Guidance for creating individual and batch latinized binomial virus species names

References

1. International Commission on Zoological Nomenclature International Code of Zoological Nomenclature, Fourth edition. London, UK: The International Trust for Zoological Nomenclature 1999; 2012
   [Google Scholar]
2. Linnaeus C. Species plantarum Stockholm, Sweden: Laurentius Salvius; 1753
   [Google Scholar]
3. Parker CT, Tindall BJ, Garrity GM. International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2008 revision). Int J Syst Evol Microbiol 2019; 69:S1–S111 [View Article]
   [Google Scholar]
4. Turland NJ, Wiersema JH, Barrie FR. International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159 Koeltz Botanical Books; 2017
   [Google Scholar]
5. International Committee on Taxonomy of Viruses Executive Committee The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks. Nat Microbiol 2020; 5:668–674 [View Article]
   [Google Scholar]
6. Calisher CH, Mahy BWJ. Taxonomy: get it right or leave it alone. Am J Trop Med Hyg 2003; 68:505–506 [View Article] [PubMed]
   [Google Scholar]
7. Kuhn JH, Jahrling PB. Clarification and guidance on the proper usage of virus and virus species names. Arch Virol 2010; 155:445–453 [View Article]
   [Google Scholar]
8. Van Regenmortel MHV. Viruses are real, virus species are man-made, taxonomic constructions. Arch Virol 2003; 148:2481–2488 [View Article]
   [Google Scholar]
9. 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]
   [Google Scholar]
10. Zerbini FM, Siddell SG, Mushegian AR, Walker PJ, Lefkowitz EJ et al. Differentiating between viruses and virus species by writing their names correctly. Arch Virol 2022; 167:1231–1234 [View Article]
    [Google Scholar]
11. Gibbs A. Binomial nomenclature for virus species: a long view. Arch Virol 2020; 165:3079–3083 [View Article]
    [Google Scholar]
12. Hull R, Rima B. Virus taxonomy and classification: naming of virus species. Arch Virol 2020; 165:2733–2736 [View Article]
    [Google Scholar]
13. Postler TS, Clawson AN, Amarasinghe GK, Basler CF, Bavari S et al. Possibility and challenges of conversion of current virus species names to Linnaean binomials. Syst Biol 2017; 66:463–473 [View Article]
    [Google Scholar]
14. Callanan J, Stockdale SR, Adriaenssens EM, Kuhn JH, 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. TaxoProp 2020.095B.R.Leviviricetes; n.d https://ictv.global/filebrowser/download/6027
15. 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]
16. Edgar RC, Taylor J, Lin V, Altman T, Barbera P et al. Petabase-scale sequence alignment catalyses viral discovery. Nature 2022; 602:142–147 [View Article] [PubMed]
    [Google Scholar]
17. Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B et al. Marine DNA viral macro- and microdiversity from pole to pole. Cell 2019; 177:1109–1123 [View Article]
    [Google Scholar]
18. Käfer S, Paraskevopoulou S, Zirkel F, Wieseke N, Donath A et al. Re-assessing the diversity of negative strand RNA viruses in insects. PLoS Pathog 2019; 15:e1008224 [View Article]
    [Google Scholar]
19. Krishnamurthy SR, Janowski AB, Zhao G, Barouch D, Wang D. Hyperexpansion of RNA bacteriophage diversity. PLoS Biol 2016; 14:e1002409 [View Article]
    [Google Scholar]
20. Li C-X, Shi M, Tian J-H, Lin X-D, Kang Y-J et al. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. Elife 2015; 4:e05378 [View Article]
    [Google Scholar]
21. Neri U, Wolf YI, Roux S, Camargo AP, Lee B et al. Expansion of the global RNA virome reveals diverse clades of bacteriophages. Cell 2022; 185:4023–4037 [View Article]
    [Google Scholar]
22. Paraskevopoulou S, Käfer S, Zirkel F, Donath A, Petersen M et al. Viromics of extant insect orders unveil the evolution of the flavi-like superfamily. Virus Evol 2021; 7:veab030 [View Article]
    [Google Scholar]
23. Shi M, Lin X-D, Chen X, Tian J-H, Chen L-J et al. The evolutionary history of vertebrate RNA viruses. Nature 2018; 556:197–202 [View Article]
    [Google Scholar]
24. 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]
    [Google Scholar]
25. 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]
    [Google Scholar]
26. Tisza MJ, Pastrana DV, Welch NL, Stewart B, Peretti A et al. Discovery of several thousand highly diverse circular DNA viruses. Elife 2020; 9:e51971 [View Article]
    [Google Scholar]
27. Zayed AA, Wainaina JM, Dominguez-Huerta G, Pelletier E, Guo J et al. Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome. Science 2022; 376:156–162 [View Article]
    [Google Scholar]
28. Pallen MJ, Telatin A, Oren A. The next million names for Archaea and Bacteria. Trends Microbiol 2021; 29:289–298 [View Article]
    [Google Scholar]
29. Pallen M, Alikhan N-F. Naming the unnamed: over 45,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database. Biology 2021 [View Article]
    [Google Scholar]
30. Callanan J, Stockdale SR, Adriaenssens EM, Kuhn JH, Rumnieks J et al. Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses. Microb Genom 2021; 7:000686 [View Article] [PubMed]
    [Google Scholar]
31. International Committee on Taxonomy of Viruses (ICTV) ICTV Master Species List 2021.v3. Master Species Lists | ICTV 2022 https://ictv.global/msl
    [Google Scholar]
32. R Core Team R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2020 https://www.R-project.org/
33. Gagolewski M. stringi: THE String Processing Package for R; 2020 https://stringi.gagolewski.com/
34. Wickham H. stringr: simple, consistent wrappers for common string operations; 2019 https://CRAN.R-project.org/package=stringr
35. Pallen MJ. Bacterial nomenclature in the era of genomics. New Microbes New Infect 2021; 44:100942 [View Article]
    [Google Scholar]