Virus classification

Virus

Virus 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 is to say they are non-living particles with some chemical characteristics similar to those of life, or non-cellular life. As such, they do not fit neatly into the established biological classification system in place for cellular organisms.

Viruses are mainly 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; some related preliminary efforts have been accomplished.[1]

Virus species definition

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Species form the basis for any biological classification system. The ICTV had adopted the principle that a virus species is a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche. 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.”[2]

ICTV classification

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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.[3]

The system shares many features with the classification system of cellular organisms, such as taxon structure. However, this system of nomenclature differs from other taxonomic codes on several points. A minor point is that names of orders and families are italicized,[4] 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 taxon suffixes given in italics[5]:

Realm (-viria)

Subrealm (-vira)

Kingdom (-viriae)

Subkingdom (-virites)

Phylum (-viricota)

Subphylum (-viricotina)

Class (-viricetes)

Subclass (-viricetidae)

Order (-virales)

Suborder (-virineae)

Family (-viridae)

Subfamily (-virinae)

Genus (-virus)

Subgenus (-virus)

Species

Species names often take the form of [Disease] virus, particularly for higher plants and animals. As of November 2018, only phylum, subphylum, class, order, suborder, family, subfamily, genus, and species are used.

The establishment of an order is based on the inference that the virus families it contains have most likely evolved from a common ancestor. The majority of virus families remain unplaced.

As of 2018, one realm, four incertae sedis orders, 46 incertae sedis families, and three incertae sedis genera are accepted:[6]

Realms: Riboviria

Incertae sedis orders: Caudovirales, Herpesvirales, Ligamenvirales, Ortervirales

Incertae sedis families: Adenoviridae, Alphasatellitidae, Ampullaviridae, Anelloviridae, Ascoviridae, Asfarviridae, Bacilladnaviridae, Baculoviridae, Bicaudaviridae, Bidnaviridae, Circoviridae, Clavaviridae, Corticoviridae, Fuselloviridae, Geminiviridae, Genomoviridae, Globuloviridae, Guttaviridae, Hepadnaviridae, Hytrosaviridae, Inoviridae, Iridoviridae, Lavidaviridae, Marseilleviridae, Microviridae, Mimiviridae, Nanoviridae, Nimaviridae, Nudiviridae, Ovaliviridae, Papillomaviridae, Parvoviridae, Phycodnaviridae, Plasmaviridae, Pleolipoviridae, Polydnaviridae, Polyomaviridae, Portogloboviridae, Poxviridae, Smacoviridae, Sphaerolipoviridae, Spiraviridae, Tectiviridae, Tolecusatellitidae, Tristromaviridae, Turriviridae

Incertae sedis genera: Dinodnavirus, Rhizidiovirus, Salterprovirus

Higher virus taxa span viruses with varying host ranges. The Ortervirales (Groups VI and VII), containing also retroviruses (infecting animals including humans e.g. HIV), retrotransposons (infecting invertebrate animals, plants and eukaryotic microorganisms) and caulimoviruses (infecting plants), are recent additions to the classification system orders.[7][8] Other variations occur between the orders: Nidovirales, for example, are isolated for their differentiation in expressing structural and nonstructural proteins separately.

Structure-based virus classification

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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.[9] 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 existing ICTV classification scheme.[10]

Baltimore classification

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Main articles: Baltimore classification and Virus Information Table

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:[11]

• I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses)

• II: ssDNA viruses (+ strand or “sense”) DNA (e.g. Parvoviruses)

• III: dsRNA viruses (e.g. Reoviruses)

• IV: (+)ssRNA viruses (+ strand or sense) RNA (e.g. Picornaviruses, Togaviruses)

• V: (−)ssRNA viruses (− strand or antisense) RNA (e.g. Orthomyxoviruses, Rhabdoviruses)

• VI: ssRNA-RT viruses (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retroviruses)

• VII: dsDNA-RT viruses DNA with RNA intermediate in life-cycle (e.g. Hepadnaviruses)

Visualization of the 7 groups of virus according to the Baltimore Classification

DNA viruses

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Further information: DNA virus

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

• Group II: viruses possess single-stranded DNA.

Virus family

Examples (common names)

Virion

naked/enveloped

Capsid

symmetry

Nucleic acid type

Group

1. Adenoviridae

Adenovirus, infectious canine hepatitis virus

Naked

Icosahedral

2. Papovaviridae

Papillomavirus, polyomaviridae, simian vacuolating virus

Naked

Icosahedral

ds circular

3. Parvoviridae

Parvovirus B19, canine parvovirus

Naked

Icosahedral

4. Herpesviridae

Herpes simplex virus, varicella-zoster virus, cytomegalovirus, Epstein–Barr virus

Enveloped

Icosahedral

5. Poxviridae

Smallpox virus, cow pox virus, sheep pox virus, orf virus, monkey pox virus, vaccinia virus

Complex coats

Complex

7. Anelloviridae

Torque teno virus

Naked

Icosahedral

ss circular

7. Pleolipoviridae

HHPV1, HRPV1, HGPV1, His2V

Enveloped

ss/ds linear/circular

I/II

RNA viruses

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Further information: RNA virus

• 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. The deadly Ebola and Marburg viruses are well known members of this group, along with influenza virus, measles, mumps and rabies.

Virus Family

Examples (common names)

Capsid

naked/enveloped

Capsid

Symmetry

Nucleic acid type

Group

1. Reoviridae

Reovirus, rotavirus

Naked

Icosahedral

III

2. Picornaviridae

Enterovirus, rhinovirus, hepatovirus, cardiovirus, aphthovirus, poliovirus, parechovirus, erbovirus, kobuvirus, teschovirus, coxsackie

Naked

Icosahedral

3. Caliciviridae

Norwalk virus

Naked

Icosahedral

4. Togaviridae

Rubella virus, alphavirus

Enveloped

Icosahedral

5. Arenaviridae

Lymphocytic choriomeningitis virus

Enveloped

Complex

ss(-)

6. Flaviviridae

Dengue virus, hepatitis C virus, yellow fever virus, Zika virus

Enveloped

Icosahedral

7. Orthomyxoviridae

Influenzavirus A, influenzavirus B, influenzavirus C, isavirus, thogotovirus

Enveloped

Helical

ss(-)

8. Paramyxoviridae

Measles virus, mumps virus, respiratory syncytial virus, Rinderpest virus, canine distemper virus

Enveloped

Helical

ss(-)

9. Bunyaviridae

California encephalitis virus, hantavirus

Enveloped

Helical

ss(-)

10. Rhabdoviridae

Rabies virus

Enveloped

Helical

ss(-)

11. Filoviridae

Ebola virus, Marburg virus

Enveloped

Helical

ss(-)

12. Coronaviridae

Corona virus

Enveloped

Helical

13. Astroviridae

Astrovirus

Naked

Icosahedral

14. Bornaviridae

Borna disease virus

Enveloped

Helical

ss(-)

15. Arteriviridae

Arterivirus, equine arteritis virus

Enveloped

Icosahedral

16. Hepeviridae

Hepatitis E virus

Naked

Icosahedral

Reverse transcribing viruses

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• 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.

Virus Family

Examples (common names)

Capsid

naked/enveloped

Capsid

Symmetry

Nucleic acid type

Group

1. Retroviridae

HIV

Enveloped

dimer RNA

2. Caulimoviridae

Caulimovirus, Cacao swollen-shoot virus (CSSV)

Naked

VII

3. Hepadnaviridae

Hepatitis B virus

Enveloped

Icosahedral

circular, partially ds

VII

Holmes classification

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Holmes (1948) used Carl Linnaeus’s system of 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)

LHT System of Virus Classification

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The LHT System of Virus Classification is based on chemical and physical characters like nucleic acid (DNA or RNA), symmetry (helical or icosahedral or complex), presence of envelope, diameter of capsid, number of capsomers.[12] This classification was approved by the Provisional Committee on Nomenclature of Virus (PNVC) of the International Association of Microbiological Societies (1962).[citation needed] It is as follows:

• Phylum Vira (divided into 2 subphyla)

• Subphylum Deoxyvira (DNA viruses)

• Class Deoxybinala (dual symmetry)

• Order Urovirales

• Family Phagoviridae

• Class Deoxyhelica (helical symmetry)

• Order Chitovirales

• Family Poxviridae

• Class Deoxycubica (cubical symmetry)

• Order Peplovirales

• Family Herpesviridae (162 capsomeres)

• Order Haplovirales (no envelope)

• Family Iridoviridae (812 capsomeres)

• Family Adenoviridae (252 capsomeres)

• Family Papiloviridae (72 capsomeres)

• Family Paroviridae (32 capsomeres)

• Family Microviridae (12 capsomeres)

• Subphylum Ribovira (RNA viruses)

• Class Ribocubica

• Order Togovirales

• Family Arboviridae

• Order Tymovirales

• Family Napoviridae

• Family Reoviridae

• Class Ribohelica

• Order Sagovirales

• Family Stomataviridae

• Family Paramyxoviridae

• Family Myxoviridae

• Order Rhabdovirales

• Suborder Flexiviridales

• Family Mesoviridae

• Family Peptoviridae

• Suborder Rigidovirales

• Family Pachyviridae

• Family Protoviridae

• Family Polichoviridae

Subviral agents

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The following agents are smaller than viruses and have only some of their properties.

Viroids

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Main article: Viroid

• Family Avsunviroidae[13]

◦ Genus Avsunviroid; type species: Avocado sunblotch viroid

◦ Genus Pelamoviroid; type species: Peach latent mosaic viroid

◦ Genus Elaviroid; type species: Eggplant latent viroid

• Family Pospiviroidae[14]

◦ 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

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Main article: Satellite (biology)

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 viruses[15]

◦ Single-stranded RNA satellite viruses

▪ Subgroup 1: Chronic bee-paralysis satellite virus

▪ Subgroup 2: Tobacco necrosis satellite virus

◦ Double-stranded DNA satellite viruses (virophages)

• Satellite nucleic acids

◦ Single-stranded satellite DNAs

◦ 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)

Prions

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Prions, named for their description as “proteinaceous and infectious particles”, lack any detectable (as of 2002) nucleic acids or virus-like particles. They resist inactivation procedures that normally affect nucleic acids.[16]

• Mammalian prions:

◦ Agents of spongiform encephalopathies

• Fungal prions:

◦ PSI+ prion of Saccharomyces cerevisiae

◦ URE3 prion of Saccharomyces cerevisiae

◦ RNQ/PIN+ prion of Saccharomyces cerevisiae

◦ Het-s prion of Podospora anserina

Defective interfering particles

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Main article: Defective interfering particle

• Defective interfering RNA

• Defective interfering D