RNA virus | classification

Classification

Classification of the RNA viruses has proven to be a difficult problem. This is in part due to the high mutation rates these genomes undergo. Classification is based principally on the type of genome (double-stranded, negative- or positive-single-strand) and gene number and organisation. Currently there are 5 orders and 47 families of RNA viruses recognised. There are also many unassigned species and genera.

Related to but distinct from the RNA viruses are the viroids and the RNA satellite viruses. These are not currently classified as RNA viruses and are described on their own pages.

Positive strand RNA viruses

This is the single largest group of RNA viruses[13] with 30 families. Attempts have been made to group these families in higher orders. These proposals were based on an analysis of the RNA polymerases and are still under consideration. To date, the suggestions proposed have not been broadly accepted because of doubts over the suitability of a single gene to determine the taxonomy of the clade.

The proposed classification of positive-strand RNA viruses is based on the RNA-dependent RNA polymerase. Three groups have been recognised:[14]

  1. Bymoviruses, comoviruses, nepoviruses, nodaviruses, picornaviruses, potyviruses, sobemoviruses and a subset of luteoviruses (beet western yellows virus and potato leafroll virus)—the picorna like group (Picornavirata).
  2. Carmoviruses, dianthoviruses, flaviviruses, pestiviruses, statoviruses, tombusviruses, single-stranded RNA bacteriophages, hepatitis C virus and a subset of luteoviruses (barley yellow dwarf virus)—the flavi like group (Flavivirata).
  3. Alphaviruses, carlaviruses, furoviruses, hordeiviruses, potexviruses, rubiviruses, tobraviruses, tricornaviruses, tymoviruses, apple chlorotic leaf spot virus, beet yellows virus and hepatitis E virus—the alpha like group (Rubivirata).

A division of the alpha-like (Sindbis-like) supergroup on the basis of a novel domain located near the N termini of the proteins involved in viral replication has been proposed.[15] The two groups proposed are: the 'altovirus' group (alphaviruses, furoviruses, hepatitis E virus, hordeiviruses, tobamoviruses, tobraviruses, tricornaviruses and probably rubiviruses); and the 'typovirus' group (apple chlorotic leaf spot virus, carlaviruses, potexviruses and tymoviruses).

The alpha like supergroup can be further divided into three clades: the rubi-like, tobamo-like, and tymo-like viruses.[16]

Additional work has identified five groups of positive-stranded RNA viruses containing four, three, three, three, and one order(s), respectively.[17] These fourteen orders contain 31 virus families (including 17 families of plant viruses) and 48 genera (including 30 genera of plant viruses). This analysis suggests that alphaviruses and flaviviruses can be separated into two families—the Togaviridae and Flaviridae, respectively—but suggests that other taxonomic assignments, such as the pestiviruses, hepatitis C virus, rubiviruses, hepatitis E virus, and arteriviruses, may be incorrect. The coronaviruses and toroviruses appear to be distinct families in distinct orders and not distinct genera of the same family as currently classified. The luteoviruses appear to be two families rather than one, and apple chlorotic leaf spot virus appears not to be a closterovirus but a new genus of the Potexviridae.

Evolution

The evolution of the picornaviruses based on an analysis of their RNA polymerases and helicases appears to date to the divergence of the eukaryotes.[18] Their putative ancestors include the bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages.

Partitiviruses are related to and may have evolved from a totivirus ancestor.[19]

Hypoviruses and barnaviruses appear to share an ancestry with the potyvirus and sobemovirus lineages respectively.[19]

Double-stranded RNA viruses

This analysis also suggests that the dsRNA viruses are not closely related to each other but instead belong to four additional classes—Birnaviridae, Cystoviridae, Partitiviridae, and Reoviridae — and one additional order (Totiviridae) of one of the classes of positive ssRNA viruses in the same subphylum as the positive-strand RNA viruses.

One study has suggested that there are two large clades: One includes the Caliciviridae, Flaviviridae, and Picornaviridae families and a second that includes the Alphatetraviridae, Birnaviridae and Cystoviridae, Nodaviridae, and Permutotretraviridae families.[20]

Negative strand RNA viruses

These viruses have multiple types of genome ranging from a single RNA molecule up to eight segments. Despite their diversity it appears that they may have originated in arthropods and to have diversified from there.[21]

Satellite viruses

A number of satellite viruses - viruses that require the assistance of another virus to complete their life cycle - are also known. Their taxonomy has yet to be settled. The following four genera have been proposed for positive sense single stranded RNA satellite viruses that infect plants - Albetovirus, Aumaivirus, Papanivirus and Virtovirus.[22] A family - Sarthroviridae which includes the genus Macronovirus - has been proposed for the positive sense single stranded RNA satellite viruses that infect arthropods.

Other Languages
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català: Virus d'ARN
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română: Ribovirus
Simple English: RNA virus
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