Can the natural system of viruses reconcile the current taxonomy with an alternative classification useful to clinicians?

Abstract

In 2022, a group of basic and clinical virologists, bioinformaticians, and evolutionary and structural biologists met in Oxford, UK, to develop a consensus on methodologies used to classify viruses. They concluded that virus taxonomy, which is hierarchical and based on evolution, is only one of many possible ways to classify viruses. This taxonomy, while satisfying the four principles they set out, faces difficulties in coordinating with other classification systems useful to clinicians, infectious disease specialists, agronomists, etc. One example discussed is the grouping of different viral strains that cause different diseases into the species Enterovirus C. Here we show that the use of a previously proposed variant of a natural virus classification system based on the use of Neural Replicator Analysis can resolve this contradiction by establishing the fine structure of the Enterovirus C species, in which strains that cause different diseases are placed in several different cells of the binomial table of viruses. A key element in enabling this is the sophisticated preprocessing of the original viral genomes using neural replicators.