Virus classification

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.[2]

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."[3] 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.[4]

The actual criteria used vary by the taxon, and can be inconsistent (arbitrary similarity thresholds) or unrelated to lineage (geography) at times.[5] The matter is, for many, not yet settled.[2]

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:[6]

Viruses sensu stricto are defined operationally by the ICTV as a type of MGE (mobile genetic element) 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.

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.[13] 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.[14]

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.[15]

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.[12]

• Group I: viruses possess double-stranded DNA. Viruses that cause chickenpox and herpes are found here.
• Group II: viruses possess single-stranded DNA.

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.[17]

• 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.
• Group V: viruses possess negative-sense single-stranded RNA genomes. Ebola and Marburg viruses are well known members of this group, along with influenza virus, measles, mumps and rabies.

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.[18]

• 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.

Holmes (1948) used a Linnaean taxonomy with binomial nomenclature to classify viruses into 3 groups under one order, Virales. They are placed as follows:

• Group I: Phaginae (attacks bacteria)
• Group II: Phytophaginae (attacks plants)
• Group III: Zoophaginae (attacks animals)

The system was not accepted by others due to its neglect of morphological similarities.[19]

• Family Avsunviroidae[23]
  • Genus Avsunviroid; type species: Avocado sunblotch viroid
  • Genus Pelamoviroid; type species: Peach latent mosaic viroid
  • Genus Elaviroid; type species: Eggplant latent viroid
• Family Pospiviroidae[24]
  • Genus Pospiviroid; type species: Potato spindle tuber viroid
  • Genus Hostuviroid; type species: Hop stunt viroid
  • Genus Cocadviroid; type species: Coconut cadang-cadang viroid
  • Genus Apscaviroid; type species: Apple scar skin viroid
  • Genus Coleviroid; type species: Coleus blumei viroid 1

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.[20]

• Satellite viruses[25]
  • Single-stranded RNA satellite viruses
    • (unnamed family)
      • Aumaivirus – Maize white line mosaic satellite virus
      • Papanivirus – Panicum mosaic satellite virus
      • Virtovirus – Tobacco mosaic satellite virus
      • Albetovirus – Tobacco necrosis satellite virus
    • Family Sarthroviridae
      • Macronovirus – Macrobrachium satellite virus 1 (extra small virus)
    • (unnamed genus) – Nilaparvata lugens commensal X virus
    • (unnamed genus) – Chronic bee-paralysis satellite virus
  • Double-stranded DNA satellite viruses
    • Family Lavidaviridae – Virophages
  • Single-stranded DNA satellite viruses
    • Genus Dependoparvovirus – Adeno-associated virus group
• Satellite nucleic acids
  • Single-stranded satellite DNAs
    • Family Alphasatellitidae (encoding a replication initiator protein)
    • Family Tolecusatellitidae (encoding a pathogenicity determinant βC1)
  • Double-stranded satellite RNAs
  • Single-stranded satellite RNAs
    • Subgroup 1: Large satellite RNAs
    • Subgroup 2: Small linear satellite RNAs
    • Subgroup 3: Circular satellite RNAs (virusoids)
    • Genus Deltavirus
    • Polerovirus-associated RNAs
  • Satellite-like RNA
  • Satellite-like DNA

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)