Virus classification is the process of naming viruses and placing them into a taxonomic system similar to the classification systems used for cellular organisms.
Viruses are 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 and, in 2013, some preliminary efforts were underway.
Species form the basis for any biological classification system. Before 1982, it was thought that viruses could not be made to fit Ernst Mayr's reproductive concept of species, and so were not amenable to such treatment. In 1982, the ICTV started to define a species as "a cluster of strains" with unique identifying qualities. In 1991, the more specific principle that a virus species is a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche was adopted.
In July 2013, the ICTV definition of species changed to state: "A species is a monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria."These criteria include the structure of the capsid, the existence of an envelope, the gene expression program for its proteins, host range, pathogenicity, and most importantly genetic sequence similarity and phylogenetic relationship.
The actual criteria used vary by the taxon, and can be inconsistent (arbitrary similarity thresholds) or unrelated to lineage (geography) at times.The matter is, for many, not yet settled.
This article is missing information about which species concept.(November 2021)
The International Committee on Taxonomy of Viruses began to devise and implement rules for the naming and classification of viruses early in the 1970s, an effort that continues to the present. The ICTV is the only body charged by the International Union of Microbiological Societies with the task of developing, refining, and maintaining a universal virus taxonomy.The system shares many features with the classification system of cellular organisms, such as taxon structure. However, some differences exist, such as the universal use of italics for all taxonomic names, unlike in the International Code of Nomenclature for algae, fungi, and plants and International Code of Zoological Nomenclature.
Viral classification starts at the level of realm and continues as follows, with the taxonomic suffixes in parentheses:
Unlike the system of binomial nomenclature adopted in cellular species, there is currently no standardized form for virus species names. At present, the ICTV mandates that a species name must contain as few words as possible while remaining distinct, and must not only contain the word virus and the host name.Species names often take the form of [Disease] virus, particularly for higher plants and animals. In 2019, the ICTV published a proposal to adopt a more formalized system of binomial nomenclature for virus species names, to be voted on in 2020. However, some virologists later objected to the potential naming system change, arguing that the debate came while many in the field were preoccupied due to the COVID-19 pandemic.
As of 2019, all levels of taxa except subrealm, subkingdom, and subclass are used. Four realms, one incertae sedis order, 24 incertae sedis families, and three incertae sedis genera are recognized:
Realms: Duplodnaviria , Monodnaviria , Adnaviria , Ribozyviria , Riboviria , and Varidnaviria
Incertae sedis families:
Incertae sedis genera: Dinodnavirus , Rhizidiovirus
It has been suggested that similarity in virion assembly and structure observed for certain viral groups infecting hosts from different domains of life (e.g., bacterial tectiviruses and eukaryotic adenoviruses or prokaryotic Caudovirales and eukaryotic herpesviruses) reflects an evolutionary relationship between these viruses.Therefore, structural relationship between viruses has been suggested to be used as a basis for defining higher-level taxa – structure-based viral lineages – that could complement the ICTV classification scheme of 2010.
The ICTV has gradually added many higher-level taxa using relationships in protein folds. All four realms defined in the 2019 release are defined by the presence of a protein of a certain structural family.
Baltimore classification (first defined in 1971) is a classification system that places viruses into one of seven groups depending on a combination of their nucleic acid (DNA or RNA), strandedness (single-stranded or double-stranded), sense, and method of replication. Named after David Baltimore, a Nobel Prize-winning biologist, these groups are designated by Roman numerals. Other classifications are determined by the disease caused by the virus or its morphology, neither of which are satisfactory due to different viruses either causing the same disease or looking very similar. In addition, viral structures are often difficult to determine under the microscope. Classifying viruses according to their genome means that those in a given category will all behave in a similar fashion, offering some indication of how to proceed with further research. Viruses can be placed in one of the seven following groups:
Viruses with a DNA genome, except for the DNA reverse transcribing viruses, are members of three of the four recognized viral realms: Duplodnaviria , Monodnaviria , and Varidnaviria . But the incertae sedis order Ligamenvirales , and many other incertae sedis families and genera, are also used to classify DNA viruses. The domains Duplodnaviria and Varidnaviria consist of double-stranded DNA viruses; other double-stranded DNA viruses are incertae sedis. The domain Monodnaviria consists of single-stranded DNA viruses that generally encode a HUH endonuclease; other single-stranded DNA viruses are incertae sedis.
|Virus family||Examples (common names)||Virion|
|Nucleic acid type||Group|
|1. Adenoviridae||Canine hepatitis virus, Some types of the common cold||Naked||Icosahedral||ds||I|
|2. Papovaviridae||JC virus, HPV||Naked||Icosahedral||ds circular||I|
|3. Parvoviridae||Human parvovirus B19, canine parvovirus||Naked||Icosahedral||ss||II|
|4. Herpesviridae||Herpes simplex virus, varicella-zoster virus, cytomegalovirus, Epstein–Barr virus||Enveloped||Icosahedral||ds||I|
|5. Poxviridae||Smallpox virus, cowpox, myxoma virus, monkeypox, vaccinia virus||Complex coats||Complex||ds||I|
|6. Anelloviridae||Torque teno virus||Naked||Icosahedral||ss circular||II|
|7. Pleolipoviridae||HHPV1, HRPV1||Enveloped||ss/ds linear/circular||I/II|
All viruses that have an RNA genome, and that encode an RNA-dependent RNA polymerase (RdRp), are members of the kingdom Orthornavirae , within the realm Riboviria .
|Virus Family||Examples (common names)||Capsid|
|Nucleic acid type||Group|
|1. Reoviridae||Reovirus, rotavirus||Naked||Icosahedral||ds||III|
|2. Picornaviridae||Enterovirus, rhinovirus, hepatovirus, cardiovirus, aphthovirus, poliovirus, parechovirus, erbovirus, kobuvirus, teschovirus, coxsackie||Naked||Icosahedral||ss||IV|
|3. Caliciviridae||Norwalk virus||Naked||Icosahedral||ss||IV|
|4. Togaviridae||Eastern equine encephalitis||Enveloped||Icosahedral||ss||IV|
|5. Arenaviridae||Lymphocytic choriomeningitis virus, Lassa fever||Enveloped||Complex||ss(-)||V|
|6. Flaviviridae||Dengue virus, hepatitis C virus, yellow fever virus, Zika virus||Enveloped||Icosahedral||ss||IV|
|7. Orthomyxoviridae||Influenzavirus A, influenzavirus B, influenzavirus C, isavirus, thogotovirus||Enveloped||Helical||ss(-)||V|
|8. Paramyxoviridae||Measles virus, mumps virus, respiratory syncytial virus, Rinderpest virus, canine distemper virus||Enveloped||Helical||ss(-)||V|
|9. Bunyaviridae||California encephalitis virus, Sin nombre virus||Enveloped||Helical||ss(-)||V|
|10. Rhabdoviridae||Rabies virus, Vesicular stomatitis||Enveloped||Helical||ss(-)||V|
|11. Filoviridae||Ebola virus, Marburg virus||Enveloped||Helical||ss(-)||V|
|12. Coronaviridae||Human coronavirus 229E, Human coronavirus NL63, Human coronavirus OC43, Human coronavirus HKU1, Middle East respiratory syndrome-related coronavirus, Severe acute respiratory syndrome coronavirus, and Severe acute respiratory syndrome coronavirus 2||Enveloped||Helical||ss||IV|
|14. Bornaviridae||Borna disease virus||Enveloped||Helical||ss(-)||V|
|15. Arteriviridae||Arterivirus, equine arteritis virus||Enveloped||Icosahedral||ss||IV|
|16. Hepeviridae||Hepatitis E virus||Naked||Icosahedral||ss||IV|
All viruses that encode a reverse transcriptase (also known as RT or RNA-dependent DNA polymerase) are members of the class Revtraviricetes , within the phylum Arterviricota, kingdom Pararnavirae, and realm Riboviria . The class Blubervirales contains the single family Hepadnaviridae of DNA RT (reverse transcribing) viruses; all other RT viruses are members of the class Ortervirales.
|Virus Family||Examples (common names)||Capsid|
|Nucleic acid type||Group|
|1. Retroviridae||HIV||Enveloped||dimer RNA||VI|
|2. Caulimoviridae||Caulimovirus, Cacao swollen-shoot virus (CSSV)||Naked||VII|
|3. Hepadnaviridae||Hepatitis B virus||Enveloped||Icosahedral||circular, partially ds||VII|
Holmes (1948) used a Linnaean taxonomy with binomial nomenclature to classify viruses into 3 groups under one order, Virales. They are placed as follows:
The system was not accepted by others due to its neglect of morphological similarities.
The following infectious agents are smaller than viruses and have only some of their properties.Since 2015, the ICTV has allowed them to be classified in a similar way as viruses are.
Satellites depend on co-infection of a host cell with a helper virus for productive multiplication. Their nucleic acids have substantially distinct nucleotide sequences from either their helper virus or host. When a satellite subviral agent encodes the coat protein in which it is encapsulated, it is then called a satellite virus.
Satellite-like nucleic acids resemble satellite nucleic acids, in that they replicate with the aid of helper viruses. However they differ in that they can encode functions that can contribute to the success of their helper viruses; while they are sometimes considered to be genomic elements of their helper viruses, they are not always found within their helper viruses.
Defective interfering particles are defective viruses that have lost their ability to replicate except in the presence of a helper virus, which is normally the parental virus. They can also interfere with the helper virus.
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An RNA virus is a virus which has RNA as its genetic material. The nucleic acid is usually single-stranded RNA (ssRNA) but it may be double-stranded RNA (dsRNA). Notable human diseases caused by RNA viruses include the common cold, influenza, SARS, MERS, COVID-19, Dengue Virus, hepatitis C, hepatitis E, West Nile fever, Ebola virus disease, rabies, polio, mumps, and measles.
Viroids are small single-stranded, circular RNAs that are infectious pathogens. Unlike viruses, they have no protein coating. All known viroids are inhabitants of angiosperms, and most cause diseases, whose respective economic importance to humans varies widely.
A satellite is a subviral agent that depends on the coinfection of a host cell with a helper virus for its replication. Satellites can be divided into two major classes: satellite viruses and satellite nucleic acids. Satellite viruses, which are most commonly associated with plants, are also found in mammals, arthropods, and bacteria. They encode structural proteins to enclose their genetic material, which are therefore distinct from the structural proteins of their helper viruses. Satellite nucleic acids, in contrast, do not encode their own structural proteins, but instead are encapsulated by proteins encoded by their helper viruses. The genomes of satellites range upward from 359 nucleotides in length for satellite tobacco ringspot virus RNA (STobRV).
Geminiviridae is a family of plant viruses that encode their genetic information on a circular genome of single-stranded (ss) DNA. There are 520 species in this family, assigned to 14 genera. Diseases associated with this family include: bright yellow mosaic, yellow mosaic, yellow mottle, leaf curling, stunting, streaks, reduced yields. They have single-stranded circular DNA genomes encoding genes that diverge in both directions from a virion strand origin of replication. According to the Baltimore classification they are considered class II viruses. It is the largest known family of single stranded DNA viruses.
The International Committee on Taxonomy of Viruses (ICTV) authorizes and organizes the taxonomic classification of and the nomenclatures for viruses. The ICTV has developed a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus that affects living organisms. The members of the International Committee on Taxonomy of Viruses are considered expert virologists. The ICTV was 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, typically is performed by study groups of experts in the families.
Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group. Seven Baltimore groups are described that take into consideration whether the viral genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), whether the genome is single- or double-stranded, and whether the sense of a single-stranded RNA genome is positive or negative.
Totivirus is a genus of double-stranded RNA viruses in the family Totiviridae. Fungi serve as natural hosts. The name of the group derives from Latin toti which means undivided or whole. There are seven species in this genus.
Double-stranded RNA viruses are a polyphyletic group of viruses that have double-stranded genomes made of ribonucleic acid. The double-stranded genome is used to transcribe a positive-strand RNA by the viral RNA-dependent RNA polymerase (RdRp). The positive-strand RNA may be used as messenger RNA (mRNA) which can be translated into viral proteins by the host cell's ribosomes. The positive-strand RNA can also be replicated by the RdRp to create a new double-stranded viral genome.
Carlavirus, formerly known as the "Carnation latent virus group", is a genus of viruses in the order Tymovirales, in the family Betaflexiviridae. Plants serve as natural hosts. There are 53 species in this genus. Diseases associated with this genus include: mosaic and ringspot symptoms.
Picobirnavirus is a genus of double-stranded RNA viruses. It is the only genus in the family Picobirnaviridae. Although amniotes, especially mammals, were thought to serve as hosts, it has been recently suggested that these viruses might infect bacteria and possibly some other invertebrates. There are three species in this genus. Associated symptoms include gastroenteritis in animals and humans, though the disease association is unclear.
Entomopoxvirinae is a subfamily of viruses, in the family Poxviridae. Insects, human, vertebrates, and arthropods serve as natural hosts. There are currently 31 species in this subfamily, divided among 4 genera with one species unassigned to a genus. Diseases associated with this subfamily include: impairment of motility and development.
Megabirnaviridae is a family of double-stranded RNA viruses with one genus Megabirnavirus which infects fungi. The group name derives from member's bipartite dsRNA genome and mega that is greater genome size than families Birnaviridae and Picobirnaviridae. There is only one species in this family: Rosellinia necatrix megabirnavirus 1. Diseases associated with this family include: reduced host virulence.
Spiraviridae is a family of viruses that replicate in hyperthermophilic archaea of the genus Aeropyrum, specifically Aeropyrum pernix. The family contains one genus, Alphaspiravirus, which contains one species, Aeropyrum coil-shaped virus. The virions of Aeropyrum coil-shaped virus (ACV) are non-enveloped and in the shape of hollow cylinders that are formed by a coiling fiber that consists of two intertwining halves of the circular DNA strand inside a capsid. An appendage protrudes from each end of the cylindrical virion. The viral genome is positive-sense, single-stranded DNA ( ssDNA) and encodes for significantly more genes than other known ssDNA viruses. ACV is also unique in that it appears to lack its own enzymes to aid replication, instead likely using the host cell's replisomes. ACV has no known relation to any other archaea-infecting viruses, but it does share its coil-like morphology with some other archaeal viruses, suggesting that such viruses may be an ancient lineage that only infect archaea.
Positive-strand RNA viruses are a group of related viruses that have positive-sense, single-stranded genomes made of ribonucleic acid. The positive-sense genome can act as messenger RNA (mRNA) and can be directly translated into viral proteins by the host cell's ribosomes. Positive-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) which is used during replication of the genome to synthesize a negative-sense antigenome that is then used as a template to create a new positive-sense viral genome.
Riboviria is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase, as well as reverse-transcribing viruses that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase (RdRp), also called RNA replicase, produces RNA from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA (mRNA) for translation of viral proteins.
In virology, realm is the highest taxonomic rank established for viruses by the International Committee on Taxonomy of Viruses (ICTV), which oversees virus taxonomy. Six virus realms are recognized and united by specific highly conserved traits:
Saccharomyces cerevisiae virus L-A, also called L-A helper virus, is a member of the Totiviridae family of viruses found primarily in Saccharomyces cerevisiae. Its discovery in the 1970s was the main starting point of research on yeast virology. It is a double-stranded RNA virus with no extracellular phase and so is inherited through vertical cytoplasmic transmission. Additionally, in many strains of the yeast, it is found along with another virus called the M virus, known to encode the killer toxin in many S. cerevisiae strains which confers the ability to kill neighboring sensitive cells that do not harbor the virus. It is indeed for this reason the virus is referred to as a helper virus, due to the M genome's dependence on it for its own survival and replication.
Orthornavirae is a kingdom of viruses that have genomes made of ribonucleic acid (RNA) and which encode an RNA-dependent RNA polymerase (RdRp). The RdRp is used to transcribe the viral RNA genome into messenger RNA (mRNA) and to replicate the genome. Viruses in this kingdom also share a number of characteristics involving evolution, including high rates of genetic mutations, recombinations, and reassortments.
Duplornaviricota is a phylum of RNA viruses, which contains all double-stranded RNA viruses, except for those in phylum Pisuviricota. Characteristic of the group is a viral capsid composed of 60 homo- or heterodimers of capsid protein on a pseudo-T=2 lattice. Duplornaviruses infect both prokaryotes and eukaryotes. The name of the group derives from Italian duplo which means double, rna for the type of virus, and -viricota which is the suffix for a virus phylum.
Tolivirales is an order of RNA viruses which infect insects and plants. Member viruses have a positive-sense single-stranded RNA genome. The virions are non-enveloped, spherical, and have an icosahedral capsid. The name of the group is a syllabic abbreviation of "tombusvirus-like" with the suffix -virales indicating a virus order.