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, 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

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

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, just one single phylum, two subphyla (Haploviricotina and Polyploviricotina), six classes, 14 orders, five suborders, 143 families, 64 subfamilies, 846 genera, and 4,958 species of viruses have been defined by the ICTV.[6][7] The orders are as follows:

  • Ortervirales contain single-stranded RNA and DNA viruses that replicate through a DNA intermediate (Groups VI and VII).
  • Picornavirales contains small (+) strand ssRNA viruses that infect a variety of plant, insect and animal hosts.
  • Tymovirales contain monopartite (+) ssRNA viruses that infect plants.
  • Bunyavirales contain tripartite (-) ssRNA viruses (Group V).

These orders 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.[8][9]

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

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 existing ICTV classification scheme.[11]

Baltimore classification

Baltimore Classification
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:[12]

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

DNA viruses

  • 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 ds I
2. Papovaviridae Papillomavirus, polyomaviridae, simian vacuolating virus Naked Icosahedral ds circular I
3. Parvoviridae 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, cow pox virus, sheep pox virus, orf virus, monkey pox virus, vaccinia virus Complex coats Complex ds I
6. Hepadnaviridae Hepatitis B virus Enveloped Icosahedral circular, partially ds VII
7. Anelloviridae Torque teno virus Naked Icosahedral ss circular II

RNA viruses

  • 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 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 Rubella virus, alphavirus Enveloped Icosahedral ss IV
5. Arenaviridae Lymphocytic choriomeningitis virus 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, hantavirus Enveloped Helical ss(-) V
10. Rhabdoviridae Rabies virus Enveloped Helical ss(-) V
11. Filoviridae Ebola virus, Marburg virus Enveloped Helical ss(-) V
12. Coronaviridae Corona virus Enveloped Helical ss IV
13. Astroviridae Astrovirus Naked Icosahedral 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
17. Retroviridae HIV Enveloped VI

Reverse transcribing viruses

  • 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 classification

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

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.[13] This classification was approved by the Provisional Committee on Nomenclature of Virus (PNVC) of the International Association of Microbiological Societies (1962). 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

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

Viroids

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 viruses[16]
  • 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

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.[17]

Defective interfering particles

  • Defective interfering RNA
  • Defective interfering DNA

See also

Notes

  1. ^ Zimmer C (5 September 2013). "A Catalog for All the World's Viruses?". New York Times. Retrieved 6 September 2013.
  2. ^ Adams MJ, Lefkowitz EJ, King AM, Carstens EB (December 2013). "Recently agreed changes to the International Code of Virus Classification and Nomenclature". Archives of Virology. 158 (12): 2633–9. doi:10.1007/s00705-013-1749-9. PMID 23836393.
  3. ^ Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG, Smith DB (January 2018). "Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)". Nucleic Acids Research. 46 (D1): D708–D717. doi:10.1093/nar/gkx932. PMC 5753373. PMID 29040670.
  4. ^ The Virus Species Concept: Introduction Archived 2007-09-27 at the Wayback Machine Virus Taxonomy Online: Seventh Report of the International Committee on Taxonomy of Viruses. 2000. Retrieved on 2007-07-14.
  5. ^ ICTV Code
  6. ^ "International Committee on Taxonomy of Viruses (ICTV)".
  7. ^ ICTV Virus Taxonomy ICTV Virus Taxonomy Release History
  8. ^ Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, et al. (June 2018). "Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses". Journal of Virology. 92 (12). doi:10.1128/JVI.00515-18. PMC 5974489. PMID 29618642.
  9. ^ "Taxonomy". International Committee on Taxonomy of Viruses (ICTV). Retrieved 2017-09-29.
  10. ^ Bamford DH (May 2003). "Do viruses form lineages across different domains of life?". Research in Microbiology. 154 (4): 231–6. doi:10.1016/S0923-2508(03)00065-2. PMID 12798226.
  11. ^ Krupovič M, Bamford DH (December 2010). "Order to the viral universe". Journal of Virology. 84 (24): 12476–9. doi:10.1128/JVI.01489-10. PMC 3004316. PMID 20926569.
  12. ^ "Baltimore Classification of Viruses" (Website.) Molecular Biology Web Book - http://web-books.com/. Retrieved on 2008-08-18.
  13. ^ Lwoff A, Horne R, Tournier P (1962). "A system of viruses". Cold Spring Harbor Symposia on Quantitative Biology. 27: 51–5. doi:10.1101/sqb.1962.027.001.008. PMID 13931895.
  14. ^ "80.002 Avsunviroidae - ICTVdB Index of Viruses." (Website.) U.S. National Institutes of Health website. Retrieved on 2007-09-27.
  15. ^ "80.001 Popsiviroidae - ICTVdB Index of Viruses." (Website.) U.S. National Institutes of Health website. Retrieved on 2007-09-27.
  16. ^ "81. Satellites - ICTVdB Index of Viruses." (Website.) U.S. National Institutes of Health website. Retrieved on 2007-09-27.
  17. ^ "90. Prions - ICTVdB Index of Viruses." (Website.) U.S. National Institutes of Health website. Retrieved on 2007-09-27.

External links

Alvernaviridae

Alvernaviridae is a family of viruses. Dinoflagellates serve as natural hosts. There is currently only one species in this family: the type species Heterocapsa circularisquama RNA virus 01. Diseases associated with this family include: control of the host population possibly through lysis of the host cell.

Bacillarnavirus

Bacillarnavirus is a genus of viruses in the order Picornavirales. Marine diatoms serve as natural hosts. There are currently three species in this genus, including the type species Rhizosolenia setigera RNA virus 01.

Baltimore classification

The Baltimore classification, developed by David Baltimore, is a virus classification system that groups viruses into families, depending on their type of genome (DNA, RNA, single-stranded (ss), double-stranded (ds), etc..) and their method of replication.

Barnaviridae

Barnaviridae is a family of viruses. Cultivated mushroom serve as natural hosts. There are currently only one genus (Barnavirus) and one species in this family: the type species Mushroom bacilliform virus. Diseases associated with this family include: La France disease.

Carmotetraviridae

Carmotetraviridae is a family of viruses; there is currently only one genus in this family, Alphacarmotetravirus, and one species in this genus, the type species Providence virus. Lepidopteran insects serve as natural hosts.

DsDNA-RT virus

dsDNA-RT viruses are the seventh group in the Baltimore virus classification.

They are not considered DNA viruses (class I of Baltimore classification),

but rather reverse transcribing viruses because they replicate through an RNA intermediate. It includes the families Hepadnaviridae and Caulimoviridae.

The term "pararetrovirus" is also used for this group. The term was introduced in 1985.

Emaravirus

Emaravirus is a genus of plant viruses. The genus has nine species. The type species European mountain ash ringspot-associated emaravirus is associated with a leaf mottling and ringspot disease of European mountain ash Sorbus aucuparia. It can be transmitted by grafting and possibly mites.

Gammaflexiviridae

Gammaflexiviridae is a family of viruses in the order Tymovirales. Fungi serve as natural hosts. There are currently only one genus, Mycoflexivirus, and one species in this family: the type species Botrytis virus F.

Hantaviridae

Hantaviridae is a family of viruses in the order Bunyavirales. It is named for the Hantan River area in South Korea where an early outbreak of one of its species was observed.

Higrevirus

Higrevirus is a genus of viruses. Plants serve as natural hosts. There is currently only one species in this genus: the type species Hibiscus green spot virus 2.

Megabirnaviridae

Megabirnaviridae is a family of viruses with one genus Megabirnavirus. Fungi serve as natural hosts. There is only one species in this family: the type species Rosellinia necatrix megabirnavirus 1. Diseases associated with this family include: reduced host virulence.

Nairoviridae

Nairoviridae is a family of viruses in the order Bunyavirales. Its name derives from Nairobi sheep disease, caused by the member Nairobi sheep disease orthonairovirus.

Nomenclature codes

Nomenclature codes or codes of nomenclature are the various rulebooks that govern biological taxonomic nomenclature, each in their own broad field of organisms. To an end-user who only deals with names of species, with some awareness that species are assignable to families, it may not be noticeable that there is more than one code, but beyond this basic level these are rather different in the way they work.

The successful introduction of two-part names for species by Linnaeus was the start for an ever-expanding system of nomenclature. With all naturalists worldwide adopting this approach to thinking up names there arose several schools of thought about the details. It became ever more apparent that a detailed body of rules was necessary to govern scientific names. From the mid-nineteenth century onwards there were several initiatives to arrive at worldwide-accepted sets of rules. Presently nomenclature codes govern the naming of:

Algae, Fungi and Plants – International Code of Nomenclature for algae, fungi, and plants (ICN), which in July 2011 replaced the International Code of Botanical Nomenclature (ICBN) and the earlier International Rules of Botanical Nomenclature.

Animals – International Code of Zoological Nomenclature (ICZN)

Bacteria – International Code of Nomenclature of Prokaryotes (ICNP), which in 2008 replaced the International Code of Nomenclature of Bacteria (ICNB)

Cultivated plants – International Code of Nomenclature for Cultivated Plants (ICNCP)

Plant associations – International Code of Phytosociological Nomenclature (ICPN)

Viruses – The International Code of Virus Classification and Nomenclature (ICVCN); see also virus classification

Pandoravirus

Pandoravirus is a genus of giant virus, first discovered in 2013. It is the second largest in physical size of any known viral genus. Pandoraviruses have double stranded DNA genomes, with the largest genome size (2.5 million base pairs) of any known viral genus.

Peribunyaviridae

Peribunyaviridae is a family of viruses in the order Bunyavirales. Its name partially derives from Bunyamwera, Uganda, where the founding species was first isolated.

Phasmaviridae

Phasmaviridae is a family of viruses with negative stranded RNA genomes. They are a member of the order Bunyavirales.

Pithovirus

Pithovirus, first described in a 2014 paper, is a genus of giant virus known from one species, Pithovirus sibericum, which infects amoebas. It is a double-stranded DNA virus, and is a member of the nucleocytoplasmic large DNA viruses clade. The 2014 discovery was made when a viable specimen was found in a 30,000-year-old ice core harvested from permafrost in Siberia, Russia.

Spiraviridae

Spiraviridae is a family of single stranded DNA viruses that infect archeae.

Turriviridae

Turriviridae is a family of viruses; it contains only one genus, Alphaturrivirus. The archaea Sulfolobus solfataricus serve as natural hosts. There are currently only two species in the genus Alphaturrivirus.

Components
Viral life cycle
Genetics
By host
Other
Baltimore (virus classification)
DNA
RNA
RT

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