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

References

1. Callanan J, Stockdale S, Adriaenssens E, Kuhn J, Pallen M et al. rename one class (leviviricetes - formerly allassoviricetes), rename one order (norzivirales - formerly levivirales), create one new order (timlovirales), and expand the class to a total of six families, 420 genera and 883 species. ICTV TaxoProp 2020.095b; 2021 https://talk.ictvonline.org/files/ictv_official_taxonomy_updates_since_the_8th_report/m/prokaryote-official/12203
2. Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM et al. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021. Arch Virol 2021; 166:2633–2648 [View Article] [PubMed]
   [Google Scholar]
3. Fiers W, Contreras R, Duerinck F, Haegeman G, Iserentant D et al. Complete nucleotide sequence of bacteriophage MS2 RNA: Primary and secondary structure of the replicase gene. Nature 1976; 260:500–507 [View Article] [PubMed]
   [Google Scholar]
4. Wildy P. Classification and nomenclature of viruses. In First report of the International Committee on Nomenclature of viruses Basel, Switzerland: S. Karger; 1971
   [Google Scholar]
5. Fenner F. Classification and nomenclature of viruses. Second report of the International Committee on Taxonomy of Viruses Intervirology 1976; 7:1–115
   [Google Scholar]
6. Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI et al. Global organization and proposed megataxonomy of the virus world. Microbiol Mol Biol Rev 2020; 84:e00061-19 [View Article] [PubMed]
   [Google Scholar]
7. Krupovic M, Kuhn JH, Wang F, Baguero DP, Dolja VV et al. Adnaviria: a new realm for archaeal filamentous viruses with linear A-form double-stranded DNA genomes. J Virol 2021; 95:e0067321
   [Google Scholar]
8. van Duin J, Olsthoorn RCL. Family Leviviridae. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. eds In Virus taxonomy. Ninth report of the International Committee on Taxonomy of Viruses Amsterdam, Netherlands: Elsevier/Academic Press; 2012 pp 1035–1043 https:// talk. ictvonline. org/ ictv- reports/ ictv_ 9th_report/ positive- sense- rna- viruses- 2011/ w/ posrna_ viruses/ 263/leviviridae
   [Google Scholar]
9. Callanan J, Stockdale SR, Shkoporov A, Draper LA, Ross RP et al. Biases in viral metagenomics-based detection, cataloguing and quantification of bacteriophage genomes in human faeces, a review. Microorganisms 2021; 9:524 [View Article] [PubMed]
   [Google Scholar]
10. Krishnamurthy SR, Janowski AB, Zhao G, Barouch D, Wang D. Hyperexpansion of RNA bacteriophage diversity. PLoS Biol 2016; 14:e1002409 [View Article] [PubMed]
    [Google Scholar]
11. Zhang T, Breitbart M, Lee WH, Run J-Q, Wei CL et al. RNA viral community in human feces: Prevalence of plant pathogenic viruses. PLoS Biol 2006; 4:e3 [View Article] [PubMed]
    [Google Scholar]
12. Callanan J, Stockdale SR, Shkoporov A, Draper LA, Ross RP et al. Expansion of known ssRNA phage genomes: From tens to over a thousand. Sci Adv 2020; 6:eaay5981 [View Article] [PubMed]
    [Google Scholar]
13. Shi M, Lin X-D, Tian J-H, Chen L-J, Chen X et al. Redefining the invertebrate RNA virosphere. Nature 2016; 540:539–543 [View Article] [PubMed]
    [Google Scholar]
14. Starr EP, Nuccio EE, Pett-Ridge J, Banfield JF, Firestone MK. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. Proc Natl Acad Sci U S A 2019; 116:25900–25908 [View Article] [PubMed]
    [Google Scholar]
15. Li L, Stoeckert CJ, Roos DS. Orthomcl: Identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [View Article] [PubMed]
    [Google Scholar]
16. Loeb T, Zinder ND. A bacteriophage containing RNA. Proc Natl Acad Sci U S A 1961; 47:282–289 [View Article] [PubMed]
    [Google Scholar]
17. August JT, Cooper S, Shapiro L, Zinder ND. RNA phage induced RNA polymerase. Cold Spring Harbor Symposia on Quantitative Biology 1963; 28:95–97 [View Article]
    [Google Scholar]
18. Atkins JF, Steitz JA, Anderson CW, Model P. Binding of mammalian ribosomes to MS2 phage RNA reveals an overlapping gene encoding a lysis function. Cell 1979; 18:247–256 [View Article] [PubMed]
    [Google Scholar]
19. Blumenthal T, Carmichael GG. RNA replication: Function and structure of Qbeta-replicase. Annu Rev Biochem 1979; 48:525–548 [View Article] [PubMed]
    [Google Scholar]
20. Kastelein RA, Remaut E, Fiers W, van Duin J. Lysis gene expression of RNA phage MS2 depends on a frameshift during translation of the overlapping coat protein gene. Nature 1982; 295:35–41 [View Article] [PubMed]
    [Google Scholar]
21. van Duin J. Single-stranded RNA bacteriophages. Calendar R. ed In The Bacteriophages [Internet] Boston, MA: Springer US; 1988 pp 117–167 https://doi.org/10.1007/978-1-4684-5424-6_4
    [Google Scholar]
22. Spiegelman S, Haruna I, Holland IB, Beaudreau G, Mills D. The synthesis of a self-propagating and infectious nucleic acid with a purified enzyme. Proc Natl Acad Sci U S A 1965; 54:919–927 [View Article] [PubMed]
    [Google Scholar]
23. Steitz JA. Polypeptide chain initiation: Nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA. Nature 1969; 224:957–964 [View Article] [PubMed]
    [Google Scholar]
24. International Committee on Taxonomy of Viruses Virus Taxonomy [Internet] 2021
    [Google Scholar]
25. Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM et al. Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020). Arch Virol 2020; 165:2737–2748 [View Article] [PubMed]
    [Google Scholar]