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.
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.
Virus 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.
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." Viruses are real physical entities produced by biological evolution and genetics, whereas virus species and higher taxa are abstract concepts produced by rational thought and logic. The virus/species relationship thus represents the front line of the interface between biology and logic.
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.
ICTV classification.
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", "Riboviria", and "Varidnaviria"
"Incertae sedis" order: "Ligamenvirales"
"Incertae sedis" families:
"Incertae sedis" genera: "Deltavirus", "Dinodnavirus", "Rhizidiovirus"
Structure-based virus classification.
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.
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:
DNA viruses.
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".
RNA viruses.
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".
Reverse transcribing viruses.
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.
Historical systems.
Holmes classification.
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.
Subviral agents.
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.
Viroids and virus-dependent agents.
Satellites.
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.
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.