form, for instance tobacco mosaic virus polymerase.
The use of italics for the name of a species as a taxonomic entity will clearly signal that it has the status of an officialy recognized species. When the taxonomic status of a new putative species is uncertain or its positioning within an established genus has not been clarified, it will be considered a “tentative” species and its name will not be given in italics, although its initial letter will be capitalized. At a later stage transition to italicisation will then signal recognition of full species status.
A uniform italicized spelling of all taxonomic levels from Order to Species will reinforce in a visible manner the status of virus species as a taxonomic entity. This new rule also removes some past oddities in orthography of species names. When a virus species name contained a Latin host name it was customary to use italics and capitals for this part of the virus name. However, when the host name was the same in botanical Latin and in English (e.g., Iris) it was unclear what the form should be. The new orthography removes such ambiguities.
Scientific names in biology are usually latin words and the use of italics indicates the Latin origin. It is a moot point whether the genus names Enterovirus or Tobamovirus should be considered Latin words, and the use of italics in such cases is simply a convenient way to indicate that these terms refer to formal taxa. The use of italics for species names serves the same function.
In biology, scientific names of organisms always include the genus name together with the species epithet. Many plant virologists tend to favour such a binomial system and will refer to Tobacco mosaic tobamovirus or Tobacco etch potyvirus. The advantage of such binomials is that it provides additional information about the virus properties in terms of the genus characteristics and that the name ends in- virus. Animal virologists are reluctant to use such a binomial system and will point out that Influenza A influenzavirus A is certainly an odd name. The rat Rattus rattus is equally odd and it cannot be excluded that in the future, virologists may opt for the binomial system of nomenclature used in the whole of biology.
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