Recently, however, there has come a move to introduce higher-level taxa such as the "supergroup" or family into plant virus classification schemes, in line with animal and human virus classification. There has also been an increasing use of genome sequence data for establishing relationships between viruses: some of these analyses have been especially illuminating in that they have revealed distant relationships between several plant virus groups and some animal virus families.
Two notable examples are the relationships between picornaviruses, comoviruses and potyviruses; and between caulimoviruses, retroviruses and hepadnaviruses.
Such sequence comparisons have largely made use of strongly-conserved predicted protein sequences that are related to replication; the inference of the analyses is that the replicases of individual viruses within these separate groups of viruses have diverged evolutionarily from a common source.
Similar sequence comparisons have been used to estimate evolutionary distances between, and make taxonomic proposals for, many different organisms, ranging from bacteria to plants to hominoids. A common approach in these studies has been the construction of phylogenetic trees for the organisms in question: these have been used to clarify lines of evolutionary descent of the organisms, and illustrate relationships with taxonomic significance. It is interesting that very few such analyses have been performed for viruses in general, and plant viruses in particular - probably both because of a general reluctance to speculate upon virus evolutionary processes, and because of a lack of sequence data. The analyses that have been done have also concentrated mainly on distance data - that is, pairwise similarity or difference estimates - for use in phenetic comparisons, rather than using the cladistic techniques which have become popular in animal and plant systematics recently.
Formerly such investigations were performed using precipitin techniques; recently, however, ELISA techniques have been used for SDI determinations: Jaegle and van Regenmortel demonstrated the general use of the technique, and Dekker et al. (1988) and Pinner et al. (1992) put it to use in determining relationships among maize streak virus (MSV) and related geminiviruses of cereals and grasses.
SDI data have been used for taxonomic purposes, in that "clusters" of related viruses can be differentiated from less-related species (van Regenmortel, 1982); they have also been used to construct relationship dendrograms: Koenig (1976) presented a comprehensive analysis of the serology of 13 tymoviruses, which included a novel "loop structure".
In fact, one can take a table of reciprocal SDI values for a group of viruses and analyse it directly for construction of a dendrogram. The SDI data is conceptually similar to the pairwise DNA hybridisation data that has often been used for construction of phylogenetic trees); thus, one may also root the dendrogram to make it into a tree, and speculate on the phylogeny of virus coat proteins from serological data.
That the approach may be comfortably used to define a taxonomic group - or genus - is shown by Gibbs (1980), where a tree that includes the furovirus beet necrotic yellow vein virus (BNYVV) clearly separates this from definitive tobamoviruses.
Fauquet et al. (1985) have also claimed that the amino acid compositions of most virus coat proteins fell into groups closely corresponding to accepted plant virus taxonomic groups: thus determination of the composition of a virus coat protein may well be a most useful exercise from a taxonomic point of view, as such data appears to define the virus taxonomic group (=genus); however, it is still an analytical undertaking of some magnitude, and difficult for most laboratories.
One group of viruses that have been studied by restriction mapping and restriction fragment pattern differences are the geminiviruses of maize and cereals (Clarke et al., 1989; Kirby et al., 1989; Rybicki et al., 1989; Hughes et al., 1990).
It is possible to directly convert a series of restriction fragment patterns of different viral DNAs on an electropherogram into a digital data matrix and analyse this by cladistic techniques; it is also possible to construct difference tables (Clarke et al., 1989; Rybicki et al., 1989) and analyse them phenetically. Detailed restriction maps of related virus DNAs may be transformed into distance matrices (Kirby et al., 1989; Hughes et al., 1990), or also treated as digital information for cladistic analysis.
With recent developments in cDNA synthesis technology, it is also possible to routinely map RNA viruses by restriction enzyme cleavage: for instance, DNA fragments obtained from human rhinoviruses by polymerase chain reaction (PCR) amplification of cDNA have been used for typing of the virus isolates by restriction endonuclease cleavage patterns; PCR has also been used for amplification and typing of viroids from cDNA. Restriction map data falls down, however, at demonstrating relationships beyond the level of about 30% sequence difference (Kirby et al., 1989); thus map comparisons may only be useful for sub-group level comparisons.
These examples could be taken as leading inexorably to a proposal for the establishment of plant virus taxa right up to the "super-familial" level: however, plant virus genome relationships are not as simple as are the phylogenetic relationships of some of their constituent parts, and any taxon higher than the familial level would be very hard to justify. For example, the Bromoviridae all have a similar genomic structure and organisation, and it could be confidently asserted that all components of all of them have a common source. Tobamoviruses also all have a similar genetic organisation. Their putative replicases are related to those of the Bromoviridae; however, there is no demonstrable relationship between any other genes of the two groups of viruses, and the genetic organisation is markedly different. Moreover, both sets of viruses share sequence similarity with the animal alphaviruses, in the family Togaviridae, which have even less similar genetic organisation. Should these viruses all be grouped in a "superfamily"?
Much the same can be said for the picorna-, como- and potyviruses. Goldbach (1987) has proposed that simple viruses have evolved by building up modules into genomes, and that different "supergroups" can be distinguished by their core modules, which consist of genes related to replication: thus there is a picornavirus-like supergroup, of viruses with similar polymerse/protease core modules, and an alphavirus supergroup, of viruses with similar "nucleotide-binding" protein/replicase cores.