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Taxonomy of prokaryotic viruses: update from the ICTV bacterial andarchaeal viruses subcommittee.
Arch Virol. 2016 Apr;161(4):1095-9. doi: 10.1007/s00705-015-2728-0. Epub 2016 Jan 5.
Krupovic M1, Dutilh BE2,3,4, Adriaenssens EM5, Wittmann J6, Vogensen FK7, Sullivan MB8,9, Rumnieks J10, Prangishvili D1, Lavigne R11, Kropinski AM12, Klumpp J13, Gillis A14, Enault F15,16, Edwards RA17, Duffy S18, Clokie MR19, Barylski J20, Ackermann HW21, Kuhn JH22.
The taxonomy of viruses should include viruses.
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 virusclassification, 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.
A taxonomy update for the family Polyomaviridae.
Arch Virol. 2016 Jun;161(6):1739-50. doi: 10.1007/s00705-016-2794-y. Epub 2016 Feb 29.
Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses, Calvignac-Spencer S1,2, Feltkamp MC3, Daugherty MD4,5, Moens U6, Ramqvist T7, Johne R8, Ehlers B9.
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.
A proposal to rationalize within-species plant virus nomenclature:benefits and implications of inaction.
Arch Virol. 2016 Jul;161(7):2051-7. doi: 10.1007/s00705-016-2848-1. Epub 2016 Apr 21.
Jones RA1,2, Kehoe MA3.
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.
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 CL1, Amarasinghe GK2, Bányai K3, Bào Y4, Basler CF5, Bavari S6, Bejerman N7,8, Blasdell KR9, Briand FX10, Briese T11, Bukreyev A12, Calisher CH13, Chandran K14, Chéng J15, Clawson AN16, Collins PL17, Dietzgen RG18, Dolnik O19, Domier LL20, Dürrwald R21, Dye JM6, Easton AJ22, Ebihara H23, Farkas SL3, Freitas-Astúa J24, Formenty P25, Fouchier RA26, Fù Y15, Ghedin E27, Goodin MM28, Hewson R29, Horie M30, Hyndman TH31, Jiāng D15, Kitajima EW32, Kobinger GP33, Kondo H34, Kurath G35, Lamb RA36,37, Lenardon S7, Leroy EM38, Li CX39, Lin XD40, Liú L15, Longdon B41, Marton S3, Maisner A19, Mühlberger E42, Netesov SV43, Nowotny N44,45, Patterson JL46, Payne SL47, Paweska JT48, Randall RE49, Rima BK50, Rota P51, Rubbenstroth D52, Schwemmle M52, Shi M53, Smither SJ54, Stenglein MD55, Stone DM56, Takada A57, Terregino C58, Tesh RB12, Tian JH59, Tomonaga K60, Tordo N61,62, Towner JS63, Vasilakis N64,65, Verbeek M66, Volchkov VE67, Wahl-Jensen V68, Walsh JA22, Walker PJ9, Wang D69, Wang LF70,71, Wetzel T72, Whitfield AE73, Xiè JT15, Yuen KY74, Zhang YZ53, Kuhn JH75.
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).
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 M1, Ghabrial SA2, Jiang D3, Varsani A4,5,6.
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.
Arch Virol. 2016 Jul 16. [Epub ahead of print]
Ratification vote on taxonomic proposals to the InternationalCommittee on Taxonomy of Viruses (2016).
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 ( http://www.ictvonline.org/statutes.asp ), 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 ( http://www.ictvonline.org/ ) 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://talk.ictvonline.org/files/proposals/ ). 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).
Adams MJ1, Lefkowitz EJ2, King AM3, Harrach B4, Harrison RL5, Knowles NJ6, Kropinski AM7, Krupovic M8, Kuhn JH9, Mushegian AR10, Nibert M11, Sabanadzovic S12, Sanfaçon H13, Siddell SG14, Simmonds P15, Varsani A16, Zerbini FM17, Gorbalenya AE18, Davison AJ19.
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