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.
In 2021, the ICTV changed the International Code of Virus Classification and Nomenclature (ICVCN) to mandate a binomial format (genus|| ||species) for naming new viral species similar to that used for cellular organisms; the names of species coined prior to 2021 are gradually being converted to the new format, a process which has been stated to be planned to be completed by end 2023.
As at 2022, the ICTV taxonomy listed 11,273 named virus species (including some classed as satellite viruses and others as viroids) in 2,818 genera, 264 families, 72 orders, 40 classes, 17 phyla, 9 kingdoms and 6 realms. [1] However, the number of named viruses considerably exceeds the number of named virus species since, by contrast to the classification systems used elsewhere in biology, a virus "species" is a collective name for a group of (presumably related) viruses sharing certain common features (see below). Also, the use of the term "kingdom" in virology does not equate to its usage in other biological groups, where it reflects high level groupings that separate completely different kinds of organisms (see Kingdom (biology)).
The currently accepted and formal definition of a 'virus' was accepted by the ICTV Executive Committee in November 2020 and ratified in March 2021, and is as follows:[2]
Viruses sensu stricto are defined operationally by the ICTV as a type of MGE that encodes at least one protein that is a major component of the virion encasing the nucleic acid of the respective MGE and therefore the gene encoding the major virion protein itself or MGEs that are clearly demonstrable to be members of a line of evolutionary descent of such major virion protein-encoding entities. Any monophyletic group of MGEs that originates from a virion protein-encoding ancestor should be classified as a group of viruses.
Species definition
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.[3]
As at 2021 (the latest edition of the ICVCN), the ICTV definition of species states: "A species is the lowest taxonomic level in the hierarchy approved by the ICTV. A species is a monophyletic group of MGEs (mobile genetic elements) whose properties can be distinguished from those of other species by multiple criteria", with the comment "The criteria by which different species within a genus are distinguished shall be established by the appropriate Study Group. These criteria may include, but are not limited to, natural and experimental host range, cell and tissue tropism, pathogenicity, vector specificity, antigenicity, and the degree of relatedness of their genomes or genes. The criteria used should be published in the relevant section of the ICTV Report and reviewed periodically by the appropriate Study Group."[4]
Below species rank (named viruses/virus strains/isolates)
Many individually named viruses (sometimes referred to as "virus strains") exist at below the rank of virus species. The ICVCN gives the examples of blackeye cowpea mosaic virus and peanut stripe virus, which are both classified in the species Bean common mosaic virus, the latter a member of the genus Potyvirus that will in due course receive a binomial name as Potyvirus [species...]. As another example, the virus SARS-CoV-1, that causes severe acute respiratory syndrome (SARS) is different from the virus SARS-CoV-2, the cause of the COVID-19 pandemic, but both are classified within the same virus species, a member of the genus Betacoronavirus that is currently known as Severe acute respiratory syndrome-related coronavirus which, per the 2021 mandate from the ICTV, will also receive a binomial name in due course. As set out in the ICVCN, section 3.4, the names [and definitions] of taxa below the rank of species are not governed by the ICTV; "Naming of such entities is not the responsibility of the ICTV but of international specialty groups. It is the responsibility of ICTV Study Groups to consider how these entities may best be classified into species."[4] Using the example given above, the virus causing the COVID-19 pandemic was given the designation "SARS-CoV-2" by the Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses in 2020; in the same publication, this Study Group recommended a naming convention for particular isolates of this virus "resembl[ing] the formats used for isolates of avian coronaviruses, filoviruses and influenza virus" in the format virus/host/location/isolate/date, with a cited example as "SARS-CoV-2/human/Wuhan/X1/2019".[5]
In parallel to the system of binomial nomenclature adopted in cellular species, the ICTV has recently (2021) mandated that new virus species be named in a binomial format (genus|| species), and that pre-existing virus species names be progressively replaced with new names in the binomial format.[7] A mid-2023 review of the status of this changeover stated: "...a large number of proposals [concerning virus nomenclature, submitted to the ICTV Executive Committee (EC) for its consideration] renamed existing species for compliance with the recently mandated binomial nomenclature format. As a result, 8,982 out of the current 11,273 species (80%) now have binomial names. The process will be concluded in 2023, with the remaining 2,291 species being renamed."[8]
As of 2021, all levels of taxa except subrealm, subkingdom, and subclass are used. Six realms, one incertae sedis class, 22 incertae sedis families, and two incertae sedis genera are recognized:[9]
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.[10] 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.[11]
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.[12]
The Baltimore Classification of viruses is based on the method of viral mRNA synthesis
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:[13]
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 HUHendonuclease; other single-stranded DNA viruses are incertae sedis.[14]
Group I: viruses possess double-stranded DNA. Viruses that cause chickenpox and herpes are found here.
Group III: viruses possess double-stranded RNA genomes, e.g. rotavirus.
Group IV: viruses possess positive-sense single-stranded RNA genomes. Many well known viruses are found in this group, including the picornaviruses (which is a family of viruses that includes well-known viruses like Hepatitis A virus, enteroviruses, rhinoviruses, poliovirus, and foot-and-mouth virus), SARS virus, hepatitis C virus, yellow fever virus, and rubella virus.
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.[16]
Group VI: viruses possess single-stranded RNA viruses that replicate through a DNA intermediate. The retroviruses are included in this group, of which HIV is a member.
Group VII: viruses possess double-stranded DNA genomes and replicate using reverse transcriptase. The hepatitis B virus can be found in this group.
The system was not accepted by others due to its neglect of morphological similarities.[17]
Subviral agents
Infectious agents are smaller than viruses and have only some of their properties.[18][19] Since 2015, the ICTV has allowed them to be classified in a similar way as viruses are.[20]
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.[18]
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.
Defective interfering particles (RNA)
Defective interfering particles (DNA)
Viriforms
Viriforms are a polyphyletic category of endogenous viral elements. Sometime in their evolution, they became "domesticated" by their host as a key part of the host's lifecycle. The prototypical example is members of the (also polyphyletic) Polydnaviriformidae, which are used by wasps to send pieces of immunity-blunting DNA into the prey by packing them into virion-like particles. Other members are so-called gene transfer agents (GTAs) found among prokaryotes. GTA particles resemble tailed phages, but are smaller and carry mostly random pieces of host DNA. GTAs are produced by the host in times of stress; releasing GTAs kills the host cell, but allows pieces of its genetic material to live on in other bacteria, usually of the same species.[24] The three known clades of GTAs, Rhodogtaviriformidae, Bartogtaviriformidae, and Brachygtaviriformidae, all arised independently from different parts of the Caudoviricetes family tree.[25]
↑ Walker PJ, Siddell SG, Lefkowitz EJ, etal. (6 July 2021). "Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)". Archives of Virology. 168 (9): 2633–2648. doi:10.1007/s00705-021-05156-1. hdl:10362/134245. PMID34231026.
↑ Zerbini F, Siddell S, Lefkowitz E, etal. (10 June 2023). "Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023)". Archives of Virology. 168 (article no. 175): 175. doi:10.1007/s00705-023-05797-4. PMID37296227.
1 2 "Subviral Agents". ICTV 9th Report (2011). International Committee on Taxonomy of Viruses. Archived from the original on Jul 7, 2022. Retrieved 2020-06-15. Updated version in sync with current release: "Subviral Agents". 10th Report. International Committee on Taxonomy of Viruses. Archived from the original on Jul 2, 2022.
An RNA virus is a virus—other than a retrovirus—that has ribonucleic acid (RNA) as its genetic material. The nucleic acid is usually single-stranded RNA (ssRNA) but it may be double-stranded (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.
Parvoviruses are a family of animal viruses that constitute the family Parvoviridae. They have linear, single-stranded DNA (ssDNA) genomes that typically contain two genes encoding for a replication initiator protein, called NS1, and the protein the viral capsid is made of. The coding portion of the genome is flanked by telomeres at each end that form into hairpin loops that are important during replication. Parvovirus virions are small compared to most viruses, at 23–28 nanometers in diameter, and contain the genome enclosed in an icosahedral capsid that has a rugged surface.
Virusoids are circular single-stranded RNA(s) dependent on viruses for replication and encapsidation. The genome of virusoids consists of several hundred (200–400) nucleotides and does not code for any proteins.
Rubella virus (RuV) is the pathogenic agent of the disease rubella, transmitted only between humans via the respiratory route, and is the main cause of congenital rubella syndrome when infection occurs during the first weeks of pregnancy.
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).
Podoviridae was a family of bacteriophage in the order Caudovirales often associated with T-7 like phages. The family and order Caudoviraleshave now been abolished, with the term podovirus now used to refer to the morphology of viruses in this former family. There were 130 species in this family, assigned to 3 subfamilies and 52 genera. This family was characterized by having very short, noncontractile tails. Many former phages in the former family Podoviriade are now classified in the Autographiviridae
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.
Tombusviridae is a family of single-stranded positive sense RNA plant viruses. There are three subfamilies, 17 genera, and 95 species in this family. The name is derived from Tomato bushy stunt virus (TBSV).
The Pospiviroidae are a incertae sedis family of ssRNA viroids with 5 genera and 39 species, including the first viroid to be discovered, PSTVd, which is part of genus Pospiviroid. Their secondary structure is key to their biological activity. The classification of this family is based on differences in the conserved central region sequence. Pospiviroidae replication occurs in an asymmetric fashion via host cell RNA polymerase, RNase, and RNA ligase. Its hosts are plants, specifically dicotyledons and some monocotyledons.
The International Committee on Taxonomy of Viruses (ICTV) authorizes and organizes the taxonomic classification of and the nomenclature for viruses. The ICTV develops a universal taxonomic scheme for viruses, and thus has the means to appropriately describe, name, and classify every virus taxon. 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 identifying new taxa and delimiting the boundaries of species, genera, families, etc. 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.
Luteovirus is a genus of viruses, in the family Tombusviridae. There are 13 species in this genus. Plants serve as natural hosts. The geographical distribution of Luteoviruses is widespread, with the virus primarily infecting plants via transmission by aphid vectors. The virus only replicates within the host cell and not within the vector. The name 'luteovirus' arises from the Latin luteus, which is translated as 'yellow'. Luteovirus was given this name due to the symptomatic yellowing of the plant that occurs as a result of infection.
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.
Lagovirus is a genus of viruses, in the family Caliciviridae. Lagomorphs serve as natural hosts. There are two species in this genus. Diseases associated with this genus include: necrotizing hepatitis leading to fatal hemorrhages.
Ferlavirus, also referred to as Ophidian paramyxovirus, is a genus of viruses in the family Paramyxoviridae, order Mononegavirales. Reptiles serve as natural hosts. There is currently only one species in this genus to accommodate a single virus, Fer-de-Lance virus (FDLV).
Spiraviridae is a family of incertae sedis 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 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 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.
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:
Thaspiviridae is a family of incertae sedis spindle-shaped viruses. The family contains a single genus, Nitmarvirus, which contains a single species, Nitmarvirus NSV1.
Ribozyviria is a realm of satellite nucleic acids — infectious agents that resemble viruses, but cannot replicate without a helper virus. Established in ICTV TaxoProp 2020.012D, the realm is named after the presence of genomic and antigenomic ribozymes of the Deltavirus type. The agents in Ribozyviria are satellite nucleic acids, which are distinct from satellite viruses in that they do not encode all of their own structural proteins but require proteins from their helper viruses in order to assemble. Additional common features include a rod-like structure, an RNA-binding "delta antigen" encoded in the genome, and animal hosts. Furthermore, the size range of the genomes of these viruses is between around 1547–1735nt, they encode a hammerhead ribozyme or a hepatitis delta virus ribozyme, and their coding capacity only involves one conserved protein. Most lineages of this realm are poorly understood, the notable exception being the genus Deltavirus, comprising the causal agents of hepatitis D in humans.
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