Abstract
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.
Highlights
The genome of the positive-sense single-stranded RNA (+ssRNA) phage MS2, which infects Escherichia coli bacteria, was the first of any biological entity ever to be sequenced [3]
To support the continued expansion of the newly organized class Leviviricetes within phylum Lenarviricota, hidden Markov models (HMMs) generated from the expanded number of available bacteria-infecting positive-sense single-stranded RNA (+ssRNA) virus proteins are available at Figshare: https://doi.org/10.6084/m9.figshare.12745394.v1
In the 1971 First Report of the International Committee on Nomenclature of Viruses (ICNV; today the International Committee on Taxonomy of Viruses [ICTV]), phage MS2 was classified as a member of the ‘ribophage group’ [4], which in the Second Report (1976) was considered a genus in the -new family Leviviridae [unitalicized at the time] [5]
Summary
The genome of the positive-sense single-stranded RNA (+ssRNA) phage MS2, which infects Escherichia coli bacteria, was the first of any biological entity ever to be sequenced [3]. To support the continued expansion of the newly organized class Leviviricetes within phylum Lenarviricota, hidden Markov models (HMMs) generated from the expanded number of available bacteria-infecting positive-sense single-stranded RNA (+ssRNA) virus proteins are available at Figshare: https://doi.org/10.6084/m9.figshare.12745394.v1. To create a novel taxonomic framework for bacteria- infecting +ssRNA viruses, 1868 genomic sequences tentatively identified as such in [10, 12,13,14] were obtained from the US National Center for Biotechnology Information (NCBI).
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