Virus species polemics: 14 senior virologists oppose a proposed change to the ICTV definition of virus species

Abstract

The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) has recently decided to modify the current definition of virus species (Code of Virus Classification and Nomenclature Rule 3.21) and will soon ask the full ICTV membership (189 voting members) to ratify the proposed controversial change. In this discussion paper, 14 senior virologists, including six Life members of the ICTV, compare the present and proposed new definition and recommend that the existing definition of virus species should be retained. Since the pros and cons of the proposal posted on the ICTV website are not widely consulted, the arguments are summarized here in order to reach a wider audience.

Revisiting the classification of curtoviruses based on genome-wide pairwise identity

“…In the case of the curtoviruses, the species demarcation criteria that we have proposed suggest the existence among the currently known curtoviruses of only three monophyletic species (Beet curly top virus, Horseradish curly top virus and Spinach severe curly top virus) that are also distinguishable by the host species from which they have been obtained. Therefore, although our genome-sequencebased approach to virus classification is not universally supported [39], it does, in this case at least, yield a completely objective classification system that is consistent with the observed biological properties of curtoviruses.…”

“…The species demarcation criteria we have applied here for curtoviruses and that which we have applied previously to mastreviruses [25] are both predominantly based on pairwise full-genome nucleotide sequence identities coupled with phylogenetic support. This approach has been critiqued by Van Regenmortel et al [39], who favour the concept of a virus species being a polythetic class of viral isolates constituting a replicating lineage in a particular ecological niche and argue against a proposal by A. King, M. Adams, E. Lefkowitz and E. Carstens (proposal 2011.002sG), which states 'A species is a monophyletic group of viruses whose properties can be distinguished from other species by multiple criteria' (the criteria include natural and experimental host ranges, pathogenicity, vector specificity, cell and tissue tropism and degrees of relatedness of their genes and genomes).…”

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

“…Over the last decade debates regarding the classification of some groups, such as viruses, have been the subject of passionate exchanges of views. Indeed, within the virus community discussions range from the definition of what a virus species is (van Regenmortel et al, 2013) to the possibility that certain viruses might represent a distinct fourth domain of life (Bandea, 2009;Williams et al, 2011;Philippe et al, 2013;Pennisi, 2013;Raoult, 2013). Finally, these discussions are complicated by the connection between viruses and a number of mobile genetic elements (more commonly referred to as transposable elements, TEs) that have been characterized in both prokaryotic and eukaryotic genomes (Weiss, 2006;Stoye et al, 2012;Desnues et al, 2012;Yutin et al, 2013).…”

Phylogenetic and Genome-Wide Pairwise Distance Analysis of the Genus Luteovirus

“…The genetic re-assortment and recombination, although, contributed to the formation of relatively stable viral entities with distinguishable biological properties, create genomes with mosaic / multiple features. The polythetic or cluster class (van Regenmortel et al, 2013), thus, could not be distinguished if one or few ORFs are considered. Whole genome information may distinguish them from other related viruses from which they evolved.…”