2020
Binomial nomenclature for virus species: a long view
https://link.springer.com/article/10.1007/s00705-020-04828-8
A brief history of the species concept in virology and an opinion on the proposal to introduce Linnaean binomial virus species names
https://link.springer.com/article/10.1007/s00705-020-04795-0
Changes to virus taxonomy and the Statutes ratified by the International Committee on Taxonomy of Viruses (2020)
https://link.springer.com/article/10.1007/s00705-020-04752-x
Virus taxonomy and classification: naming of virus species
https://link.springer.com/article/10.1007/s00705-020-04748-7
2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
https://link.springer.com/article/10.1007/s00705-020-04731-2
Pleomorphic archaeal viruses: the family Pleolipoviridae is expanding by seven new species
https://link.springer.com/article/10.1007/s00705-020-04689-1
Reorganizing the family Parvoviridae: a revised taxonomy independent of the canonical approach based on host association
https://link.springer.com/article/10.1007/s00705-020-04632-4
Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
https://link.springer.com/article/10.1007/s00705-020-04577-8
Recommendations for the nomenclature of enteroviruses and rhinoviruses
https://link.springer.com/article/10.1007/s00705-019-04520-6
2019
Binomial nomenclature for virus species: a consultation
https://link.springer.com/article/10.1007/s00705-019-04477-6
Proposed revision of the family Secoviridae taxonomy to create three subgenera, “Satsumavirus”, “Stramovirus” and “Cholivirus”, in the genus Sadwavirus
https://link.springer.com/article/10.1007/s00705-019-04468-7
Changes to virus taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2019)
https://link.springer.com/article/10.1007/s00705-019-04306-w
Michael Adams: new life member of the International Committee on Taxonomy of Viruses (ICTV)
https://link.springer.com/article/10.1007/s00705-019-04290-1
Taxonomy of the order Mononegavirales: update 2019
https://link.springer.com/article/10.1007/s00705-019-04247-4
Taxonomy of the order Bunyavirales: update 2019
https://link.springer.com/article/10.1007/s00705-019-04253-6
Hepatitis C virus 3b strains in injection drug users in Guangdong Province, China, may have originated in Yunnan Province
https://link.springer.com/article/10.1007/s00705-019-04260-7
Taxonomy of the order Bunyavirales: second update 2018
https://link.springer.com/article/10.1007/s00705-018-04127-3
Taxonomy of the order Mononegavirales: second update 2018
https://link.springer.com/article/10.1007/s00705-018-04126-4
“Tupanvirus”, a new genus in the family Mimiviridae
https://link.springer.com/article/10.1007/s00705-018-4067-4
2018
Increasing the number of available ranks in virus taxonomy from five to ten and adopting the Baltimore classes as taxa at the basal rank
This opinion article makes a case for increasing the number of ranks used in virus taxonomy from the current five to ten (as are used to classify cellular life forms) and placing the Baltimore classes in the p. .
Alexander E. Gorbalenya in Archives of Virology (2018)
Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018)
This article lists the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2018. A total of 451 species, 69 genera, 11 subfamilies, 9 families and . .
Andrew M. Q. King, Elliot J. Lefkowitz, Arcady R. Mushegian… in Archives of Virology (2018)
Alphasatellitidae: a new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites
Nanoviruses and geminiviruses are circular, single stranded DNA viruses that infect many plant species around the world. Nanoviruses and certain geminiviruses that belong to the Begomovirus and Mastrevirusgenera. .
Rob W. Briddon, Darren P. Martin, Philippe Roumagnac… in Archives of Virology (2018)
Virus taxonomy—a taxing task
Ulrich Desselberger in Archives of Virology (2018)
Taxonomy of the family Arenaviridae and the order Bunyavirales: update 2018
In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the up. .
Piet Maes, Sergey V. Alkhovsky, Yīmíng Bào, Martin Beer… in Archives of Virology (2018)
Taxonomy of the order Mononegavirales: update 2018
In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Commi. .
Gaya K. Amarasinghe, Nidia G. Aréchiga Ceballos, Ashley C. Banyard… in Archives of Virology (2018)
Smacoviridae: a new family of animal-associated single-stranded DNA viruses
Smacoviruses have small (∼2.3-2.9 kb), circular single-stranded DNA genomes encoding rolling circle replication-associated proteins (Rep) and unique capsid proteins. Although smacoviruses are prevalent in faec. .
Arvind Varsani, Mart Krupovic in Archives of Virology (2018)
Problems of classification in the family Paramyxoviridae.
Rima B, Collins P, Easton A, Fouchier R, Kurath G, Lamb RA, Lee B, Maisner A, Rota P, Wang LF.
A number of unassigned viruses in the family Paramyxoviridae need to be classified either as a new genus or placed into one of the seven genera currently recognized in this family. Furthermore, numerous new paramyxoviruses continue to be discovered. However, attempts at classification have highlighted the difficulties that arise by applying historic criteria or criteria based on sequence alone to the classification of the viruses in this family. While the recent taxonomic change that elevated the previous subfamily Pneumovirinae into a separate family Pneumoviridae is readily justified on the basis of RNA dependent -RNA polymerase (RdRp or L protein) sequence motifs, using RdRp sequence comparisons for assignment to lower level taxa raises problems that would require an overhaul of the current criteria for assignment into genera in the family Paramyxoviridae. Arbitrary cut off points to delineate genera and species would have to be set if classification was based on the amino acid sequence of the RdRp alone or on pairwise analysis of sequence complementarity (PASC) of all open reading frames (ORFs). While these cut-offs cannot be made consistent with the current classification in this family, resorting to genus-level demarcation criteria with additional input from the biological context may afford a way forward. Such criteria would reflect the increasingly dynamic nature of virus taxonomy even if it would require a complete revision of the current classification.
Arch Virol. 2018 May;163(5):1395-1404. doi: 10.1007/s00705-018-3720-2. DOI: 10.1007/s00705-018-3720-2 PMID: 29372404.
Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.
Adriaenssens EM, Wittmann J, Kuhn JH, Turner D, Sullivan MB, Dutilh BE, Jang HB, van Zyl LJ, Klumpp J, Lobocka M, Moreno Switt AI, Rumnieks J, Edwards RA, Uchiyama J, Alfenas-Zerbini P, Petty NK, Kropinski AM, Barylski J, Gillis A, Clokie MRC, Prangishvili D, Lavigne R, Aziz RK, Duffy S, Krupovic M, Poranen MM, Knezevic P, Enault F, Tong Y, Oksanen HM, Rodney Brister J.
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. 2018 Apr;163(4):1125-1129. doi:10.1007/s00705-018-3723-z. PubMed PMID: 29356990.
Rymovirus: a cautionary tale.
Gibbs AJ, Gibbs MJ.
A recent proposal that the genus Rymovirus be assimilated into the genus Potyvirus is examined, discussed, and rejected. It illustrates the danger of using 'sequence identity' as a proxy for phylogenetic relatedness to distinguish closely related but distinct groups of viruses.
Arch Virol. 2018 Mar;163(3):815-817. doi: 10.1007/s00705-017-3676-7. DOI: 10.1007/s00705-017-3676-7 PMID: 29224129
Recognition of six additional cystoviruses: Pseudomonas virus phi6 is no longer the sole species of the family Cystoviridae.
Mäntynen S, Sundberg LR, Poranen MM.
Cystoviridae is a family of bacterial viruses (bacteriophages) with a tri-segmented dsRNA genome. It includes a single genus Cystovirus, which has presently only one recognised virus species, Pseudomonas virus phi6. However, a large number of additional dsRNA phages have been isolated from various environmental samples, indicating that such viruses are more widespread and abundant than previously recognised. Six of the additional dsRNA phage isolates (Pseudomonas phages phi8, phi12, phi13, phi2954, phiNN and phiYY) have been fully sequenced. They all infect Pseudomonas species, primarily plant pathogenic Pseudomonas syringae strains. Due to the notable genetic and structural similarities with Pseudomonas phage phi6, we propose that these viruses should be included into the Cystovirus genus (and consequently into the Cystoviridae family). Here, we present an updated taxonomy of the family Cystoviridae and give a short overview of the properties of the type member phi6 as well as the putative new members of the family.
Arch Virol. 2018 Apr;163(4):1117-1124. doi: 10.1007/s00705-017-3679-4. DOI: 10.1007/s00705-017-3679-4. PMID: 29260329.
2017
Is it time to retire the genus Rymovirus from the family Potyviridae?
Ward CW.
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.
PMID: 28265774
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.
PMID: 28213872
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.
PMID: 28155197
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.
PMID: 28078475
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]
PMID: 28434098
Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee.
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 [8], 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.
PMID: 28040838
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]
PMID: 28389807
2016
Eric Carstens: new life member of the International Committee on Taxonomy of Viruses (ICTV).
Adams MJ, Davison AJ.
We are delighted to announce that Professor Eric B Carstens has recently been elected as a Life Member of the ICTV. This follows nomination by the whole Executive Committee at its meeting in London in July 2015 and subsequent ratification by the entire voting membership. Eric is currently a Professor in the Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada, and has a particular research interest in large DNA viruses that infect insects.
Arch Virol. 2016 Sep 2.
PMID: 27589978
Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016).
Adams MJ, Lefkowitz EJ, King AM, 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 April 2016.Changes to virus taxonomy (the Universal Scheme of Virus Classification of the International Committee on Taxonomy of Viruses [ICTV]) now take place annually and are the result of a multi-stage process. In accordance with the ICTV Statutes ( https://ictv.global/about/statutes ), proposals submitted to the ICTV Executive Committee (EC) undergo a review process that involves input from the ICTV Study Groups (SGs) and Subcommittees (SCs), other interested virologists, and the EC. After final approval by the EC, proposals are then presented for ratification to the full ICTV membership by publication on an ICTV web site ( https://ictv.global ) followed by an electronic vote. The latest set of proposals approved by the EC was made available on the ICTV website by January 2016 ( https://ictv.global/files/proposals/approved ). A list of these proposals was then emailed on 28 March 2016 to the 148 members of ICTV, namely the EC Members, Life Members, ICTV Subcommittee Members (including the SG chairs) and ICTV National Representatives. Members were then requested to vote on whether to ratify the taxonomic proposals (voting closed on 29 April 2016).
Arch Virol. 2016 Oct;161(10):2921-49. doi: 10.1007/s00705-016-2977-6. Epub 2016 Jul 16. Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ,
PMID: 27424026
Taxonomy of prokaryotic viruses: update from the ICTV bacterial andarchaeal viruses subcommittee.
Krupovic M, Dutilh BE, Adriaenssens EM, Wittmann J, Vogensen FK, Sullivan MB, Rumnieks J, Prangishvili D, Lavigne R, Kropinski AM, Klumpp J, Gillis A, Enault F, Edwards RA, Duffy S, Clokie MR, Barylski J, Ackermann HW, Kuhn JH.
The prokaryotic virus community is represented on the International Committee on Taxonomy of Viruses (ICTV) by the Bacterial and Archaeal Viruses Subcommittee. In 2008, the three caudoviral families Myoviridae, Podoviridae, and Siphoviridae included only 18 genera and 36 species. Under the able chairmanship of Rob Lavigne (KU Leuven, Belgium), major advances were made in the classification of prokaryotic viruses and the order Caudovirales was expanded dramatically, to reflect the genome-based relationships between phages. Today, the order includes six subfamilies, 80 genera, and 441 species. This year, additional changes in prokaryotic virus taxonomy have been brought forward under the new subcommittee chair, Andrew M. Kropinski (University of Guelph, Canada).
Arch Virol. 2016 Apr;161(4):1095-9. doi: 10.1007/s00705-015-2728-0. Epub 2016 Jan 5.
PMID: 26733293
The taxonomy of viruses should include viruses.
Calisher CH
Arch Virol. 2016 May;161(5):1419-22. doi: 10.1007/s00705-016-2779-x. Epub 2016 Feb 25.
Having lost sight of its goal, the International Committee on Taxonomy of Viruses has redoubled its efforts. That goal is to arrive at a consensus regarding virus classification, i.e., proper placement of viruses in a hierarchical taxonomic scheme; not an easy task given the wide variety of recognized viruses. Rather than suggesting a continuation of the bureaucratic machinations of the past, this opinion piece is a call for insertion of common sense in sorting out the avalanche of information already, and soon-to-be, accrued data. In this way information about viruses ideally would be taxonomically correct as well as useful to working virologists and journal editors, rather than being lost, minimized, or ignored.
PMID: 26914357
A taxonomy update for the family Polyomaviridae.
Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses, Calvignac-Spencer S, Feltkamp MC, Daugherty MD, Moens U, Ramqvist T, Johne R, Ehlers B.
Arch. Virol. 2016 Jun;161(6):1739-50. doi: 10.1007/s00705-016-2794-y. Epub 2016 Feb 29.
Many distinct polyomaviruses infecting a variety of vertebrate hosts have recently been discovered, and their complete genome sequence could often be determined. To accommodate this fast-growing diversity, the International Committee on Taxonomy of Viruses (ICTV) Polyomaviridae Study Group designed a host- and sequence-based rationale for an updated taxonomy of the family Polyomaviridae. Applying this resulted in numerous recommendations of taxonomical revisions, which were accepted by the Executive Committee of the ICTV in December 2015. New criteria for definition and creation of polyomavirus species were established that were based on the observed distance between large T antigen coding sequences. Four genera (Alpha-, Beta, Gamma- and Deltapolyomavirus) were delineated that together include 73 species. Species naming was made as systematic as possible - most species names now consist of the binomial name of the host species followed by polyomavirus and a number reflecting the order of discovery. It is hoped that this important update of the family taxonomy will serve as a stable basis for future taxonomical developments.
PMID: 26923930
A proposal to rationalize within-species plant virus nomenclature:benefits and implications of inaction.
Jones RA, Kehoe MA.
Arch Virol. 2016 Jul;161(7):2051-7. doi: 10.1007/s00705-016-2848-1. Epub 2016 Apr 21.
Current approaches used to name within-species, plant virus phylogenetic groups are often misleading and illogical. They involve names based on biological properties, sequence differences and geographical, country or place-association designations, or any combination of these. This type of nomenclature is becoming increasingly unsustainable as numbers of sequences of the same virus from new host species and different parts of the world increase. Moreover, this increase is accelerating as world trade and agriculture expand, and climate change progresses. Serious consequences for virus research and disease management might arise from incorrect assumptions made when current within-species phylogenetic group names incorrectly identify properties of group members. This could result in development of molecular tools that incorrectly target dangerous virus strains, potentially leading to unjustified impediments to international trade or failure to prevent such strains being introduced to countries, regions or continents formerly free of them. Dangerous strains might be missed or misdiagnosed by diagnostic laboratories and monitoring programs, and new cultivars with incorrect strain-specific resistances released. Incorrect deductions are possible during phylogenetic analysis of plant virus sequences and errors from strain misidentification during molecular and biological virus research activities. A nomenclature system for within-species plant virus phylogenetic group names is needed which avoids such problems. We suggest replacing all other naming approaches with Latinized numerals, restricting biologically based names only to biological strains and removing geographically based names altogether. Our recommendations have implications for biosecurity authorities, diagnostic laboratories, disease-management programs, plant breeders and researchers.
PMID: 27101071
Taxonomy of the order Mononegavirales: update 2016.
Arch Virol. 2016 Aug;161(8):2351-60. doi: 10.1007/s00705-016-2880-1. Epub 2016 May 23.
Afonso CL, Amarasinghe GK, Bányai K, Bào Y, Basler CF, Bavari S, Bejerman N,, Blasdell KR, Briand FX, Briese T, Bukreyev A, Calisher CH, Chandran K, Chéng J, Clawson AN, Collins PL, Dietzgen RG, Dolnik O, Domier LL, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Farkas SL, Freitas-Astúa J, Formenty P, Fouchier RA, Fù Y, Ghedin E, Goodin MM, Hewson R, Horie M, Hyndman TH, Jiāng D, Kitajima EW, Kobinger GP, Kondo H, Kurath G, Lamb RA,, Lenardon S, Leroy EM, Li CX, Lin XD, Liú L, Longdon B, Marton S, Maisner A, Mühlberger E, Netesov SV, Nowotny N,, Patterson JL, Payne SL, Paweska JT, Randall RE, Rima BK, Rota P, Rubbenstroth D, Schwemmle M, Shi M, Smither SJ, Stenglein MD, Stone DM, Takada A, Terregino C, Tesh RB, Tian JH, Tomonaga K, Tordo N,, Towner JS, Vasilakis N,, Verbeek M, Volchkov VE, Wahl-Jensen V, Walsh JA, Walker PJ, Wang D, Wang LF,, Wetzel T, Whitfield AE, Xiè JT, Yuen KY, Zhang YZ, Kuhn JH.
In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
PMID: 27216929
PMCID: PMC4947412
Genomoviridae: a new family of widespread single-stranded DNAviruses.
Arch Virol. 2016 Sep;161(9):2633-43. doi: 10.1007/s00705-016-2943-3. Epub 2016 Jun 24.
Krupovic M, Ghabrial SA, Jiang D, Varsani A
Here, we introduce a new family of eukaryote-infecting single-stranded (ss) DNA viruses that was created recently by the International Committee on Taxonomy of Viruses(ICTV). The family, named Genomoviridae, contains a single genus, Gemycircularvirus, which currently has one recognized virus species, Sclerotinia gemycircularvirus 1. Sclerotinia sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) is currently the sole representative isolate of the family; however, a great number of SsHADV-1-like ssDNA virus genomes has been sequenced from various environmental, plant- and animal-associated samples, indicating that members of family Genomoviridae are widespread and abundant in the environment.
PMID: 27343045
Ratification vote on taxonomic proposals to the InternationalCommittee on Taxonomy of Viruses (2016).
Arch Virol. 2016 Jul 16. [Epub ahead of print]
Adams MJ, Lefkowitz EJ, King AM, 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 April 2016.Changes to virus taxonomy (the Universal Scheme of Virus Classification of the International Committee on Taxonomy of Viruses [ICTV]) now take place annually and are the result of a multi-stage process. In accordance with the ICTV Statutes ( https://ictv.global/about/statutes ), proposals submitted to the ICTV Executive Committee (EC) undergo a review process that involves input from the ICTV Study Groups (SGs) and Subcommittees (SCs), other interested virologists, and the EC. After final approval by the EC,proposals are then presented for ratification to the full ICTV membership by publication on an ICTV web site ( hhttps://ictv.global ) followed by an electronic vote. The latest set of proposals approved by the EC was made available on the ICTV website by January 2016 ( https://ictv.global/files/proposals/approvedproposals/ ). A list of theseproposals was then emailed on 28 March 2016 to the 148 members of ICTV, namely the EC Members, Life Members, ICTV Subcommittee Members (including the SG chairs) and ICTV National Representatives. Members were then requested to vote on whether to ratify the taxonomic proposals (voting closed on 29 April 2016).
PMID: 27424026
Obituary Craig R. Pringle (1930-2015).
Easton AJ.
Arch Virol. 2016 Mar;161(3):769-770. doi: 10.1007/s00705-015-2725-3. PMID: 26695769
Reorganization and expansion of the nidoviral family Arteriviridae.
Kuhn JH, Lauck M, Bailey AL, Shchetinin AM, Vishnevskaya TV, Bào Y, Ng TF, LeBreton M, Schneider BS, Gillis A, Tamoufe U, Diffo JL, Takuo JM, Kondov NO, Coffey LL, Wolfe ND, Delwart E, Clawson AN, Postnikova E, Bollinger L, Lackemeyer MG, Radoshitzky SR, Palacios G, Wada J, Shevtsova ZV, Jahrling PB, Lapin BA, Deriabin PG, Dunowska M, Alkhovsky SV, Rogers J, Friedrich TC, O'Connor DH, Goldberg TL.
The family Arteriviridae presently includes a single genus Arterivirus. This genus includes four species as the taxonomic homes for equine arteritis virus (EAV), lactate dehydrogenase-elevating virus (LDV), porcine respiratory and reproductive syndrome virus (PRRSV), and simian hemorrhagic fever virus (SHFV), respectively. A revision of this classification is urgently needed to accommodate the recent description of eleven highly divergent simian arteriviruses in diverse African nonhuman primates, one novel arterivirus in an African forest giant pouched rat, and a novel arterivirus in common brushtails in New Zealand. In addition, the current arterivirus nomenclature is not in accordance with the most recent version of the International Code of Virus Classification and Nomenclature. Here we outline an updated, amended, and improved arterivirus taxonomy based on current data. Taxon-specific sequence cut-offs are established relying on a newly established open reading frame 1b phylogeny and pairwise sequence comparison (PASC) of coding-complete arterivirus genomes. As a result, the current genus Arterivirus is replaced by five genera: Equartevirus (for EAV), Rodartevirus (LDV + PRRSV), Simartevirus (SHFV + simian arteriviruses), Nesartevirus (for the arterivirus from forest giant pouched rats), and Dipartevirus (common brushtail arterivirus). The current species Porcine reproductive and respiratory syndrome virus is divided into two species to accommodate the clear divergence of the European and American "types" of PRRSV, both of which now receive virus status. The current species Simian hemorrhagic fever virus is divided into nine species to accommodate the twelve known simian arteriviruses. Non-Latinized binomial species names are introduced to replace all current species names to clearly differentiate them from virus names, which remain largely unchanged.
Arch Virol. 2016 Mar; 161(3): 755-768. doi: 10.1007/s00705-015-2672-z. Epub 2015 Nov 25. PMID: 26608064
Pietilä MK, Roine E, Sencilo A, Bamford DH, Oksanen HM.
Viruses infecting archaea show a variety of virion morphotypes, and they are currently classified into more than ten viral families or corresponding groups. A pleomorphic virus morphotype is very common among haloarchaeal viruses, and to date, several such viruses have been isolated. Here, we propose the classification of eight such viruses and formation of a new family, Pleolipoviridae (from the Greek pleo for more or many and lipos for lipid), containing three genera, Alpha-, Beta-, and Gammapleolipovirus. The proposal is currently under review by the International Committee on Taxonomy of Viruses (ICTV). The members of the proposed family Pleolipoviridae infect halophilic archaea and are nonlytic. They share structural and genomic features and differ from any other classified virus. The virion of pleolipoviruses is composed of a pleomorphic membrane vesicle enclosing the genome. All pleolipoviruses have two major structural protein species, internal membrane and spike proteins. Although the genomes of the pleolipoviruses are single- or double-stranded, linear or circular DNA molecules, they share the same genome organization and gene synteny and show significant similarity at the amino acid level. The canonical features common to all members of the proposed family Pleolipoviridae show that they are closely related and thus form a new viral family.
Arch Virol. 2016 Jan;161(1):249-56. doi: 10.1007/s00705-015-2613-x. Epub 2015 Oct 12. PMID: 26459284
Krupovic M, Kuhn JH, Fischer MG.
Satellite viruses encode structural proteins required for the formation of infectious particles but depend on helper viruses for completing their replication cycles. Because of this unique property, satellite viruses that infect plants, arthropods, or mammals, as well as the more recently discovered satellite-like viruses that infect protists (virophages), have been grouped with other, so-called "sub-viral agents." For the most part, satellite viruses are therefore not classified. We argue that possession of a coat-protein-encoding gene and the ability to form virions are the defining features of a bona fide virus. Accordingly, all satellite viruses and virophages should be consistently classified within appropriate taxa. We propose to create four new genera - Albetovirus, Aumaivirus, Papanivirus, and Virtovirus - for positive-sense single-stranded (+) RNA satellite viruses that infect plants and the family Sarthroviridae, including the genus Macronovirus, for (+)RNA satellite viruses that infect arthopods. For double-stranded DNA virophages, we propose to establish the family Lavidaviridae, including two genera, Sputnikvirus and Mavirus.
Arch Virol. 2016 Jan;161(1):233-47. doi: 10.1007/s00705-015-2622-9. Epub 2015 Oct 7. PMID: 26446887
2015
Pantó L, Podgorski II, Jánoska M, Márkó O, Harrach B.
A species classification regarding Old World monkey adenoviruses is proposed. We determined the nucleotide sequences of PCR-amplified fragments from the genes of the IVa2, DNA-dependent DNA polymerase, penton base, and hexon proteins from every simian adenovirus (SAdV) serotype that originated from Old World monkeys for which the full genome sequence had not yet been published. We confirmed that the majority of Old Word monkey SAdVs belong to two previously established species. Interestingly, one is the most recently established human AdV species, Human mastadenovirus G, which includes a single human virus, HAdV-52, as well as SAdV-1, -2, -7, -11, -12, and -15. The other approved species, Simian mastadenovirus A includes SAdV-3, -4, -6, -9, -10, -14, and -48. Several SAdVs (SAdV-5, -8, -49, -50) together with baboon AdV-1 and rhesus monkey AdV strains A1139, A1163, A1173, A1258, A1285, A1296, A1312, A1327 and A1335 have been proposed to be classified into an additional species, Simian mastadenovirus B. Another proposed species, Simian mastadenovirus C has been described for SAdV-19, baboon AdV-2/4 and -3. Our study revealed the existence of four additional AdV lineages. The corresponding new candidate species are Simian mastadenovirus D (for SAdV-13), Simian mastadenovirus E (for SAdV-16), Simian mastadenovirus F (for SAdV-17 and -18), and Simian mastadenovirus G (for SAdV-20). Several biological and genomic properties, such as the host origin, haemagglutination profile, number of fibre genes, and G+C content of the genome, strongly support this classification. Three SAdV strains originating from the American Type Culture Collection turned out to be mixtures of at least two virus types, either of the same species (SAdV-12 and -15 types from Human mastadenovirus G) or of two different species (SAdV-5 types from Simian mastadenovirus B and Human mastadenovirus G).
Arch Virol. 2015 Dec;160(12):3165-77. doi: 10.1007/s00705-015-2575-z. Epub 2015 Sep 14. PMID: 26370792
Scheets K, Jordan R, White KA, Hernández C.
Currently, the family Tombusviridae encompasses thirteen viral genera that contain single-stranded, positive-sense RNA genomes and isometric virions; the exception being the genus Umbravirus, whose members do not encode a coat protein (CP). A new genus, tentatively named Pelarspovirus, is proposed to be added to this family and would include five members, with Pelargonium line pattern virus recommended as the type species. Viruses assigned to this proposed genus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal CP that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. Distinguishing characteristics of these viruses include i) production of a single, tricistronic subgenomic RNA for expression of MP and CP genes, ii) presence of a non-AUG start codon (CUG or GUG) initiating the MP2 ORF, iii) absence of AUG codons in any frame between the AUG initiation codons of MP1 and CP genes, and iv) sequence-based phylogenetic clustering of all encoded proteins in separate clades from those of other family members.
Arch Virol. 2015 Sep;160(9):2385-93. doi: 10.1007/s00705-015-2500-5. Epub 2015 Jul 7. PMID: 26149249
Radoshitzky SR, Bào Y, Buchmeier MJ, Charrel RN, Clawson AN, Clegg CS, DeRisi JL, Emonet S, Gonzalez JP, Kuhn JH, Lukashevich IS, Peters CJ, Romanowski V, Salvato MS, Stenglein MD, de la Torre JC.
Until recently, members of the monogeneric family Arenaviridae (arenaviruses) have been known to infect only muroid rodents and, in one case, possibly phyllostomid bats. The paradigm of arenaviruses exclusively infecting small mammals shifted dramatically when several groups independently published the detection and isolation of a divergent group of arenaviruses in captive alethinophidian snakes. Preliminary phylogenetic analyses suggest that these reptilian arenaviruses constitute a sister clade to mammalian arenaviruses. Here, the members of the International Committee on Taxonomy of Viruses (ICTV) Arenaviridae Study Group, together with other experts, outline the taxonomic reorganization of the family Arenaviridae to accommodate reptilian arenaviruses and other recently discovered mammalian arenaviruses and to improve compliance with the Rules of the International Code of Virus Classification and Nomenclature (ICVCN). PAirwise Sequence Comparison (PASC) of arenavirus genomes and NP amino acid pairwise distances support the modification of the present classification. As a result, the current genus Arenavirus is replaced by two genera, Mammarenavirus and Reptarenavirus, which are established to accommodate mammalian and reptilian arenaviruses, respectively, in the same family. The current species landscape among mammalian arenaviruses is upheld, with two new species added for Lunk and Merino Walk viruses and minor corrections to the spelling of some names. The published snake arenaviruses are distributed among three new separate reptarenavirus species. Finally, a non-Latinized binomial species name scheme is adopted for all arenavirus species. In addition, the current virus abbreviations have been evaluated, and some changes are introduced to unequivocally identify each virus in electronic databases, manuscripts, and oral proceedings.
Arch Virol. 2015 Jul;160(7):1851-74. doi: 10.1007/s00705-015-2418-y. PMID: 25935216
Adams MJ, Lefkowitz EJ, King AM, Bamford DH, Breitbart M, Davison AJ, Ghabrial SA, Gorbalenya AE, Knowles NJ, Krell P, Lavigne R, Prangishvili D, Sanfaçon H, Siddell SG, Simmonds P, Carstens EB.
Changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2015 are listed.
Arch Virol. 2015 Jul;160(7):1837-50. doi: 10.1007/s00705-015-2425-z. PMID: 25913692
Brown JK, Zerbini FM, Navas-Castillo J, Moriones E, Ramos-Sobrinho R, Silva JC, Fiallo-Olivé E, Briddon RW, Hernández-Zepeda C, Idris A, Malathi VG, Martin DP, Rivera-Bustamante R, Ueda S, Varsani A.
Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.
Arch Virol. 2015 Jun;160(6):1593-619. doi: 10.1007/s00705-015-2398-y. Epub 2015 Apr 18. PMID: 25894478
Adams MJ, Hendrickson RC, Dempsey DM, Lefkowitz EJ.
A database and website (
https://ictv.global/taxonomy/history ) have been established where the history of changes in virus taxonomy from 1971 to the present day can easily be traced. Each change is linked to a source document confirming the change or, for most changes since 2002, to the taxonomic proposal approved by the International Committee on Taxonomy of Viruses (ICTV).
Arch Virol. 2015 May;160(5):1375-83. doi: 10.1007/s00705-015-2376-4. Epub 2015 Feb 25. PMID: 25708839
Kuhn JH, Dürrwald R, Bào Y, Briese T, Carbone K, Clawson AN, deRisi JL, Garten W, Jahrling PB, Kolodziejek J, Rubbenstroth D, Schwemmle M, Stenglein M, Tomonaga K, Weissenböck H, Nowotny N.
Knowledge of bornaviruses has expanded considerably during the last decade. A possible reservoir of mammalian Borna disease virus has been identified, divergent bornaviruses have been detected in birds and reptiles, and endogenous bornavirus-like elements have been discovered in the genomes of vertebrates of several species. Previous sequence comparisons and alignments have indicated that the members of the current family Bornaviridae are phylogenetically diverse and are not adequately classified in the existing bornavirus taxonomy supported by the International Committee on Taxonomy of Viruses (ICTV). We provide an update of these analyses and describe their implications for taxonomy. We propose retaining the family name Bornaviridae and the genus Bornavirus but reorganizing species classification. PAirwise Sequence Comparison (PASC) of bornavirus genomes and Basic Local Alignment Search Tool (BLAST) comparison of genomic and protein sequences, in combination with other already published phylogenetic analyses and known biological characteristics of bornaviruses, indicate that this genus should include at least five species: Mammalian 1 bornavirus (classical Borna disease virus and divergent Borna disease virus isolate No/98), Psittaciform 1 bornavirus (avian/psittacine bornaviruses 1, 2, 3, 4, 7), Passeriform 1 bornavirus (avian/canary bornaviruses C1, C2, C3, LS), Passeriform 2 bornavirus (estrildid finch bornavirus EF), and Waterbird 1 bornavirus (avian bornavirus 062CG). This classification is also in line with biological characteristics of these viruses and their vertebrate hosts. A snake bornavirus, proposed to be named Loveridge's garter snake virus 1, should be classified as a member of an additional species (Elapid 1 bornavirus), unassigned to a genus, in the family Bornaviridae. Avian bornaviruses 5, 6, MALL, and another "reptile bornavirus" ("Gaboon viper virus") should stay unclassified until further information becomes available. Finally, we propose new virus names and abbreviations when necessary to achieve clear differentiation and unique identification.
Arch Virol. 2015 Feb;160(2):621-32. doi: 10.1007/s00705-014-2276-z. Epub 2014 Dec 2. PubMed PMID: 25449305; PubMed Central PMCID: PMC4315759.
2014
Di Serio F, Flores R, Verhoeven JT, Li SF, Pallás V, Randles JW, Sano T, Vidalakis G, Owens RA.
Viroids are the smallest autonomous infectious nucleic acids known so far. With a small circular RNA genome of about 250-400 nt, which apparently does not code for any protein, viroids replicate and move systemically in host plants. Since the discovery of the first viroid almost forty-five years ago, many different viroids have been isolated, characterized and, frequently, identified as the causal agents of plant diseases. The first viroid classification scheme was proposed in the early 1990s and adopted by the International Committee on Taxonomy of Viruses (ICTV) a few years later. Here, the current viroid taxonomy scheme and the criteria for viroid species demarcation are discussed, highlighting the main taxonomic questions currently under consideration by the ICTV Viroid Study Group. The impact of correct taxonomic annotation of viroid sequence variants is also addressed, taking into consideration the increasing application of next-generation sequencing and bioinformatics for known and previously unrecognized viroids.
Arch Virol. 2014 Dec;159(12):3467-78. doi: 10.1007/s00705-014-2200-6. Epub 2014 Sep 13.
Adams MJ, Lefkowitz EJ, King AM, Carstens EB.
Changes to virus taxonomy approved by a vote of all ICTV members in February-March 2014 are reported.
Arch Virol. 2014 Oct;159(10):2831-41. doi: 10.1007/s00705-014-2114-3. Epub 2014 Jun 7. PubMed PMID: 24906522.
M. J. Adams, E. B. Carstens
Following discussions at the Executive Committee meeting of the International Committee on Taxonomy of Viruses (ICTV) in Edinburgh, UK, in July 2013, it was agreed to propose changes to the Statutes to allow the appointment of a third Secretary, with particular responsibility for virus data. These changes have now been formally adopted, following approval by the ICTV voting membership (in a ballot conducted by e-mail) and by IUMS Virology Division, as required by the Statutes.
Arch Virol. 2014 Oct;159(10):2829-30. doi: 10.1007/s00705-014-2145-9. Epub 2014 Jun 7. PubMed PMID: 24906527.
Varsani A, Navas-Castillo J, Moriones E, Hernández-Zepeda C, Idris A, Brown JK, Murilo Zerbini F, Martin DP.
The family Geminiviridae includes plant-infecting circular single-stranded DNA viruses that have geminate particle morphology. Members of this family infect both monocotyledonous and dicotyledonous plants and have a nearly global distribution. With the advent of new molecular tools and low-cost sequencing, there has been a significant increase in the discovery of new geminiviruses in various cultivated and non-cultivated plants. In this communication, we highlight the establishment of three new genera (Becurtovirus, Eragrovirus and Turncurtovirus) to accommodate various recently discovered geminiviruses that are highly divergent and, in some cases, have unique genome architectures. The genus Becurtovirus has two viral species, Beet curly top Iran virus (28 isolates; leafhopper vector Circulifer haematoceps) and Spinach curly top Arizona virus (1 isolate; unknown vector), whereas the genera Eragrovirus and Turncurtovirus each have a single assigned species: Eragrostis curvula streak virus (6 isolates; unknown vector) and Turnip curly top virus (20 isolates; leafhopper vector Circulifer haematoceps), respectively. Based on analysis of all of the genome sequences available in public databases for each of the three new genera, we provide guidelines and protocols for species and strain classification within these three new genera.
Arch Virol. 2014 Aug;159(8):2193-203. doi: 10.1007/s00705-014-2050-2. Epub 2014 Mar 22.
Calisher CH, Tesh RB.
Arch Virol. 2014 Aug;159(8):2189-91. doi: 10.1007/s00705-014-2008-4. Epub 2014 Feb 18.
Varsani A, Martin DP, Navas-Castillo J, Moriones E, Hernández-Zepeda C, Idris A, Murilo Zerbini F, Brown JK.
Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77 % genome-wide pairwise identity as a species demarcation threshold and 94 % genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77 % genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94 % identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe curly top virus (SpSCTV) and Horseradish curly top virus (HrCTV).
Arch Virol. 2014 Jul;159(7):1873-82. doi: 10.1007/s00705-014-1982-x. Epub 2014 Jan 25. PMID: 24463952
Pawlowski A, Rissanen I, Bamford JK, Krupovic M, Jalasvuori M.
A new family of viruses named Sphaerolipoviridae has been proposed recently. It comprises icosahedral, tailless haloarchaeal viruses with an internal lipid membrane located between the protein capsid and the dsDNA genome. The proposed family Sphaerolipoviridae was divided into two genera: Alphasphaerolipovirus, including Haloarcula hispanica viruses SH1, PH1 and HHIV-2, and Betasphaerolipovirus, including Natrinema virus SNJ1. Here, we propose to expand the family Sphaerolipoviridae to include a group of bacteriophages infecting extreme thermophilic Thermus thermophilus and sharing a number of structural and genomic properties with archaeal sphaerolipoviruses. This new group comprises two members, lytic phage P23-77 and temperate phage IN93, as well as putative members P23-72 and P23-65H. In addition, several related proviruses have been discovered as integrated elements in bacterial genomes of the families Thermus and Meiothermus. Morphology of the virus particles and the overall capsid architecture of these bacteriophages resembles that of archaeal members of the Sphaerolipoviridae, including an unusual capsid arrangement in a T = 28 dextro lattice. Alpha- and betasphaerolipoviruses share with P23-77-like bacteriophages a conserved block of core genes that encode a putative genome-packaging ATPase and the two major capsid proteins (MCPs). The recently determined X-ray structure of the small and large MCPs of P23-77 revealed a single beta-barrel (jelly-roll) fold that is superimposable with the cryo-EM density maps of the SH1 capsomers. Given the common features of these viruses, we propose to include the so far unclassified P23-77-like bacteriophages into a new genus, "Gammasphaerolipovirus", within the family Sphaerolipoviridae.
Arch Virol. 2014 Jun;159(6):1541-54. doi: 10.1007/s00705-013-1970-6. Epub 2014 Jan 7. PMID: 24395078
Kuhn JH, Bào Y, Bavari S, Becker S, Bradfute S, Brauburger K, Rodney Brister J, Bukreyev AA, Caì Y, Chandran K, Davey RA, Dolnik O, Dye JM, Enterlein S, Gonzalez JP, Formenty P, Freiberg AN, Hensley LE, Hoenen T, Honko AN, Ignatyev GM, Jahrling PB, Johnson KM, Klenk HD, Kobinger G, Lackemeyer MG, Leroy EM, Lever MS, Mühlberger E, Netesov SV, Olinger GG, Palacios G, Patterson JL, Paweska JT, Pitt L, Radoshitzky SR, Ryabchikova EI, Saphire EO, Shestopalov AM, Smither SJ, Sullivan NJ, Swanepoel R, Takada A, Towner JS, van der Groen G, Volchkov VE, Volchkova VA, Wahl-Jensen V, Warren TK, Warfield KL, Weidmann M, Nichol ST.
Specific alterations (mutations, deletions, insertions) of virus genomes are crucial for the functional characterization of their regulatory elements and their expression products, as well as a prerequisite for the creation of attenuated viruses that could serve as vaccine candidates. Virus genome tailoring can be performed either by using traditionally cloned genomes as starting materials, followed by site-directed mutagenesis, or by de novo synthesis of modified virus genomes or parts thereof. A systematic nomenclature for such recombinant viruses is necessary to set them apart from wild-type and laboratory-adapted viruses, and to improve communication and collaborations among researchers who may want to use recombinant viruses or create novel viruses based on them. A large group of filovirus experts has recently proposed nomenclatures for natural and laboratory animal-adapted filoviruses that aim to simplify the retrieval of sequence data from electronic databases. Here, this work is extended to include nomenclature for filoviruses obtained in the laboratory via reverse genetics systems. The previously developed template for natural filovirus genetic variant naming, (/)///-, is retained, but we propose to adapt the type of information added to each field for cDNA clone-derived filoviruses. For instance, the full-length designation of an Ebola virus Kikwit variant rescued from a plasmid developed at the US Centers for Disease Control and Prevention could be akin to "Ebola virus H.sapiens-rec/COD/1995/Kikwit-abc1" (with the suffix "rec" identifying the recombinant nature of the virus and "abc1" being a placeholder for any meaningful isolate designator). Such a full-length designation should be used in databases and the methods section of publications. Shortened designations (such as "EBOV H.sap/COD/95/Kik-abc1") and abbreviations (such as "EBOV/Kik-abc1") could be used in the remainder of the text, depending on how critical it is to convey information contained in the full-length name. "EBOV" would suffice if only one EBOV strain/variant/isolate is addressed.
Arch Virol. 2014 May;159(5):1229-37. doi: 10.1007/s00705-013-1877-2. Epub 2013 Nov 5. PMID: 24190508
Cotmore SF, Agbandje-McKenna M, Chiorini JA, Mukha DV, Pintel DJ, Qiu J, Soderlund-Venermo M, Tattersall P, Tijssen P, Gatherer D, Davison AJ.
A set of proposals to rationalize and extend the taxonomy of the family Parvoviridae is currently under review by the International Committee on Taxonomy of Viruses (ICTV). Viruses in this family infect a wide range of hosts, as reflected by the longstanding division into two subfamilies: the Parvovirinae, which contains viruses that infect vertebrate hosts, and the Densovirinae, encompassing viruses that infect arthropod hosts. Using a modified definition for classification into the family that no longer demands isolation as long as the biological context is strong, but does require a near-complete DNA sequence, 134 new viruses and virus variants were identified. The proposals introduce new species and genera into both subfamilies, resolve one misclassified species, and improve taxonomic clarity by employing a series of systematic changes. These include identifying a precise level of sequence similarity required for viruses to belong to the same genus and decreasing the level of sequence similarity required for viruses to belong to the same species. These steps will facilitate recognition of the major phylogenetic branches within genera and eliminate the confusion caused by the near-identity of species and viruses. Changes to taxon nomenclature will establish numbered, non-Latinized binomial names for species, indicating genus affiliation and host range rather than recapitulating virus names. Also, affixes will be included in the names of genera to clarify subfamily affiliation and reduce the ambiguity that results from the vernacular use of "parvovirus" and "densovirus" to denote multiple taxon levels.
Arch Virol. 2014 May;159(5):1239-47. doi: 10.1007/s00705-013-1914-1. Epub 2013 Nov 9. PMID: 24212889
Bukreyev AA, Chandran K, Dolnik O, Dye JM, Ebihara H, Leroy EM, Mühlberger E, Netesov SV, Patterson JL, Paweska JT, Saphire EO, Smither SJ, Takada A, Towner JS, Volchkov VE, Warren TK, Kuhn JH.
The International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group prepares proposals on the classification and nomenclature of filoviruses to reflect current knowledge or to correct disagreements with the International Code of Virus Classification and Nomenclature (ICVCN). In recent years, filovirus taxonomy has been corrected and updated, but parts of it remain controversial, and several topics remain to be debated. This article summarizes the decisions and discussion of the currently acting ICTV Filoviridae Study Group since its inauguration in January 2012.
Archives of Virology, 2014 Apr;159(4):821-30. doi: 10.1007/s00705-013-1834-0. Epub 2013 Oct 13. PMID 24122154
Dietzgen RG, Kuhn JH, Clawson AN, Freitas-Astúa J, Goodin MM, Kitajima EW, Kondo H, Wetzel T, Whitfield AE.
Orchid fleck virus (OFV) is an unassigned negative-sense, single-stranded (-)ssRNA plant virus that was previously suggested to be included in the family Rhabdoviridae, order Mononegavirales. Although OFV shares some biological characteristics, including nuclear cytopathological effects, gene order, and sequence similarities, with nucleorhabdoviruses, its taxonomic status is unclear because unlike all mononegaviruses, OFV has a segmented genome and its particles are not enveloped. This article analyses the available biological, physico-chemical, and nucleotide sequence evidence that seems to indicate that OFV and several other Brevipalpus mite-transmitted short bacilliform (-)ssRNA viruses are likely related and may be classified taxonomically in novel species in a new free-floating genus dichorhavirus.
Archives of Virology, 2014 Mar;159(3):607-19. doi: 10.1007/s00705-013-1834-0. Epub 2013 Oct 1. PMID 24081823
Gutiérrez D, Adriaenssens EM, Martínez B, Rodríguez A, Lavigne R, Kropinski AM, García P.
To date, most members of the Siphoviridae family of bacteriophages remain unclassified, including the 46 staphylococcal phages for which the complete genome sequences have been deposited in public databases. Comparative nucleotide and protein sequence analysis, in addition to available data on phage morphology, allowed us to propose three new phage genera within the family Siphoviridae: "3alikevirus", "77likevirus" and "Phietalikevirus", which include related phages infecting Staphylococcus aureus and Staphylococcus epidermidis. However, six phages infecting S. aureus, Staphylococcus pasteuri, Staphylococcus hominis and Staphylococcus capitis strains remain to be classified (orphan phages). Overall, the former phages share morphological features and genome organization. The three groups have conserved domains containing peptidoglycan hydrolytic activities clearly identified as part of tape measure proteins ("3alikevirus" and "77likevirus") or as individual virionassociated proteins ("Phietalikevirus"). In addition, bacteriophages belonging to the genus "3alikevirus" share closely related DNA-processing and packaging proteins, while bacteriophages included in the genus "Phietalikevirus" encode specific tail proteins for host interaction. These properties are considered distinctive for these genera. Orphan phages seem to have a more divergent organization, but they share some properties with members of these proposed genera.
Archives of Virology, 2014 Feb;159(2):389-98. PMID 24022640.
Javed MA, Ackermann HW, Azeredo J, Carvalho CM, Connerton I, Evoy S, Hammerl JA, Hertwig S, Lavigne R, Singh A, Szymanski CM, Timms A, Kropinski AM.
Most Campylobacter bacteriophages isolated to date have long contractile tails and belong to the family Myoviridae. Based on their morphology, genome size and endonuclease restriction profile, Campylobacter phages were originally divided into three groups. The recent genome sequencing of seven virulent campylophages reveal further details of the relationships between these phages at the genome organization level. This article details the morphological and genomic features among the campylophages, investigates their taxonomic position, and proposes the creation of two new genera, the "Cp220likevirus" and "Cp8unalikevirus" within a proposed subfamily, the "Eucampyvirinae"
Archives of Virology, 2014 Jan;159(1):181-90. doi: 10.1007/s00705-013-1788-2. Epub 2013 Jul 24. PMID 23881082.
Archives of Virology, January 2014, Volume 159, Issue 1, pp 175-180. PMID 23836392
2013
Archives of Virology, December 2013, Volume 158, Issue 12, pp
2633-2639. PMID 23836393
Kuhn JH, Bekal S, Caì Y, Clawson AN, Domier LL, Herrel M, Jahrling PB, Kondo H, Lambert KN, Mihindukulasuriya KA, Nowotny N, Radoshitzky SR, Schneider U, Staeheli P, Suzuki N, Tesh RB, Wang D, Wang LF, Dietzgen RG.
Nyamanini virus (NYMV) and Midway virus (MIDWV) are unclassified tick-borne agents that infect land birds and seabirds, respectively. The recent molecular characterization of both viruses confirmed their already known close serological relationship and revealed them to be nonsegmented, single- and negative-stranded RNA viruses that are clearly related to, but quite distinct from, members of the order Mononegavirales (bornaviruses, filoviruses, paramyxoviruses, and rhabdoviruses). A third agent, soybean cyst nematode virus 1 (SbCNV-1, previously named soybean cyst nematode nyavirus), was recently found to be an additional member of this new virus group. Here, we review the current knowledge about all three viruses and propose classifying them as members of a new mononegaviral family, Nyamiviridae.
Archives of Virology, October 2013, Volume 158, Issue 10, pp
2209-2226. PMID 23636404
Archives of Virology, 2013 Sep;158(9):2023-30. PMID: 23580178
The International Committee on Taxonomy of Viruses (ICTV) is responsible for the classification of viruses into taxa. Importantly, the ICTV is currently not responsible for the nomenclature of viruses or their subclassification into strains, lineages, or genotypes. ICTV rules for classification of viruses and nomenclature of taxa are laid out in a code, the International Code of Virus Classification and Nomenclature (ICVCN). The most recent version of the Code makes it difficult for the unfamiliar reader to distinguish between viruses and taxa, thereby often giving the impression that certain Rules apply to viruses. Here, Code text changes are proposed to address this problem.
Archives of Virology, July 2013, Volume 158, Issue 7, pp 1621-1629
Jens H. Kuhn,
Yiming Bao,
Sina Bavari,
Stephan Becker,
Steven Bradfute,
J. Rodney Brister,
Alexander A. Bukreyev,
Yíngyún Caì,
Kartik Chandran,
Robert A. Davey,
Olga Dolnik,
John M. Dye,
Sven Enterlein,
Jean-Paul Gonzalez,
Pierre Formenty,
Alexander N. Freiberg,
Lisa E. Hensley,
Anna N. Honko,
Georgy M. Ignatyev,
Peter B. Jahrling,
Karl M. Johnson,
Hans-Dieter Klenk,
Gary Kobinger,
Matthew G. Lackemeyer,
Eric M. Leroy,
Mark S. Lever,
Loreen L. Lofts,
Elke Mühlberger,
Sergey V. Netesov,
Gene G. Olinger,
Gustavo Palacios,
Jean L. Patterson,
Janusz T. Paweska,
Louise Pitt,
Sheli R. Radoshitzky,
Elena I. Ryabchikova,
Erica Ollmann Saphire,
Aleksandr M. Shestopalov,
Sophie J. Smither,
Nancy J. Sullivan,
Robert Swanepoel,
Ayato Takada,
Jonathan S. Towner,
Guido van der Groen,
Viktor E. Volchkov,
Victoria Wahl-Jensen,
Travis K. Warren,
Kelly L. Warfield,
Manfred Weidmann,
Stuart T. Nichol
The International Committee on Taxonomy of Viruses (ICTV) organizes the classification of viruses into taxa, but is not responsible for the nomenclature for taxa members. International experts groups, such as the ICTV Study Groups, recommend the classification and naming of viruses and their strains, variants, and isolates. The ICTV Filoviridae Study Group has recently introduced an updated classification and nomenclature for filoviruses. Subsequently, and together with numerous other filovirus experts, a consistent nomenclature for their natural genetic variants and isolates was developed that aims at simplifying the retrieval of sequence data from electronic databases. This is a first important step toward a viral genome annotation standard as sought by the US National Center for Biotechnology Information (NCBI). Here, this work is extended to include filoviruses obtained in the laboratory by artificial selection through passage in laboratory hosts. The previously developed template for natural filovirus genetic variant naming (<virus name> <isolation host-suffix>/<country of sampling>/ <year of sampling>/<genetic variant designation>-<isolate designation>) is retained, but it is proposed to adapt the type of information added to each field for laboratory animal-adapted variants. For instance, the full-length designation of an Ebola virus Mayinga variant adapted at the State Research Center for Virology and Biotechnology “Vector” to cause disease in guinea pigs after seven passages would be akin to “Ebola virus VECTOR/C.porcellus-lab/COD/1976/Mayinga-GPA-P7”. As was proposed for the names of natural filovirus variants, we suggest using the full-length designation in databases, as well as in the method section of publications. Shortened designations (such as “EBOV VECTOR/C.por/COD/76/May-GPA-P7”) and abbreviations (such as “EBOV/May-GPA-P7”) could be used in the remainder of the text depending on how critical it is to convey information contained in the full-length name. “EBOV” would suffice if only one EBOV strain/variant/isolate is addressed.
Archives of Virology, June 2013, Volume 158, Issue 6, pp 1425-1432
Recent advances in the ease with which the genomes of small circular single-stranded DNA viruses can be amplified, cloned, and sequenced have greatly accelerated the rate at which full genome sequences of mastreviruses (family Geminiviridae, genus Mastrevirus) are being deposited in public sequence databases. Although guidelines currently exist for species-level classification of newly determined, complete mastrevirus genome sequences, these are difficult to apply to large sequence datasets and are permissive enough that, effectively, a high degree of leeway exists for the proposal of new species and strains. The lack of a standardised and rigorous method for testing whether a new genome sequence deserves such a classification is resulting in increasing numbers of questionable mastrevirus species proposals. Importantly, the recommended sequence alignment and pairwise identity calculation protocols of the current guidelines could easily be modified to make the classification of newly determined mastrevirus genome sequences significantly more objective. Here, we propose modified versions of these protocols that should substantially minimise the degree of classification inconsistency that is permissible under the current system. To facilitate the objective application of these guidelines for mastrevirus species demarcation, we additionally present a user-friendly computer program, SDT (species demarcation tool), for calculating and graphically displaying pairwise genome identity scores. We apply SDT to the 939 full genome sequences of mastreviruses that were publically available in May 2012, and based on the distribution of pairwise identity scores yielded by our protocol, we propose mastrevirus species and strain demarcation thresholds of >78 % and >94 % identity, respectively.
Archives of Virology, June 2013, Volume 158, Issue 6, pp 1411-1424
Marc H. V. Van Regenmortel,
Hans-Wolfgang Ackermann,
Charles H. Calisher,
Ralf G. Dietzgen,
Marian C. Horzinek,
Gunther M. Keil,
Brian W. J. Mahy,
Giovanni P. Martelli,
Frederick A. Murphy,
Craig Pringle,
Bert K. Rima,
Tim Skern,
H.-J. Vetten,
Scott C. Weaver
The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) has recently decided to modify the current definition of virus species (Code of Virus Classification and Nomenclature Rule 3.21) and will soon ask the full ICTV membership (189 voting members) to ratify the proposed controversial change. In this discussion paper, 14 senior virologists, including six Life members of the ICTV, compare the present and proposed new definition and recommend that the existing definition of virus species should be retained. Since the pros and cons of the proposal posted on the ICTV website are not widely consulted, the arguments are summarized here in order to reach a wider audience.
Archives of Virology, May 2013, Volume 158, Issue 5, pp 1115-1119
The family "Marseilleviridae" is a new proposed taxon for giant viruses that infect amoebae. Its first member, Acanthamoeba polyphagamarseillevirus (APMaV), was isolated in 2007 by culturing on amoebae a water sample collected from a cooling tower in Paris, France. APMaV has an icosahedral shape with a diameter of ≈250 nm. Its genome is a double-stranded circular DNA that is 368,454 base pairs (bp) in length. The genome has a GC content of 44.7 % and is predicted to encode 457 proteins. Phylogenetic reconstructions showed that APMaV belongs to a new viral family among nucleocytoplasmic large DNA viruses, a group of viruses that also includes Acanthamoeba polyphaga mimivirus (APMV) and the other members of the family Mimiviridae as well as the members of the families Poxviridae, Phycodnaviridae, Iridoviridae, Ascoviridae, and Asfarviridae. In 2011, Acanthamoeba castellanii lausannevirus (ACLaV), another close relative of APMaV, was isolated from river water in France. The ACLaV genome is 346,754 bp in size and encodes 450 genes, among which 320 have an APMaV protein as the closest homolog. Two other giant viruses closely related to APMaV and ACLaV have been recovered in our laboratory from a freshwater sample and a human stool sample using an amoebal co-culture method. The only currently identified hosts for “marseilleviruses” are Acanthamoebaspp. The prevalence of these viruses in the environment and in animals and humans remains to be determined.
Archives of Virology, April 2013, Volume 158, Issue 4, pp 915-920
Jens H. Kuhn,
Yiming Bao,
Sina Bavari,
Stephan Becker,
Steven Bradfute,
J. Rodney Brister,
Alexander A. Bukreyev,
Kartik Chandran,
Robert A. Davey,
Olga Dolnik,
John M. Dye,
Sven Enterlein,
Lisa E. Hensley,
Anna N. Honko,
Peter B. Jahrling,
Karl M. Johnson,
Gary Kobinger,
Eric M. Leroy,
Mark S. Lever,
Elke Mühlberger,
Sergey V. Netesov,
Gene G. Olinger,
Gustavo Palacios,
Jean L. Patterson,
Janusz T. Paweska,
Louise Pitt,
Sheli R. Radoshitzky,
Erica Ollmann Saphire,
Sophie J. Smither,
Robert Swanepoel,
Jonathan S. Towner,
Guido van der Groen,
Viktor E. Volchkov,
Victoria Wahl-Jensen,
Travis K. Warren,
Manfred Weidmann,
Stuart T. Nichol
The task of international expert groups is to recommend the classification and naming of viruses. The International Committee on Taxonomy of Viruses Filoviridae Study Group and other experts have recently established an almost consistent classification and nomenclature for filoviruses. Here, further guidelines are suggested to include their natural genetic variants. First, this term is defined. Second, a template for full-length virus names (such as “Ebola virus H.sapiens-tc/COD/1995/Kikwit-9510621”) is proposed. These names contain information on the identity of the virus (e.g., Ebola virus), isolation host (e.g., members of the species Homo sapiens), sampling location (e.g., Democratic Republic of the Congo (COD)), sampling year, genetic variant (e.g., Kikwit), and isolate (e.g., 9510621). Suffixes are proposed for individual names that clarify whether a given genetic variant has been characterized based on passage zero material (-wt), has been passaged in tissue/cell culture (-tc), is known from consensus sequence fragments only (-frag), or does (most likely) not exist anymore (-hist). We suggest that these comprehensive names are to be used specifically in the methods section of publications. Suitable abbreviations, also proposed here, could then be used throughout the text, while the full names could be used again in phylograms, tables, or figures if the contained information aids the interpretation of presented data. The proposed system is very similar to the well-known influenzavirus nomenclature and the nomenclature recently proposed for rotaviruses. If applied consistently, it would considerably simplify retrieval of sequence data from electronic databases and be a first important step toward a viral genome annotation standard as sought by the National Center for Biotechnology Information (NCBI). Furthermore, adoption of this nomenclature would increase the general understanding of filovirus-related publications and presentations and improve figures such as phylograms, alignments, and diagrams. Most importantly, it would counter the increasing confusion in genetic variant naming due to the identification of ever more sequences through technological breakthroughs in high-throughput sequencing and environmental sampling.
Archives of Virology, January 2013, Volume 158, Issue 1, pp 301-311
It is proposed to delete Rule 3.41 of the International Code of Virus Classification and Nomenclature, which requires the name of a virus taxon to precede the term for the taxonomic unit.
Archives of Virology, January 2013, Volume 158, Issue 1, pp 297-299
2012
Evelien M. Adriaenssens,
Hans-Wolfgang Ackermann,
Hany Anany,
Bob Blasdel,
Ian F. Connerton,
David Goulding,
Mansel W. Griffiths,
Steven P. Hooton,
Elizabeth M. Kutter,
Andrew M. Kropinski,
Ju-Hoon Lee,
Martine Maes,
Derek Pickard,
Sangryeol Ryu,
Zargham Sepehrizadeh,
S. Sabouri Shahrbabak,
Ana L. Toribio,
Rob Lavigne
We suggest a bacteriophage genus, “Viunalikevirus”, as a new genus within the family Myoviridae. To date, this genus includes seven sequenced members: Salmonella phages ViI, SFP10 and FSH19; Escherichia phages CBA120 and PhaxI; Shigella phage phiSboM-AG3; and Dickeya phage LIMEstone1. Their shared myovirus morphology, with comparable head sizes and tail dimensions, and genome organization are considered distinguishing features. They appear to have conserved regulatory sequences, a horizontally acquired tRNA set and the probable substitution of an alternate base for thymine in the DNA. A close examination of the tail spike region in the DNA revealed four distinct tail spike proteins, an arrangement which might lead to the umbrella-like structures of the tails visible on electron micrographs. These properties set the suggested genus apart from the recently ratified subfamily Tevenvirinae, although a significant evolutionary relationship can be observed.
Archives of Virology, October 2012, Volume 157, Issue 10, pp 2035-2046
Tepovirus is a new monotypic genus of plant viruses typified by potato virus T (PVT), a virus with helically constructed filamentous particles that are 640 nm long, previously classified as unassigned species in the family Betaflexiviridae. Virions have a single-stranded positive-sense polyadenylated RNA genome that is 6.5 kb in size, and a single type of coat protein with a size of 24 kDa. The viral genome contains three slightly overlapping ORFs encoding, respectively, the replication-related proteins (ORF1), a putative movement protein of the 30 K type (ORF2) and the coat protein (ORF3). Its structure and organization (number and order of genes) resembles that of trichoviruses and of citrus leaf blotch virus (CLBV, genus Citrivirus) but has a smaller size. Besides potato, the primary host, PVT can experimentally infect herbaceous hosts by mechanical inoculation. No vector is known, and transmission is through propagating material (tubers), seeds and pollen. PVT has a number of biological, physical and molecular properties that differentiate it from betaflexiviruses with a 30K-type movement protein. It is phylogenetically distant from all these viruses, but least so from grapevine virus A (GVA), the type member of the genus Vitivirus, with which it groups in trees constructed using the sequences of all of the genes.
Archives of Virology, August 2012, Volume 157, Issue 8, pp 1629-1633
Recently, two independent surveillance studies in Côte d’Ivoire and Vietnam, respectively, led to the discovery of two mosquito-borne viruses, Cavally virus and Nam Dinh virus, with genome and proteome properties typical for viruses of the order Nidovirales. Using a state-of-the-art approach, we show that the two insect nidoviruses are (i) sufficiently different from other nidoviruses to represent a new virus family, and (ii) related to each other closely enough to be placed in the same virus species. We propose to name this new family Mesoniviridae. Meso is derived from the Greek word “mesos” (in English "in the middle") and refers to the distinctive genome size of these insect nidoviruses, which is intermediate between that of the families Arteriviridae and Coronaviridae, while ni is an abbreviation for “nido”. A taxonomic proposal to establish the new family Mesoniviridae, genus Alphamesonivirus, and species Alphamesonivirus 1 has been approved for consideration by the Executive Committee of the ICTV.
Archives of Virology, August 2012, Volume 157, Issue 8, pp 1623-1628
Archives of Virology, July 2012, Volume 157, Issue 7, pp 1411-1422
Linear viruses with double-stranded DNA genomes are classified into two families, Lipothrixviridae and Rudiviridae. The members of these two families, all of which infect hyperhermophilic members of the domain Archaea, differ significantly in the complexity of their virions as well as in their mechanisms of genome replication. However, recent structural and genomic studies have revealed a robust evolutionary link between members of the two families. To acknowledge this relationship we propose to unify the two families into the new taxonomic order "Ligamenvirales".
Archives of Virology, April 2012, Volume 157, Issue 4, pp 791-795
2011
Archives of Virology, Volume 156, Number 2 / February 2011, 363 - 367
Archives of Virology, Volume 156, Number 1 / January 2011, 181 - 182
The family Totiviridae includes a number of viruses with monosegmented dsRNA genomes and isometric virions that infect either fungi or a number of medically important protozoan parasites such as Leishmania and Giardia . A new genus, Trichomonasvirus , was recently approved for this family. Its name is based on the genus of its host organism, Trichomonas vaginalis , a protozoan parasite that colonizes the human genitourinary mucosa and is the most common non-viral sexually transmitted infection in the world. The type species of this new genus is Trichomonas vaginalis virus 1 . Distinguishing characteristics of the new genus include infection of a human sexually transmitted parasite, stable mixed infection with more than one distinct Trichomonasvirus species, and sequence-based phylogenetic divergence that distinguishes it from all other family members.
Archives of Virology, Volume 156, Number 1 / January 2011, 171 - 179
2010
Jens Kuhn,
Stephan Becker,
Hideki Ebihara,
Thomas Geisbert,
Karl Johnson,
Yoshihiro Kawaoka,
W. Lipkin,
Ana Negredo,
Sergey Netesov,
Stuart Nichol,
Gustavo Palacios,
Clarence Peters,
Antonio Tenorio,
Viktor Volchkov, and
Peter Jahrling
The taxonomy of the family Filoviridae (marburgviruses and ebolaviruses) has changed several times since the discovery of its members, resulting in a plethora of species and virus names and abbreviations. The current taxonomy has only been partially accepted by most laboratory virologists. Confusion likely arose for several reasons: species names that consist of several words or which (should) contain diacritical marks, the current orthographic identity of species and virus names, and the similar pronunciation of several virus abbreviations in the absence of guidance for the correct use of vernacular names. To rectify this problem, we suggest (1) to retain the current species names Reston ebolavirus , Sudan ebolavirus , and Zaire ebolavirus , but to replace the name Cote d’Ivoire ebolavirus [sic] with Taï Forest ebolavirus and Lake Victoria marburgvirus with Marburg marburgvirus ; (2) to revert the virus names of the type marburgviruses and ebolaviruses to those used for decades in the field (Marburg virus instead of Lake Victoria marburgvirus and Ebola virus instead of Zaire ebolavirus); (3) to introduce names for the remaining viruses reminiscent of jargon used by laboratory virologists but nevertheless different from species names (Reston virus, Sudan virus, Taï Forest virus), and (4) to introduce distinct abbreviations for the individual viruses (RESTV for Reston virus, SUDV for Sudan virus, and TAFV for Taï Forest virus), while retaining that for Marburg virus (MARV) and reintroducing that used over decades for Ebola virus (EBOV). Paying tribute to developments in the field, we propose (a) to create a new ebolavirus species ( Bundibugyo ebolavirus ) for one member virus (Bundibugyo virus, BDBV); (b) to assign a second virus to the species Marburg marburgvirus (Ravn virus, RAVV) for better reflection of now available high-resolution phylogeny; and (c) to create a new tentative genus ( Cuevavirus ) with one tentative species ( Lloviu cuevavirus ) for the recently discovered Lloviu virus (LLOV). Furthermore, we explain the etymological derivation of individual names, their pronunciation, and their correct use, and we elaborate on demarcation criteria for each taxon and virus.
Archives of Virology, Volume 155, Number 12 / December 2010, 2083 - 2103
Archives of Virology, Volume 155, Number 11 / November 2010, 1907 - 1908
Archives of Virology, Volume 155, Number 1 / January 2010, 133 - 146
Endogenous members of the family Caulimoviridae have now been found in the genomes of many plant species. Although these sequences are usually fragmented and rearranged and show varying degrees of decay, the genomes of the ancestral viruses can often be reassembled in silico , allowing classification within the existing viral taxonomic framework. In this paper, we describe analyses of endogenous members of the family Caulimoviridae in the genomes of Oryza sativa , Nicotiana tabacum and Solanum spp. and on the basis of phylogeny, genome organization and genetic distance within the pol gene, propose two new virus genera called Orendovirus and Solendovirus. A system of nomenclature for endogenous virus sequences in plants is also proposed.
Archives of Virology, Volume 155, Number 1 / January 2010, 123 - 131
Archives of Virology, Volume 155, Number 1 / January 2010, 3 - 5
Archives of Virology, Volume 155, Number 1 / January 2010, 1 - 2
2009
The new plant virus family Virgaviridae is described. The family is named because its members have rod-shaped virions (from the Latin virga = rod), and it includes the genera Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus and Tobravirus . The chief characteristics of members of the family are presented with phylogenetic analyses of selected genes to support the creation of the family. Species demarcation criteria within the genera are examined and discussed.
Archives of Virology, Volume 154, Number 12 / December 2009, 1967 - 1972
The family Partitiviridae includes plant and fungal viruses with bisegmented dsRNA genomes and isometric virions in which the two genome segments are packaged separately and used as templates for semiconservative transcription by the viral polymerase. A new genus, Cryspovirus , has been approved for this family. Its name is based on that of the host genus, Cryptosporidium , which encompasses several species of apicomplexan parasites that infect a wide range of mammals, birds, and reptiles, and are a major cause of human diarrheal illness worldwide. The type species of the new genus is Cryptosporidium parvum virus 1 . Distinguishing characteristics include infection of a protozoan host, a smaller capsid protein than found in other members of the family Partitiviridae , and sequence-based phylogenetic divergence.
Archives of Virology, Volume 154, Number 12 / December 2009, 1959 - 1965
The Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) held its 40th meeting at the Istanbul Convention and Exhibition Centre in Istanbul, Turkey, from August 7 to 9, 2008. This was just prior to the XIV International Congress of Virology (ICV), part of the joint meeting organized by the International Union of Microbiological Societies (IUMS), also in Istanbul, Turkey, from August 11 to 15, 2008. Most of the EC meeting was concerned with the discussion of taxonomic proposals. This communication reports the principal items of business discussed at the meeting.
Archives of Virology, Volume 154, Number 9 / September 2009, 1571 - 1574
Archives of Virology, Volume 154, Number 7 / July 2009, 1189 - 1193
In accordance with the Statutes of the International Committee of Taxonomy of Viruses (ICTV), the final stage in the process of making changes to the Universal Scheme of Virus Classification is the ratification of taxonomic proposals by ICTV Members. This can occur either at a Plenary meeting of ICTV, held during an International Congress of Virology meeting, or by circulation of proposals by mail followed by a ballot. Therefore, a list of proposals that had been subjected to the full, multi-stage review process was prepared and presented on the ICTVonline web pages in March 2008. This review process involved input from the ICTV Study Groups and Subcommittees, other interested virologists, and the ICTV Executive Committee. For the first time, the ratification process was performed entirely by email. The proposals were sent electronically via email on 18 March 2008 to ICTV Life Members (11), ICTV Subcommittee Members (74), and ICTV National Representatives (53).
Archives of Virology, Volume 154, Number 7 / July 2009, 1181 - 1188
Salivary gland hypertrophy viruses (SGHVs) have been identified from different dipteran species, such as the tsetse fly Glossina pallidipes (GpSGHV), the housefly Musca domestica (MdSGHV) and the narcissus bulbfly Merodon equestris (MeSGHV). These viruses share the following characteristics: (i) they produce non-occluded, enveloped, rod-shaped virions that measure 500–1,000 nm in length and 50–100 nm in diameter; (ii) they possess a large circular double-stranded DNA (dsDNA) genome ranging in size from 120 to 190 kbp and having G + C ratios ranging from 28 to 44%; (iii) they cause overt salivary gland hypertrophy (SGH) symptoms in dipteran adults and partial to complete sterility. The available information on the complete genome sequence of GpSGHV and MdSGHV indicates significant co-linearity between the two viral genomes, whereas no co-linearity was observed with baculoviruses, ascoviruses, entomopoxviruses, iridoviruses and nudiviruses, other large invertebrate DNA viruses. The DNA polymerases encoded by the SGHVs are of the type B and closely related, but they are phylogenetically distant from DNA polymerases encoded by other large dsDNA viruses. The great majority of SGHV ORFs could not be assigned by sequence comparison. Phylogenetic analysis of conserved genes clustered both SGHVs, but distantly from the nudiviruses and baculoviruses. On the basis of the available morphological, (patho)biological, genomic and phylogenetic data, we propose that the two viruses are members of a new virus family named Hytrosaviridae. This proposed family currently comprises two unassigned species, G. pallidipes salivary gland hypertrophy virus and M. domestica salivary gland hypertrophy virus, and a tentative unassigned species, M. equestris salivary gland hypertrophy virus. Here, we present the characteristics and the justification for establishing this new virus family.
Archives of Virology, Volume 154, Number 6 / June 2009, 909 - 918
The order Picornavirales includes several plant viruses that are currently classified into the families Comoviridae (genera Comovirus , Fabavirus and Nepovirus ) and Sequiviridae (genera Sequivirus and Waikavirus ) and into the unassigned genera Cheravirus and Sadwavirus . These viruses share properties in common with other picornavirales (particle structure, positive-strand RNA genome with a polyprotein expression strategy, a common replication block including type III helicase, a 3C-like cysteine proteinase and type I RNA-dependent RNA polymerase). However, they also share unique properties that distinguish them from other picornavirales. They infect plants and use specialized proteins or protein domains to move through their host. In phylogenetic analysis based on their replication proteins, these viruses form a separate distinct lineage within the picornavirales branch. To recognize these common properties at the taxonomic level, we propose to create a new family termed “Secoviridae” to include the genera Comovirus , Fabavirus , Nepovirus , Cheravirus , Sadwavirus , Sequivirus and Waikavirus . Two newly discovered plant viruses share common properties with members of the proposed family Secoviridae but have distinct specific genomic organizations. In phylogenetic reconstructions, they form a separate sub-branch within the Secoviridae lineage. We propose to create a new genus termed Torradovirus (type species, Tomato torrado virus) and to assign this genus to the proposed family Secoviridae.
Archives of Virology, Volume 154, Number 5 / May 2009, 899 - 907
Archives of Virology, Volume 154, Number 4 / April 2009, 731 - 732
Archives of Virology, Volume 154, Number 3 / March 2009, 545 - 546
The family Totiviridae comprises viruses with nonsegmented dsRNA genomes and isometric virions. A new genus, Victorivirus, has been approved for this family, named from the specific epithet of Helminthosporium victoriae, host of the type species, Helminthosporium victoriae virus 190S. Distinguishing characteristics of the 11 viruses so far assigned to this genus include infection of filamentous fungi, an apparently coupled termination–reinitiation mechanism for translating the RNA-dependent RNA polymerase as a separate product from the upstream capsid protein, and sequence-based phylogenetic grouping in a distinct clade from other family members.
Archives of Virology, Volume 154, Number 2 / February 2009, 373 - 379
The taxonomy of herpesviruses has been updated by the International Committee on Taxonomy of Viruses (ICTV). The former family Herpesviridae has been split into three families, which have been incorporated into the new order Herpesvirales. The revised family Herpesviridae retains the mammal, bird and reptile viruses, the new family Alloherpesviridae incorporates the fish and frog viruses, and the new family Malacoherpesviridae contains a bivalve virus. Three new genera have been created in the family Herpesviridae, namely Proboscivirus in the subfamily Betaherpesvirinae and Macavirus and Percavirus in the subfamily Gammaherpesvirinae. These genera have been formed by the transfer of species from established genera and the erection of new species, and other new species have been added to some of the established genera. In addition, the names of some nonhuman primate virus species have been changed. The family Alloherpesviridae has been populated by transfer of the genus Ictalurivirus and addition of the new species Cyprinid herpesvirus 3. The family Malacoherpesviridae incorporates the new genus Ostreavirus containing the new species Ostreid herpesvirus 1.
Archives of Virology, Volume 154, Number 1 / January 2009, 171 - 177
Rotavirus was present in 1,367 of 7,060 stool samples (19.4%) collected in Gyeonggi province of South Korea from 2003 through 2005. The predominant genotypes were confirmed as G4/P2A (19.0%) followed by G3/P1A (15.6%), G2/P1B[4] (9.3%), and G1/P1A (6.5%). The predominant types of rotavirus by year were G3/P in 2003, G4/P in 2004, and G1/Pin 2005. The prevalent rotavirus genotypes changed constantly from 2003 to 2005.
Archives of Virology, Volume 154, Number 1 / January 2009, 167 - 170
2008
Jelle Matthijnssens,
Max Ciarlet,
Mustafizur Rahman,
Houssam Attoui,
Krisztián Bányai,
Mary Estes,
Jon Gentsch,
Miren Iturriza-Gómara,
Carl Kirkwood,
Vito Martella,
Peter Mertens,
Osamu Nakagomi,
John Patton,
Franco Ruggeri,
Linda Saif,
Norma Santos,
Andrej Steyer,
Koki Taniguchi,
Ulrich Desselberger, and
Marc Van Ranst
Recently, a classification system was proposed for rotaviruses in which all the 11 genomic RNA segments are used (Matthijnssens et al. in J Virol 82:
3204–3219, 2008). Based on nucleotide identity cut-off percentages, different genotypes were defined for each genome segment. A nomenclature for the comparison of complete rotavirus genomes was considered in which the notations Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx are used for the VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 encoding genes, respectively. This classification system is an extension of the previously applied genotype-based system which made use of the rotavirus gene segments encoding VP4, VP7, VP6, and NSP4. In order to assign rotavirus strains to one of the established genotypes or a new genotype, a standard procedure is proposed in this report. As more human and animal rotavirus genomes will be completely sequenced, new genotypes for each of the 11 gene segments may be identified. A Rotavirus Classification Working Group (RCWG) including specialists in molecular virology, infectious diseases, epidemiology, and public health was formed, which can assist in the appropriate delineation of new genotypes, thus avoiding duplications and helping minimize errors. Scientists discovering a potentially new rotavirus genotype for any of the 11 gene segments are invited to send the novel sequence to the RCWG, where the sequence will be analyzed, and a new nomenclature will be advised as appropriate. The RCWG will update the list of classified strains regularly and make this accessible on a website. Close collaboration with the Study Group Reoviridae of the International Committee on the Taxonomy of Viruses will be maintained.
Archives of Virology, Volume 153, Number 8 / August 2008, 1621 - 1629
An infectious cDNA clone of a Norwegian isolate of Poinsettia mosaic virus (PnMV) was generated. It consisted of 6,098 nucleotides and encoded a polyprotein of 219.5 kDa. Sequence comparisons indicated that this isolate shared 98.6% (nucleotide) and 97.1% (amino acid) identity with the previously sequenced isolate from Germany. RNA transcripts derived from this cDNA were infectious in Nicotiana benthamiana. However, plants did not present typical PnMV symptoms. Furthermore, RNA transcripts from this cDNA clone were not infectious in poinsettia. Serial propagation of this cDNA clone in N. benthamiana plants restored symptom induction in this host but did not re-establish infectivity in poinsettia.
Archives of Virology, Volume 153, Number 7 / July 2008, 1347 - 1351
Archives of Virology, Volume 153, Number 7 / July 2008, 1207 - 1208
The existence of infectious agents smaller than bacteria was demonstrated already during the 1890s. After this discovery it took more than 50 years before a resilient definition of viruses could be given. There were separate developments of knowledge concerning plant viruses, bacterial viruses and animal viruses. In the mid-1930s, Wendell Stanley at the Rockefeller Institute for Medical Research at Princeton described the purification and crystallization of tobacco mosaic virus. The finding of an “infectious protein” led to him receiving a Nobel Prize in Chemistry in 1946. In studies initiated at the end of the 1930s, bacteriophages were used as a model for replicating genes. They led to important insights into the unique characteristics of virus-cell interactions. However, an understanding of the chemical nature of animal virus particles and their mode of replication was slow in coming. Not until the early 1950s did tissue culture techniques become available, which allowed studies also of an extended number of animal viruses. This article discusses the emergence of concepts which eventually allowed a description of viruses. The unique real-time analyses of the state of knowledge provided by the Nobel Prize archives were used in the investigation. These archives remain secret for 50 years. Besides all of the underlying documents of the Prize to Stanley, comprehensive investigations made in the mid 1950s of Seymour E. Cohen, Max Delbrück, Alfred D. Hershey and Salvador D. Luria (the latter three received a Prize in Medicine in 1969) and of André Lwoff (he shared a Prize in Medicine with Francois Jacob and Jaques Monod in 1965) were reviewed. The final phase of the evolution of our understanding of the virus concept closely paralleled the eventual insight into the chemical nature of the genetic material. Understanding the principle nature of barriers to the development of new concepts is of timeless value for fostering and facilitating new discoveries in science.
Archives of Virology, Volume 153, Number 6 / June 2008, 1109 - 1123
This study constitutes the first evaluation and application of quantitative taxonomy to the family Caulimoviridae and the first in-depth phylogenetic study of the family Caulimoviridae that integrates the common origin between LTR retrotransposons and caulimoviruses. The phylogenetic trees and PASC analyses derived from the full genome and from the corresponding partial RT concurred, providing strong support for the current genus classification based mainly on genome organisation and use of partial RT sequence as a molecular marker. The PASC distributions obtained are multimodal, making it possible to distinguish between genus, species and strain. The taxonomy of badnaviruses infecting banana (Musa spp.) was clarified, and the consequence of endogenous badnaviruses on the genetic diversity and evolution of caulimoviruses is discussed. The use of LTR retrotransposons as outgroups reveals a structured bipolar topology separating the genus Badnavirus from the other genera. Badnaviruses appear to be the most recent genus, with the genus Tungrovirus in an intermediary position. This structuring intersects the one established by genomic and biological properties and allows us to make a correlation between phylogeny and biogeography. The variability shown between members of the family Caulimoviridae is in a similiar range to that reported within other DNA and RNA plant virus families.
Archives of Virology, Volume 153, Number 6 / June 2008, 1085 - 1102
Geminivirus taxonomy and nomenclature is growing in complexity with the number of genomic sequences deposited in sequence databases. Taxonomic and nomenclatural updates are published at regular intervals (Fauquet et al. in Arch Virol 145:1743–1761, 2000, Arch Virol 148:405–421, 2003). A system to standardize virus names, and corresponding guidelines, has been proposed (Fauquet et al. in Arch Virol 145:1743–1761, 2000). This system is now followed by a large number of geminivirologists in the world, making geminivirus nomenclature more transparent and useful. In 2003, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% nucleotide (nt) identity threshold between full-length DNA-A component nucleotide sequences for begomovirus species. This threshold has been utilised since with general satisfaction. More recently, an article has been published to clarify the terminology used to describe virus entities below the species level [5]. The present publication is proposing demarcation criteria and guidelines to classify and name geminiviruses below the species level. Using the Clustal V algorithm (DNAStar MegAlign software), the distribution of pairwise sequence comparisons, for pairs of sequences below the species taxonomic level, identified two peaks: one at 85–94% nt identity that is proposed to correspond to “strain” comparisons and one at 92–100% identity that corresponds to “variant” comparisons. Guidelines for descriptors for each of these levels are proposed to standardize nomenclature under the species level. In this publication we review the status of geminivirus species and strain demarcation as well as providing updated isolate descriptors for a total of 672 begomovirus isolates. As a consequence, we have revised the status of some virus isolates to classify them as “strains”, whereas several others previously classified as “strains” have been upgraded to “species”. In all other respects, the classification system has remained robust, and we therefore propose to continue using it. An updated list of all geminivirus isolates and a phylogenetic tree with one representative isolate per species are provided.
Archives of Virology, Volume 153, Number 4 / April 2008, 783 - 821
The symptom-modulating, single-stranded DNA satellites (known as DNA-ß) associated with begomoviruses (family Geminiviridae) have proven to be widespread and important components of a large number of plant diseases across the Old World. Since they were first identified in 2000, over 260 full-length sequences (~1,360 nucleotides) have been deposited with databases, and this number increases daily. This has highlighted the need for a standardised, concise and unambiguous nomenclature for these components, as well as a meaningful and robust classification system. Pairwise comparisons of all available full-length DNA-ß sequences indicate that the minimum numbers of pairs occur at a sequence identity of 78%, which we propose as the species demarcation threshold for a distinct DNA-ß. This threshold value divides the presently known DNA-ß sequences into 51 distinct satellite species. In addition, we propose a naming convention for the satellites that is based upon the system already in use for geminiviruses. This maintains, whenever possible, the association with the helper begomovirus, the disease symptoms and the host plant and provides a logical and consistent system for referring to already recognised and newly identified satellites.
Archives of Virology, Volume 153, Number 4 / April 2008, 763 - 781
Despite the apparent natural grouping of “picorna-like” viruses, the taxonomical significance of this putative “supergroup” was never addressed adequately. We recently proposed to the ICTV that an order should be created and named Picornavirales, to include viruses infecting eukaryotes that share similar properties: (i) a positive-sense RNA genome, usually with a 5'-bound VPg and 3'-polyadenylated, (ii) genome translation into autoproteolytically processed polyprotein(s), (iii) capsid proteins organized in a module containing three related jelly-roll domains which form small icosahedral, non-enveloped particles with a pseudo-T = 3 symmetry, and (iv) a three-domain module containing a superfamily III helicase, a (cysteine) proteinase with a chymotrypsin-like fold and an RNA-dependent RNA polymerase. According to the above criteria, the order Picornavirales includes the families Picornaviridae, Comoviridae, Dicistroviridae, Marnaviridae, Sequiviridae and the unassigned genera Cheravirus, Iflavirus and Sadwavirus. Other taxa of “picorna-like” viruses, e.g. Potyviridae, Caliciviridae, Hypoviridae, do not conform to several of the above criteria and are more remotely related: therefore they are not being proposed as members of the new order. Newly described viruses, not yet assigned to an existing taxon by ICTV, may belong to the proposed order.
Archives of Virology, Volume 153, Number 4 / April 2008, 715 - 727
2007
The genus Nepovirus (family Comoviridae) was known both for a good level of homogeneity and for the presence of atypical members. In particular, the atypical members of the genus differed by the number of capsid protein (CP) subunits. While typical nepoviruses have a single CP subunit with three structural domains, atypical nepoviruses have either three small CP subunits, probably corresponding to the three individual domains, or a large and a small subunit, probably containing two and one structural domains, respectively. These differences are corroborated by hierarchical clustering based on sequences derived from both genomic RNAs. Therefore, these atypical viruses are now classified in two distinct genera, Cheravirus (three CP subunits; type species Cherry rasp leaf virus) and Sadwavirus (two CP subunits; type species Satsuma dwarf virus).
Archives of Virology, Volume 152, Number 9 / September 2007, 1767 - 1774
Archives of Virology, Volume 152, Number 3 / March 2007, 649 - 653
2006
Without Abstract
Archives of Virology, Volume 151, Number 12 / December 2006, 2547 - 2548
We propose that the formal definition of a virus species by the International Committee on Taxonomy of Viruses (ICTV) should be broadened by removing the restrictive word “polythetic” from the current definition, so that any characters can be used to define species. This change will bring the definition of virus species into line with the species definitions of cellular organisms and broaden the range of characters available for describing virus species.
Archives of Virology, Volume 151, Number 7 / July 2006, 1419 - 1422
Recent evidence from genome sequence analyses demands a substantial revision of the taxonomy and classification of the family Baculoviridae. Comparisons of 29 baculovirus genomes indicated that baculovirus phylogeny followed the classification of the hosts more closely than morphological traits that have previously been used for classification of this virus family. On this basis, dipteran- and hymenopteran-specific nucleopolyhedroviruses (NPV) should be separated from lepidopteran-specific NPVs and accommodated into different genera. We propose a new classification and nomenclature for the genera within the baculovirus family. According to this proposal the updated classification should include four genera: Alphabaculovirus (lepidopteran-specific NPV), Betabaculovirus (lepidopteran-specific Granuloviruses), Gammabaculovirus (hymenopteran-specific NPV) and Deltabaculovirus (dipteran-specific NPV).
Archives of Virology, Volume 151, Number 7 / July 2006, 1257 - 1266
Archives of Virology, Volume 151, Number 6 / June 2006, 1249 - 1250
Archives of Virology, Volume 151, Number 5 / May 2006, 1031 - 1037
Archives of Virology, Volume 151, Number 2 / February 2006, 413 - 422
2005
Geminivirus taxonomy and nomenclature is increasing in complexity with time, and the growing number of geminivirus sequences deposited in gene banks requires regular taxonomic updates and calls for new descriptors to identify virus isolates unambiguously. Fauquet et al. [1] proposed a system to standardize the names of the viruses, and corresponding guidelines have been followed since, rendering nomenclature much easier. Recently, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% identity threshold between complete DNA-A component nucleotide sequences of begomoviruses. This threshold has been utilised since with general satisfaction. In this paper, we review the status of geminivirus species demarcation and nomenclature for a total of 389 isolates. A small number of corrections have been made to comply with the adopted demarcation criteria but otherwise the classification system has remained robust and therefore we propose to continue using it. However, the large numbers of geminivirus sequences that have become available have led us to recognize the need for a better description of virus isolates. The pairwise comparison distribution below the taxonomic level of species identified two peaks, one at 90–91% identity that may correspond to “strains” and one at 96–98% identity that may correspond to “variants”. Guidelines for descriptors for each of these levels are proposed to standardize nomenclature. As a consequence, we have revisited the status of some virus isolates to elevate them to “strains”. An updated list of all geminivirus isolates currently available is provided.
Archives of Virology, Volume 150, Number 10 / October 2005, 2151 - 2179
Obituary: In Memoriam Patricia Ann Webb (1925-2005)
Archives of Virology, Volume 150, Number 6 / June 2005, 1268 - 1270
Archives of Virology, Volume 150, Number 5 / May 2005, 1045 - 1046
Obituary: In Memoriam Jean Cohen (1941-2004)
Archives of Virology, Volume 150, Number 4 / April 2005, 840 - 840
Obituary: In Memoriam William C. Reeves (1916-2004)
Archives of Virology, Volume 150, Number 4 / April 2005, 841 - 843
ICTV Meetings at the International Congress of Virology, San Francisco
Archives of Virology, Volume 150, Number 4 / April 2005, 844 - 844
Archives of Virology, Volume 150, Number 3 / March 2005, 629 - 635
Obituary: In Memoriam Guido Boccardo (1944–2002)
Archives of Virology, Volume 150, Number 2 / February 2005, 412 - 413
Archives of Virology, Volume 150, Number 2 / February 2005, 407 - 411
Obituary: In Memoriam Fred Brown (1925–2004)
Archives of Virology, Volume 150, Number 1 / January 2005, 199 - 200
Archives of Virology, Volume 150, Number 1 / January 2005, 189 - 198
2004
Obituary: In Memoriam Peter Hans Hofschneider (1929–2004)
Archives of Virology, Volume 149, Number 12 / December 2004, 2473 - 2474
1998
(The Statutes of the ICTV printed below were revised at a Meeting of the Executive Committee of the ICTV at the National Library of Medicine, Bethesda, USA, in April 1955, and were ratified subsequently by postal ballot of the full membership of the ICTV. A further revision of the Statutes is in progress and after ratification any amendment will be published in Virology Division News and in the 7th Report of the ICTV, prior to the International Congress of Virology in Sydney in August 1999).
Archives of Virology, Volume 143, Number 5 / April 1998, 1035 - 1040
1993
Archives of Virology, Volume 133, Number 3 / September 1993, 491 - 498
Archives of Virology, Volume 133, Number 1 / March 1993, 233 - 233
1992
Archives of Virology, Volume 124, Number 3 / September 1992, 397 - 398
