Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses

The vast majority of described prokaryotic viruses have double-stranded or single-stranded DNA or double-stranded RNA genomes. Until 2020, a mere four prokaryotic single-stranded, positive -sense RNA viruses have been classified in two genera (Riboviria; Lenarviricota; Allassoviricetes; Leviviridae). Several recent metagenomic and metatranscriptomic studies revealed a vastly greater diversity of these viruses in prokaryotic soil communities than ever anticipated. Phylogenetic analysis of these newly discovered viruses prompted the reorganization of class Allassoviricetes, now renamed Leviviricetes, to include two orders, Norzivirales and Timlovirales, and a total of six families, 428 genera and 882 species. Here we outline the new taxonomy of Leviviricetes, approved and ratified in 2021 by the International Committee on Taxonomy of Viruses, and describe open-access hidden Markov models to accommodate the anticipated identification and future classification of hundreds, if not thousands, of additional class members into this new taxonomic framework.

Automated summary

The majority of prokaryotic viruses have double-stranded or single-stranded DNA or RNA genomes. However, recent studies have revealed a much greater diversity of single-stranded positive-sense RNA viruses in prokaryotic soil communities than previously thought. Phylogenetic analysis has led to the reorganization of the class Allassoviricetes into Leviviricetes, with two new orders and a total of six families, 428 genera, and 882 species.