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 expert 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:

  • Stability
  • To avoid or reject the use of names which might cause error or confusion
  • To avoid the unnecessary creation of names

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 taxon, exclude members which might one day belong to that taxon, 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]

ICTV reports

The ICTV has published reports of virus taxonomy about twice a decade since 1971 (listed below - "Reports"). The ninth ICTV report was published in December 2011;[9] the content is now freely available through the ICTV website.[10] Beginning in 2017 the tenth ICTV report will be published online on the ICTV website[11] and will be free to access with individual chapters updated on a rolling basis. The 2018 taxonomy is available online.[12], including a downloadable Excel spreadsheet of all recognized species.

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.[13] 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.[14]

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]

History

The International Classification of Viruses was a group established in 1966 to standardize the naming of viruses. The group was renamed International Committee on Taxonomy of Viruses in 1975.

In 1971 the ICTV classification for viruses infecting vertebrates included 19 genera, 2 families, and a further 24 unclassified groups.

See also

Reports

  • Viruses, International Committee on Nomenclature of; Wildy, Peter (1971). Classification and nomenclature of viruses. 1st report. Out of print
  • Viruses, International Committee on Taxonomy of; Fenner, Frank (1976). Classification and nomenclature of viruses. 2nd report. ISBN 978-3805524186.
  • Viruses, International Committee on Taxonomy of; Matthews, Richard Ellis Ford; Section On Virology, International Association of Microbiological Societies (1979). Classification and nomenclature of viruses. 3rd report. ISBN 978-3805505239.
  • Ellis, Richard; Matthews, Ford, eds. (1982). Classification and nomenclature of viruses. 4th report. Karger. p. 199. ISBN 9783805535571.
  • Viruses, International Committee on Taxonomy of; Francki, R. I. B (1991). Classification and nomenclature of viruses. 5th report. ISBN 978-3211822869.
  • Murphy, Frederik A (1995). Virus taxonomy: classification and nomenclature of viruses. 6th report. ISBN 978-3211825945.
  • Viruses, International Committee On Taxonomy Of; Van Regenmortel, M. H. V; Fauquet, C. M; Bishop, D. H. L (2000). Virus taxonomy: classification and nomenclature of viruses. 7th report. ISBN 978-0123702005.
  • Fauquet, C.M., ed. (2005). Virus taxonomy: classification and nomenclature of viruses. 8th report. Elsevier/Academic Press. ISBN 978-0080575483.
  • King, Andrew M. Q.; Lefkowitz, Elliot; Adams, Michael J.; et al., eds. (2011). Virus taxonomy: classification and nomenclature of viruses. 9th report. Elsevier/Academic Press. p. 1338. ISBN 9780123846846. Also available online.[10]
  • ICTV 10th (online) Report[11]

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. ^ a b c d e Fauquet CM, Fargette D (2005). "International Committee on Taxonomy of Viruses and the 3,142 unassigned species". Virol. J. 2: 64. doi:10.1186/1743-422X-2-64. PMC 1208960. PMID 16105179.
  3. ^ a b c Gibbs AJ (2013). "Viral taxonomy needs a spring clean; its exploration era is over". Virol. J. 10: 254. doi:10.1186/1743-422X-10-254. PMC 3751428. PMID 23938184.
  4. ^ "Banking Diverse Data - The Origins of ICTVdB". 13 November 2005. Archived from the original on 13 November 2005. Retrieved 6 April 2018.
  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. PMID 27052507.
  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". Nature Reviews Microbiology. 15 (3): 161–168. doi:10.1038/nrmicro.2016.177. PMID 28134265.
  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". Archives of Virology. 162 (5): 1441–1446. doi:10.1007/s00705-016-3215-y. PMID 28078475.
  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 978-0123846846. Retrieved 9 December 2014.
  10. ^ a b "ICTV Ninth Report".
  11. ^ a b "ICTV Tenth Report".
  12. ^ "Taxonomy".
  13. ^ Maddison DR, Swofford DL, Maddison WP (December 1997). "NEXUS: an extensible file format for systematic information". Syst. Biol. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590. PMID 11975335.
  14. ^ Boxed data, The origin of ICTVdB, webpage, retrieved 22 June 2006

External links

Bacilladnavirus

Bacilladnavirus is a genus of single stranded DNA viruses. Species in this genus infect diatoms. The name is derived from the phrase: ssDNA virus infecting Bacillariophytes. Although other single-stranded DNA viruses which infect diatoms have been discovered (Chaetoceros debilis DNA virus (CdebDNAV), C. tenuissimus DNA virus (CtenDNAV), C. lorenzianus DNA virus (ClorDNAV), C. sp. strain TG07-C28 DNA virus (Csp05DNAV), C. setoensis DNA virus (CsetDNAV), and Thalassionema nitzschioides DNA virus (TnitDNAV)), the only species officially classified in this genus is Chaetoceros salsugineum DNA virus 01 (CsalDNAV01.) In addition, 4 genomes of uncultured bacilladnaviruses have been sequenced directly from environmental samples. It was suggested that the family Bacilladnaviridae be used to classify these viruses. This was accepted by the International Committee on Taxonomy of Viruses with its Master Species List (MSL) as of fall 2018.

Filoviridae

The family Filoviridae (), a member of the order Mononegavirales, is the taxonomic home of several related viruses (filoviruses or filovirids) that form filamentous infectious viral particles (virions), and encode their genome in the form of single-stranded negative-sense RNA. Two members of the family that are commonly known are Ebola virus and Marburg virus. Both viruses, and some of their lesser known relatives, cause severe disease in humans and nonhuman primates in the form of viral hemorrhagic fevers. All filoviruses are Select Agents, World Health Organization Risk Group 4 Pathogens (requiring Biosafety Level 4-equivalent containment), National Institutes of Health/National Institute of Allergy and Infectious Diseases Category A Priority Pathogens, Centers for Disease Control and Prevention Category A Bioterrorism Agents, and listed as Biological Agents for Export Control by the Australia Group.

Flexiviridae

The Flexiviridae were a new family of viruses in the 2004 classification of viruses, but have since the 2009 classification been split into the three new families Alphaflexiviridae, Betaflexiviridae and Gammaflexiviridae. These have in turn been subsumed under the new order Tymovirales along with the old family Tymoviridae by the International Committee on Taxonomy of Viruses based on molecular phylogenetic systematic analyses of proteins (RNA polymerase and viral coat). The viruses are positive-sense ssRNA viruses, placing them in Group IV of the Baltimore classification. These viruses are filamentous and named for being highly flexible.

Members of these families are readily transmitted mechanically and have other vectors of transmission. Species tend to be confined to a single host plant, many species preferring woody hosts, but a diversity of angiosperm hosts are known to the Flexiviridae. Viral aggregates are known to form in the cytoplasm of plant cells.

Hantaviridae

Hantaviridae is a family of viruses in the order Bunyavirales. It is named for the Hantan River area in South Korea where an early outbreak of one of its species was observed.

Lloviu cuevavirus

The species Lloviu cuevavirus ( YOV-yoo KWEV-ə-VY-rəs) is the taxonomic home of a virus that forms filamentous virion, Lloviu virus (LLOV). The species is included in the genus Cuevavirus. LLOV is a distant relative of the commonly known Ebola virus and Marburg virus.

Lloviu virus

Lloviu virus ( YOV-yoo; LLOV) is a virus distantly related to the well-known pathogens Ebola virus and Marburg virus.Lloviu virus is the sole member of the species Lloviu cuevavirus, which is included genus Cuevavirus, family Filoviridae, order Mononegavirales. The name Lloviu virus is derived from Cueva del Lloviu, the name of a Spanish cave in which it was first discovered.According to the rules for taxon naming established by the International Committee on Taxonomy of Viruses (ICTV), the name Lloviu virus is always to be capitalized (because "Lloviu" is a proper noun), but is never italicized, and may be abbreviated (with LLOV being the official abbreviation).

Marburg marburgvirus

The species Marburg marburgvirus is the taxonomic home of two related viruses that form filamentous virions, Marburg virus (MARV) and Ravn virus (RAVV). Both viruses cause Marburg virus disease in humans and nonhuman primates, a form of viral hemorrhagic fever, and both are Select agents, World Health Organization Risk Group 4 Pathogens (requiring Biosafety Level 4-equivalent containment), National Institutes of Health/National Institute of Allergy and Infectious Diseases Category A Priority Pathogens, Centers for Disease Control and Prevention Category A Bioterrorism Agents, and are listed as a Biological Agents for Export Control by the Australia Group.

Marnaviridae

Marnaviridae is a family of positive-stranded RNA viruses in the order Picornavirales. The first marnavirus that was isolated, and which is the type species for the family, infects a Microphyte: the toxic bloom-forming Raphidophyte, Heterosigma akashiwo. Algae therefore seem to serve as natural hosts. There is only one genus (Marnavirus) and one species in this family, the type species Heterosigma akashiwo RNA virus (HaRNAV).HaRNAV was isolated from water collected in the Strait of Georgia in British Columbia, Canada, from a concentrated virus assemblage using the host Heterosigma akashiwo (NEPCC 522).Although the International Committee on the Taxonomy of Viruses currently only recognizes one member of the family, environmental sequencing of the RNA-dependent RNA polymerase has shown that there are many related viruses in the sea that show a high degree of temporal and spatial diversity.

Marseilleviridae

Marseilleviridae is a family of viruses first named in 2012. The genomes of these viruses are double-stranded DNA. Amoeba are often hosts, but there is evidence that they are found in humans as well. As of 2016, the International Committee on Taxonomy of Viruses recognize four species in this family, divided among 2 genera. It is a member of the nucleocytoplasmic large DNA viruses clade.

Mononegavirales

The order Mononegavirales is the taxonomic home of numerous related viruses. Members of the order that are commonly known are, for instance, Ebola virus, human respiratory syncytial virus, measles virus, mumps virus, Nipah virus, and rabies virus. All of these viruses cause significant disease in humans. Many very important pathogens of nonhuman animals and plants are also members of this order.

Nairoviridae

Nairoviridae is a family of viruses in the order Bunyavirales. Its name derives from Nairobi sheep disease, caused by the member Nairobi sheep disease orthonairovirus.

Peribunyaviridae

Peribunyaviridae is a family of viruses in the order Bunyavirales. Its name partially derives from Bunyamwera, Uganda, where the founding species was first isolated.

Phenuiviridae

Phenuiviridae is a virus family belonging to the order Bunyavirales established by ICTV in 2016. Ruminants, camels, humans, and mosquitoes are the known hosts of members of this negative-sense single-stranded RNA virus family. Of the four genera, Phlebovirus is the only genera that includes viruses that infect humans and are associated with known disease in humans (e.g. Rift Valley Fever Phlebovirus).

Picornavirales

Picornavirales is an order of viruses with vertebrate, insect, algal or plant hosts. The name has a dual etymology. First, picorna- is an acronym for poliovirus, insensitivity to ether, coxsackievirus, orphan virus, rhinovirus, and ribonucleic acid. Secondly, pico-, meaning extremely small, combines with RNA to describe these very small RNA viruses.The families within this order share a number of common features:

The virions are non-enveloped, icosahedral, and about 30 nanometers in diameter.

The capsid has a "pseudo T=3" structure, and is composed of 60 protomers each made of three similar-sized but nonidentical beta barrels.

The genome is made of one or a few single-stranded RNA(s) serving directly as mRNA, without overlapping open reading frames.

The genome has a small protein, VPg, covalently attached to its 5' end, and usually a poly-adenylated 3' end.

Each genome RNA is translated into polyprotein(s) yielding mature viral proteins through one or several virus-encoded proteinase(s).

A hallmark of the Picornavirales is a conserved module of sequence domains, Hel-Pro-Pol, which is typical of (from the amino- to the carboxy-end of the polyprotein):

A Helicase belonging to superfamily III

[the VPg is encoded between these two domains]

A chymotrypsin-like Proteinase where the catalytic residue is typically a cysteine rather than a serine,

A polymerase belonging to superfamily I; this conserved module is a hallmark of the PicornaviralesThe evolution of picorna-like viruses seems to have antedated the separation of eukaryotes into the extant crown groups.

Realm (virology)

In virology, realm is the highest taxonomic rank established by the International Committee on Taxonomy of Viruses (ICTV). The names of realms are terminated with the suffix -viria. A realm is divided into subrealms.To date there is only one taxon described at this rank, Riboviria.

Sphaerolipoviridae

Sphaerolipoviridae is a family of double-stranded DNA viruses that infect thermophilic bacteria and halophilic archea, formally approved by the International Committee on Taxonomy of Viruses in 2015. Viruses of this family have tailless icosahedral virions with an internal lipid membrane located between the protein capsid and the double-stranded DNA genome. Overall virion organization of sphaerolipoviruses is similar to that of viruses belonging to the families Tectiviridae, Corticoviridae and Turriviridae.

There are three genera in this family. Members of the genera Alphasphaerolipovirus and Betasphaerolipovirus infect halophilic archaea, while those of the genus Gammasphaerolipovirus replicate in thermophilic bacteria.

Subrealm

In virology, subrealm is the second highest taxonomic rank established by the International Committee on Taxonomy of Viruses (ICTV), after realm. The names of subrealms are terminated with the suffix -vira. A realm is divided into kingdoms.There are currently no taxa described at this rank.

Sudan ebolavirus

The species Sudan ebolavirus is a virological taxon included in the genus Ebolavirus, family Filoviridae, order Mononegavirales. The species has a single virus member, Sudan virus (SUDV). The members of the species are called Sudan ebolaviruses.

Virus classification

Virus classification is the process of naming viruses and placing them into a taxonomic system. Similar to the classification systems used for cellular organisms, virus classification is the subject of ongoing debate and proposals. This is mainly due to the pseudo-living nature of viruses, which is to say they are non-living particles with some chemical characteristics similar to those of life, or non-cellular life. As such, they do not fit neatly into the established biological classification system in place for cellular organisms.

Viruses are mainly classified by phenotypic characteristics, such as morphology, nucleic acid type, mode of replication, host organisms, and the type of disease they cause. The formal taxonomic classification of viruses is the responsibility of the International Committee on Taxonomy of Viruses (ICTV) system, although the Baltimore classification system can be used to place viruses into one of seven groups based on their manner of mRNA synthesis. Specific naming conventions and further classification guidelines are set out by the ICTV.

A catalogue of all the world's known viruses has been proposed; some related preliminary efforts have been accomplished.

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