Viroid taxonomy: state of the art and perspectives in the high-throughput sequencing era

Proposed in the early 1990s (Elena et al., Proc. Natl. Acad. Sci. USA 1991), the first viroid classification scheme that grouped viroids into species was officially adopted in 1995 by the International Committee on Taxonomy of Viruses (ICTV, https://talk.ictvonline.org). Higher taxa (genera and family) were then proposed (Flores et al., Arch. Virology 1998) and nowadays 32 species, five genera and the two families (Pospiviroidae and Avsunviroidae) have been created by ICTV. As a general rule, ICTV demarcating criteria for viroid species include sequence identity below 90% with respect to members of other viroid species, together with different biological features. While the first criterion is relatively easy to apply, this is not the case for the second, the application of which is generally time-consuming, particularly for viroids i) with restricted or similar host range, ii) inducing latent infections, and/or iii) infecting woody plants. In the last few years, the availability of high-throughput sequencing technologies (HTS) has allowed discovery of several new viroids, especially from latently-infected woody hosts. In the absence of the biological data requested for their proper classification, including autonomous replication and systemic trafficking, several of these viroids are still considered tentative species, a situation that most likely will not change in the short term if not even worsens, as the list of unclassified viroids becomes longer. The strengths and weaknesses of the current viroid species demarcation criteria adopted by ICTV, along with the opportunity of proposing an order, Viroidales, as the higher taxonomic rank for viroids, will be discussed.