International Committee on Taxonomy of Viruses
Encyclopedia
The International Committee on Taxonomy of Viruses (ICTV) is a committee which authorizes and organizes the taxonomic
classification of virus
es. They have developed a universal taxonomic scheme for viruses and aim to describe all the viruses of living organisms. Members of the committee are considered to be world experts on viruses. The committee formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work such as delimiting the boundaries of species within a family is typically done by study groups, which consist of experts in the families.
The committee also operates an authoritative database (ICTVdB) containing taxonomic information for 1,950 virus species, as of 2005. It is open to the public and is searchable by several different means.
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). The number of unidentified virus sequences is only expected to increase as the rate of virus sequencing increases dramatically.
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.
The name of a taxon
has no 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.
s 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.
.
s. 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.
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. 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 USA.
Taxonomy
Taxonomy is the science of identifying and naming species, and arranging them into a classification. The field of taxonomy, sometimes referred to as "biological taxonomy", revolves around the description and use of taxonomic units, known as taxa...
classification of virus
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
es. They have developed a universal taxonomic scheme for viruses and aim to describe all the viruses of living organisms. Members of the committee are considered to be world experts on viruses. The committee formed from and is governed by the Virology Division of the International Union of Microbiological Societies. Detailed work such as delimiting the boundaries of species within a family is typically done by study groups, which consist of experts in the families.
The committee also operates an authoritative database (ICTVdB) containing taxonomic information for 1,950 virus species, as of 2005. It is open to the public and is searchable by several different means.
Objectives
The official objectives of the ICTV are:- To develop an internationally agreed taxonomy for viruses
- To develop internationally agreed names for virus taxa, including species and subviral agents
- To communicate taxonomic decisions to all users of virus names, in particular the international community of virologists, by publications and via the Internet
- To maintain an index of virus names
- To maintain an ICTV database on the Internet, that records the data that characterize each named viral taxon, together with the common names of each taxon in all major languages
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
Biological classification
Biological classification, or scientific classification in biology, is a method to group and categorize organisms by biological type, such as genus or species. Biological classification is part of scientific taxonomy....
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
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence...
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). The number of unidentified virus sequences is only expected to increase as the rate of virus sequencing increases dramatically.
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.
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
Taxon
|thumb|270px|[[African elephants]] form a widely-accepted taxon, the [[genus]] LoxodontaA taxon is a group of organisms, which a taxonomist adjudges to be a unit. Usually a taxon is given a name and a rank, although neither is a requirement...
has no 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.
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 epithetEpithet
An epithet or byname is a descriptive term accompanying or occurring in place of a name and having entered common usage. It has various shades of meaning when applied to seemingly real or fictitious people, divinities, objects, and binomial nomenclature. It is also a descriptive title...
s 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 virus. Approval of a new genus must be accompanied by the approval of a type speciesType species
In biological nomenclature, a type species is both a concept and a practical system which is used in the classification and nomenclature of animals and plants. The value of a "type species" lies in the fact that it makes clear what is meant by a particular genus name. A type species is the 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 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 viridae.Orders
An order is a group of families sharing certain common characters. An order name must be a single word ending in virales.Rules for sub-viral agents
Rules concerned with the classification of viruses shall also apply to the classification of viroidViroid
Viroids are plant pathogens that consist of a short stretch of highly complementary, circular, single-stranded RNA without the protein coat that is typical for viruses. The smallest discovered is a 220 nucleobase scRNA associated with the rice yellow mottle sobemovirus...
s. 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
- 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.
- 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.
- In formal usage, the name of the taxon shall precede the term for the taxonomic unit.
Decimal code
The ICTV classification uses an eight position decimal code to represent order, family, subfamily, genus, species, subspecies, serotype or subtype, and strain or isolate. Each position in the code uses 1, 2, or 3 numerical digits. The decimal code identifies a virus to the level of strain or isolate. Two examples are shown in the table below.| Taxon | Decimal Code | Name |
|---|---|---|
| Poliovirus-1 Brunhilde | ||
| Order | 00. | |
| Family | Picornaviridae | |
| Subfamily | 00.052.0. | |
| Genus | Enterovirus | |
| Species | 00.052.0.01.007. | Poliovirus 1 |
| Subspecies | 00.052.0.01.007.00. | |
| Serotype | 00.052.0.01.007.00.001. | Poliovirus 1 |
| Strain or Isolate | 00.052.0.01.007.00.001.001. | PV-1 Brunhilde |
| Influenza A virus, A/Puerto Rico/8/34 (H1N1) isolate | ||
| Order | 00. | |
| Family | Orthomyxoviridae | |
| Subfamily | 00.046.0. | |
| Genus | Influenzavirus A | |
| Species | Influenza A virus | |
| Subspecies | 00.046.0.01.001.00. | |
| Serotype | 00.046.0.01.001.00.001. | H1N1 |
| Strain or Isolate | 00.046.0.01.001.00.001.001. | A/Puerto Rico/8/34 |
Notes
|
||
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, genomicGenome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
type, nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
replication, diseases, vectors, and geographical distribution, among other characteristics.
The database was developed at the Australian National University
Australian National University
The Australian National University is a teaching and research university located in the Australian capital, Canberra.As of 2009, the ANU employs 3,945 administrative staff who teach approximately 10,000 undergraduates, and 7,500 postgraduate students...
with support of the US National Science Foundation
National Science Foundation
The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
, and sponsored by the American Type Culture Collection
American Type Culture Collection
The American Type Culture Collection is a private, not-for-profit biological resource center whose mission focuses on the acquisition, authentication, production, preservation, development and distribution of standard reference microorganisms, cell lines and other materials for research in the...
. It uses the Description Language for Taxonomy (DELTA
DELTA (taxonomy)
DELTA is a data format used in taxonomy for recording descriptions of living things. It is designed for computer processing, allowing the generation of identification keys, diagnosis, etc....
) system, a world standard for taxonomic data exchange, developed at Australia's Commonwealth Scientific and Industrial Research Organisation
Commonwealth Scientific and Industrial Research Organisation
The Commonwealth Scientific and Industrial Research Organisation is the national government body for scientific research in Australia...
(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. 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 USA.
See also
- Virus classificationVirus classificationVirus 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...
- BioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
- DELTA (taxonomy)DELTA (taxonomy)DELTA is a data format used in taxonomy for recording descriptions of living things. It is designed for computer processing, allowing the generation of identification keys, diagnosis, etc....
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