International Committee on Taxonomy of Viruses

The International Committee on Taxonomy of Viruses (ICTV) authorizes and organizes the taxonomic classification of and the nomenclatures for viruses.[1][2][3] The ICTV have developed a universal taxonomic-scheme for viruses, and means to describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered experts virologists.[4] The ICTV was formed from and is governed by the Virology Division of the International Union of Microbiological Societies.[5] Detailed work, such as delimiting the boundaries of species within a family, typically is performed by study groups of experts in the families.[2]

Objectives

The objectives of the International Committee on Taxonomy of Viruses are:

  1. To develop an internationally agreed taxonomy for viruses
  2. To establish internationally agreed names for virus taxa.
  3. To communicate the decisions reached concerning the classification and nomenclature of viruses to virologists by holding meetings and publishing reports.
  4. To maintain an Official Index of agreed names of virus taxa.
  5. To study the virus effects in modern society and their behaviour.

Principles of nomenclature

The ICTV's essential principles of virus nomenclature are:

The ICTV's universal virus classification system uses a slightly modified version of the standard biological classification system. It only recognises the taxa order, family, subfamily, genus, and species. When it is uncertain how to classify a species into a genus but its classification in a family is clear, it will be classified as an unassigned species of that family. Many taxa remain unranked. There are also, as of 2005, GenBank sequences assigned to 3,142 "species" which are not accounted for in the ICTV report (due to the way GenBank works, however, the actual number of proper species is probably significantly smaller).[2] The number of unidentified virus sequences is only expected to increase as the rate of virus sequencing increases dramatically.[2]

The ICTV has been strikingly successful in achieving stability, since their inception in 1962. Every genus and family recognized in the 1980s continued to be in use as of 2005, for example.[2]

Naming and changing taxa

Proposals for new names, name changes, and the establishment and taxonomic placement of taxa are handled by the Executive Committee of the ICTV in the form of proposals. All relevant ICTV subcommittees and study groups are consulted prior to a decision being taken.

The name of a taxon has no official status until it has been approved by ICTV, and names will only be accepted if they are linked to approved hierarchical taxa. If no suitable name is proposed for a taxon, the taxon may be approved and the name be left undecided until the adoption of an acceptable international name, when one is proposed to and accepted by ICTV. Names must not convey a meaning for the taxon which would seem to either exclude viruses which are rightfully members of that taxa, exclude members which might one day belong to that taxa, or include viruses which are members of different taxa.

Rules for taxa

Species

A species name shall consist of as few words as practicable but must not consist only of a host name and the word virus. A species name must provide an appropriately unambiguous identification of the species. Numbers, letters, or combinations thereof may be used as species epithets where such numbers and letters are already widely used. However, newly designated serial numbers, letters or combinations thereof are not acceptable alone as species epithets. If a number or letter series is in existence it may be continued.

Genera

A virus genus is a group of related species that share some significant properties and often only differ in host range and virulence. A genus name must be a single word ending in the suffix -virus. Approval of a new genus must be accompanied by the approval of a type species.

Subfamilies

A subfamily is a group of genera sharing certain common characters. The taxon shall be used only when it is needed to solve a complex hierarchical problem. A subfamily name must be a single word ending in the suffix -virinae.

Families

A family is a group of genera, whether or not these are organized into subfamilies, sharing certain common characters. A family name must be a single word ending in the suffix -viridae.

Orders

An order is a group of families sharing certain common characters. An order name must be a single word ending in the suffix -virales.

Rules for sub-viral agents

Rules concerned with the classification of viruses shall also apply to the classification of viroids. The formal endings for taxa of viroids are the word viroid for species, the suffix -viroid for genera, the suffix -viroinae for sub-families, should this taxon be needed, and -viroidae for families.

Retrotransposons are considered to be viruses in classification and nomenclature. Satellites and prions are not classified as viruses but are assigned an arbitrary classification as seems useful to workers in the particular fields.

Rules for orthography

  1. In formal taxonomic usage the accepted names of virus orders, families, subfamilies, and genera are printed in italics and the first letters of the names are capitalized.[6]
  2. Species names are printed in italics and have the first letter of the first word capitalized. Other words are not capitalized unless they are proper nouns, or parts of proper nouns.
  3. In formal usage, the name of the taxon shall precede the term for the taxonomic unit.

Classification of viruses discovered by metagenomics

Acknowledging the importance of viral metagenomics, the ICTV recognizes that genomes assembled from metagenomic data represent actual viruses and encourages their official classification following the same procedures as those used for viruses isolated and characterized using classical virology approaches.[7][8]

Ninth report

The ninth ICTV report was published in December 2011.[9]

ICTVdb database

ICTVdb is a species and isolate database that has been intended to serve as a companion to the ICTV taxonomy database. The development of ICTVdB has been supported by the ICTV since 1991 and was initially intended to aid taxonomic research. The database classifies viruses based primarily on their chemical characteristics, genomic type, nucleic acid replication, diseases, vectors, and geographical distribution, among other characteristics.

The database was developed at the Australian National University with support of the US National Science Foundation, and sponsored by the American Type Culture Collection. It uses the Description Language for Taxonomy (DELTA) system, a world standard for taxonomic data exchange, developed at Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO). DELTA is able to store a wide diversity of data and translate it into a language suitable for traditional reports and web publication. For example, ICTVdB does not itself contain genomic sequence information but can convert DELTA data into NEXUS format.[10] It can also handle large data inputs and is suited to compiling long lists of virus properties, text comments, and images.

ICTVdB has grown in concept and capability to become a major reference resource and research tool, in 1999 it was receiving over 30,000 combined online hits per day from its main site at the Australian National University, and two mirror sites based in the UK and United States.[11]

In 2011, the ICTV decided to suspend the ICTVdb project and web site. This decision was made after it became apparent that the taxonomy provided on the site was many years out of date, and that some of the information on the site was inaccurate due to problems with how the database was being queried and processed to support the natural language output of the ICTVdb web site. The ICTV has begun discussions on how best to fix these problems, but decided that the time frame for updates and error correction were sufficiently long that it was best to take the site down rather than perpetuate the release of inaccurate information. As of August 2013, the database remains on hold.[3] According to some views, "ICTV should also promote the use of a public database to replace the ICTV database as a store of the primary metadata of individual viruses, and should publish abstracts of the ICTV Reports in that database, so that they are ‘Open Access’."[3]

See also

Reports

References

  1. ↑ King, Andrew M.Q.; Lefkowitz, E.; Adams, M.J.; Carstens, E.B. (2012). Virus Taxonomy Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier. ISBN 978-0-12-384684-6.
  2. 1 2 3 4 5 Fauquet CM, Fargette D (2005). "International Committee on Taxonomy of Viruses and the 3,142 unassigned species". Virol. J. 2: 64. PMC 1208960 Freely accessible. PMID 16105179. doi:10.1186/1743-422X-2-64.
  3. 1 2 3 Gibbs AJ (2013). "Viral taxonomy needs a spring clean; its exploration era is over". Virol. J. 10: 254. PMC 3751428 Freely accessible. PMID 23938184. doi:10.1186/1743-422X-10-254.
  4. ↑ The Origin of ICTVdB, webpage, retrieved 22 June 2006
  5. ↑ http://www.nas.edu/gateway/international/1177.html
  6. ↑ Ali, Muhammad (2016). "Towards a coherent nomenclature of plant viruses". Virologica Sinica. 31 (3): 197–198. doi:10.1007/s12250-016-3741-5.
  7. ↑ Simmonds P, Adams MJ, Benkő M, Breitbart M, Brister JR, Carstens EB, Davison AJ, Delwart E, Gorbalenya AE, Harrach B, Hull R, King AMQ, Koonin EV, Krupovic M, Kuhn JH, Lefkowitz EJ, Nibert ML, Orton R, Roossinck MJ, Sabanadzovic S, Sullivan MB, Suttle CA, Tesh RB, van der Vlugt RA, Varsani A, Zerbini FM (2017). "Consensus statement: Virus taxonomy in the age of metagenomics" (PDF). Nature Reviews Microbiology. 15 (3): 161–168. PMID 28134265. doi:10.1038/nrmicro.2016.177.
  8. ↑ 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 (2017). "50 years of the International Committee on Taxonomy of Viruses: progress and prospects" (PDF). Archives of Virology. 162 (5): 1441–1446. PMID 28078475. doi:10.1007/s00705-016-3215-y.
  9. ↑ King, Andrew M. Q.; et al., eds. (2012). Virus taxonomy : classification and nomenclature of viruses : ninth report of the International Committee on Taxonomy of Viruses. London: Academic Press. ISBN 0123846846. Retrieved 9 December 2014.
  10. ↑ Maddison DR, Swofford DL, Maddison WP (December 1997). "NEXUS: an extensible file format for systematic information". Syst. Biol. 46 (4): 590–621. PMID 11975335. doi:10.1093/sysbio/46.4.590.
  11. ↑ Boxed data, The origin of ICTVdB, webpage, retrieved 22 June 2006
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