Is it time to retire the genus Rymovirus from the family Potyviridae?
In the most recent Report of the International Committee on Taxonomy of Viruses (9th Report, 2011) (King et al., Virus Taxonomy, Elsevier, New York, 2011) the family Potyviridae is described as comprising seven genera - Potyvirus, Ipomovirus, Macluravirus, Rymovirus, Tritimovirus, Brambyvirus and Bymovirus - despite previous suggestions questioning the validity of the taxonomic status of the genus Rymovirus. Since then the ICTV website records that an eighth genus Poacevirus has been approved for the Potyviridae family. The creation of the genus Rymovirus at the 1990 Potyvirus Taxonomy Workshop in Braunschweig, Germany was based on two things: (i) the incorrect assumption that the genomes of all mite-transmitted members of the Potyviridae would have strong sequence similarity to that of wheat streak mosaic virus, the only mite-transmitted member of this genus for which sequence data were available at that time, and (ii) that the genus should be named Rymovirus (based on a virus for which there was no sequence information) rather than a name based on wheat streak mosaic virus (e.g., "Whestremovirus") because ryegrass mosaic virus (RGMV) was the first mite-transmitted virus to be described and thus should take precedence. When sequence data for RGMV became available in 1995, these data showed that RGMV was very different from wheat streak mosaic virus (WSMV) and should not be assigned to the same genus. WSMV was subsequently re-assigned to a new genus, Tritimovirus, while the genus Rymovirus was retained. In this author's opinion, this retention is not justified, and the removal of Rymovirus as a distinct genus in the family Potyviridae is recommended. There may be merit when assigning it to the genus Potyvirus in sequestering these viruses in a rymovirus subgroup, as is done with other potyviruses, to reflect their different mode of transmission.
Arch Virol. 2017 Jul;162(7):2175-2179. doi: 10.1007/s00705-017-3301-9. Epub 2017 Mar 7.
Capulavirus and Grablovirus: two new genera in the family Geminiviridae.
Varsani A, Roumagnac P, Fuchs M, Navas-Castillo J, Moriones E, Idris A, Briddon RW, Rivera-Bustamante R, Murilo Zerbini F, Martin DP.
Geminiviruses are plant-infecting single-stranded DNA viruses that occur in most parts of the world. Currently, there are seven genera within the family Geminiviridae (Becurtovirus, Begomovirus, Curtovirus, Eragrovirus, Mastrevirus, Topocuvirus and Turncurtovirus). The rate of discovery of new geminiviruses has increased significantly over the last decade as a result of new molecular tools and approaches (rolling-circle amplification and deep sequencing) that allow for high-throughput workflows. Here, we report the establishment of two new genera: Capulavirus, with four new species (Alfalfa leaf curl virus, Euphorbia caput-medusae latent virus, French bean severe leaf curl virus and Plantago lanceolata latent virus), and Grablovirus, with one new species (Grapevine red blotch virus). The aphid species Aphis craccivora has been shown to be a vector for Alfalfa leaf curl virus, and the treehopper species Spissistilus festinus is the likely vector of Grapevine red blotch virus. In addition, two highly divergent groups of viruses found infecting citrus and mulberry plants have been assigned to the new species Citrus chlorotic dwarf associated virus and Mulberry mosaic dwarf associated virus, respectively. These species have been left unassigned to a genus by the ICTV because their particle morphology and insect vectors are unknown.
Arch Virol. 2017 Jun;162(6):1819-1831. doi: 10.1007/s00705-017-3268-6. Epub 2017 Feb 17.
Revisiting the taxonomy of the family Circoviridae: establishment of the genus Cyclovirus and removal of the genus Gyrovirus.
Rosario K, Breitbart M, Harrach B, Segalés J, Delwart E, Biagini P, Varsani A.
The family Circoviridae contains viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, including the smallest known autonomously replicating, capsid-encoding animal pathogens. Members of this family are known to cause fatal diseases in birds and pigs and have been historically classified in one of two genera: Circovirus, which contains avian and porcine pathogens, and Gyrovirus, which includes a single species (Chicken anemia virus). However, over the course of the past six years, viral metagenomic approaches as well as degenerate PCR detection in unconventional hosts and environmental samples have elucidated a broader host range, including fish, a diversity of mammals, and invertebrates, for members of the family Circoviridae. Notably, these methods have uncovered a distinct group of viruses that are closely related to members of the genus Circovirus and comprise a new genus, Cyclovirus. The discovery of new viruses and a re-evaluation of genomic features that characterize members of the Circoviridae prompted a revision of the classification criteria used for this family of animal viruses. Here we provide details on an updated Circoviridae taxonomy ratified by the International Committee on the Taxonomy of Viruses in 2016, which establishes the genus Cyclovirus and reassigns the genus Gyrovirus to the family Anelloviridae, a separate lineage of animal viruses that also contains circular ssDNA genomes. In addition, we provide a new species demarcation threshold of 80% genome-wide pairwise identity for members of the family Circoviridae, based on pairwise identity distribution analysis, and list guidelines to distinguish between members of this family and other eukaryotic viruses with circular, ssDNA genomes.
Arch Virol. 2017 May;162(5):1447-1463. doi: 10.1007/s00705-017-3247-y. Epub 2017 Feb 2.
50 years of the International Committee on Taxonomy of Viruses: progress and prospects.
Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert ML, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Orton RJ, Smith DB, Gorbalenya AE, Davison AJ.
We mark the 50th anniversary of the International Committee on Taxonomy of Viruses (ICTV) by presenting a brief history of the organization since its foundation, showing how it has adapted to advancements in our knowledge of virus diversity and the methods used to characterize it. We also outline recent developments, supported by a grant from the Wellcome Trust (UK), that are facilitating substantial changes in the operations of the ICTV and promoting dialogue with the virology community. These developments will generate improved online resources, including a freely available and regularly updated ICTV Virus Taxonomy Report. They also include a series of meetings between the ICTV and the broader community focused on some of the major challenges facing virus taxonomy, with the outcomes helping to inform the future policy and practice of the ICTV.
Arch Virol. 2017 May;162(5):1441-1446. doi: 10.1007/s00705-016-3215-y. Epub 2017 Jan 11.
Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2017).
Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfaçon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ.
This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2017.
Arch Virol. 2017 Apr 22. doi: 10.1007/s00705-017-3358-5. [Epub ahead of print]
Adriaenssens EM, Krupovic M, Knezevic P, Ackermann HW, Barylski J, Brister JR, Clokie MR, Duffy S, Dutilh BE, Edwards RA, Enault F, Jang HB, Klumpp J, Kropinski AM, Lavigne R, Poranen MM, Prangishvili D, Rumnieks J, Sullivan MB, Wittmann J, Oksanen HM, Gillis A, Kuhn JH.
The prokaryotic virus community is represented at the International Committee on Taxonomy of Viruses (ICTV) by the Bacterial and Archaeal Viruses Subcommittee. Since our last report , the committee composition has changed, and a large number of taxonomic proposals (TaxoProps) were submitted to the ICTV Executive Committee (EC) for approval.
Arch Virol. 2017 Apr;162(4):1153-1157. doi: 10.1007/s00705-016-3173-4. Epub 2016 Dec 31. No abstract available.
Taxonomy of the order Mononegavirales: update 2017.
Amarasinghe GK, Bào Y, Basler CF, Bavari S, Beer M, Bejerman N, Blasdell KR, Bochnowski A, Briese T, Bukreyev A, Calisher CH, Chandran K, Collins PL, Dietzgen RG, Dolnik O, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Fang Q, Formenty P, Fouchier RA, Ghedin E, Harding RM, Hewson R, Higgins CM, Hong J, Horie M, James AP, Jiāng D, Kobinger GP, Kondo H, Kurath G, Lamb RA, Lee B, Leroy EM, Li M, Maisner A, Mühlberger E, Netesov SV, Nowotny N, Patterson JL, Payne SL, Paweska JT, Pearson MN, Randall RE, Revill PA, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Smither SJ, Song Q, Stone DM, Takada A, Terregino C, Tesh RB, Tomonaga K, Tordo N, Towner JS, Vasilakis N, Volchkov VE, Wahl-Jensen V, Walker PJ, Wang B, Wang D, Wang F, Wang LF, Werren JH, Whitfield AE, Yan Z, Ye G, Kuhn JH.
In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Arch Virol. 2017 Apr 7. doi: 10.1007/s00705-017-3311-7. [Epub ahead of print]