An expert group convened by the International Committee on Taxonomy of Viruses (ICTV) in 2016 debated and affirmed a policy to allow viruses known from their genome sequences alone to be incorporated into virus taxonomy [1]. This policy enables taxonomic assignments without requiring prior knowledge of a virus phenotypic properties, such as host range, type of disease, virus vector, pathogenicity, etc. Nevertheless the use of only non-processed genome sequences and their compairement after alignment leads to the situations when highly clinically diverse viruses are characterized as belonging to the same species because their genomes differ in only a small degree. Actually, it motivates virologists to separate their taxonomic systems from classification suited for clinicysts, plant biologists, etc.
In 2022 a group of basic and clinical virologists, bioinformaticians, and evolutionary and structural biologists met in Oxford, United Kingdom, to develop a consensus on methodologies used for virus classification [2]. They formulated four principles of virus taxonomy: 1) virus taxa should be monophyletic; 2) phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks; 3) alternative classifications that consider phenotypic attributes, such as being vector-borne, infecting a certain type of host or displaying specific pathogenicity, may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships; 4) evolution based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy under suitable control [2].
The second principle suggests that such classification schemes based on the use of phenotypic and ecological features cannot be considered or called taxonomies. It was already mentioned in [3] that in natural virus system these properties should be directly derived from the place of the virus genome in the system which can have the form of a table. It was also shown that such properties as virus vectors can be really derived to some extent from their place in the table for the genus Flavivirus [4]. The type of disease is defined by the position in the table for the cases of Human papillomaviruses and Caulimoviruses, and the viral hosts is defined by the position in the table for the Caulimoviruses and Polyomoviruses, etc. [3]. This permits to avoid or at least to delay the “divorse” of taxonomy based on the use of virus genomes only and of classification systems useful for clinicycts, plant biologists and other specialists (as it was stated in [2]: “numerous widely used clinical or veterinary virus designations cannot be supported by taxonomic assignments but often better serve clinical and regulatory purposes”).
It seems that such a divorse is partly connected with the difficulty which was mentioned by virologists in [2]: diversity of clinical symptoms is observed for the viruses considered as representing the member of the same species on the basis of the close similarity of their aligned genome sequencies. As the example they considered the case of the species Enterovirus C which strains have essentially distinct properties. This was considered as a form of “mismatch” that can occur between taxonomy and classification desired by clinicians, veterinarians, agronomists, etc.
The species Enterovirus C, in the family Picornaviridae, includes a clinically highly diverse range of member viruses, such as poliovirus types 1, 2, and 3 causing poliomyelitis, as well as also other enterovirus types which can cause different diseases of gastrointestinal tract, repiratory and also of nervous system. The assignment of these viruses to the same species is motivated by their high degree of sequence similarity and their ability to recombine [2, 6]. Note, that the poliovirus-associated neuroinvasive phenotype ultimately derives from a difference in the receptors used by these viruses, which is caused by only of small difference in the gene encoding the capsid protein VP1.
Here, using the example of Enterovirus C viruses, we show that this difficulty disappears when using an approach to constructing a natural viral system using the Neural Replicator Analysis (NRA) [5]. The main advantage of this approach is that it allows the nonlinear preprocessing of original viral genome sequences by converting them into replicator tables and replicator transmitted motifs that exhibit distinct periodic properties [3,4.5].