The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks

Abstract

Virus taxonomy emerged as a discipline in the middle of the twentieth century. Traditionally, classification by virus taxonomists has been focussed on the grouping of relatively closely related viruses. However, during the past few years, the International Committee on Taxonomy of Viruses (ICTV) has recognized that the taxonomy it develops can be usefully extended to include the basal evolutionary relationships among distantly related viruses. Consequently, the ICTV has changed its Code to allow a 15-rank classification hierarchy that closely aligns with the Linnaean taxonomic system and may accommodate the entire spectrum of genetic divergence in the virosphere. The current taxonomies of three human pathogens, Ebola virus, severe acute respiratory syndrome coronavirus and herpes simplex virus 1 are used to illustrate the impact of the expanded rank structure. This new rank hierarchy of virus taxonomy will stimulate further research on virus origins and evolution, and vice versa, and could promote crosstalk with the taxonomies of cellular organisms.

Fig. 1. A comparison of the ICTV taxonomic rank hierarchy in 1991–2017 and 2019.

Taxonomic ranks are shown in relation to the distribution pattern of taxa. The number of taxa assigned to each rank (as recorded in the current ICTV Master Species List, release 2018b, MSL34 (ref. )) are shown in white font on the 15-rank structure. When the ranks are described as a hierarchy, the species rank is often referred to as the lowest rank and the realm rank as the highest rank. However, when the ranks are used as phylogenetic terms, the realm rank can be described as basal and the species rank as apical or terminal. Both conventions are used in this Consensus Statement. Black arrows, ranks common to the five- and 15-rank structure; pink arrows, ranks introduced in the 15-rank structure.

Fig. 2. Classification of EBOV, SARS-CoV and herpes simplex virus 1 in the 15-rank taxonomic hierarchy.

Intra-cluster virus divergence, which increases from the virus to the species rank to the realm rank, is represented by the increasing width of the respective rectangles, which are not drawn to scale. EBOV is most closely related to, but distinct from, Bombali, Bundibugyo, Reston, Sudan and Taï Forest viruses, which belong to separate species included in the Ebolavirus genus. SARS-CoV is one of several closely related coronaviruses isolated from humans and animals, such as palm civets and bats, and are included in the species Severe acute respiratory syndrome-related coronavirus. Herpes simplex virus 1 is one of two human herpesviruses belonging to different species in the Simplexvirus genus. Ranks that were introduced with the extended rank structure are indicated by an asterisk.