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AnRNA virus is avirus characterized by a ribonucleic acid (RNA) basedgenome.[1] The genome can besingle-stranded RNA (ssRNA) or double-stranded (dsRNA).[2] Notable human diseases caused by RNA viruses includeinfluenza,SARS,MERS,COVID-19,Dengue virus,hepatitis C,hepatitis E,West Nile fever,Ebola virus disease,rabies,polio,mumps, andmeasles.
All RNA viruses use a homologous RNA-dependent polymerase for replication and are categorized by theInternational Committee on Taxonomy of Viruses (ICTV) into the realmRiboviria.[3] This includes viruses belonging toGroup III,Group IV,Group V, andGroup VI of theBaltimore classification system. Group VI comprises theretroviruses, which have RNA genetic material but useDNA intermediates in theirlife cycle.Riboviria does not includeviroids andsatellite nucleic acids:Deltavirus,Avsunviroidae, andPospiviroidae are taxa that were mistakenly included in 2019,[a] but this was corrected in 2020.[4]
RNA viruses can be further classified according to the sense or polarity of their RNA intonegative-sense andpositive-sense, orambisense RNA viruses. Positive-sense viral RNA is similar tomRNA and thus can be immediatelytranslated by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by anRNA-dependent RNA polymerase before translation. Purified RNA of a positive-sense virus can directly cause infection though it may be less infectious than the whole virus particle. In contrast, purified RNA of a negative-sense virus is not infectious by itself as it needs to betranscribed into positive-sense RNA; eachvirion can be transcribed to several positive-sense RNAs. Ambisense RNA viruses resemble negative-sense RNA viruses, except they translate genes from their negative and positive strands.[5]
Thedouble-stranded (ds)RNA viruses represent a diverse group of viruses that vary widely in host range (humans, animals, plants,fungi,[b] andbacteria),genome segment number (one to twelve), andvirion organization (Triangulation number,capsid layers, spikes, turrets, etc.). Members of this group include therotaviruses, which are the most common cause ofgastroenteritis in young children, andpicobirnaviruses, which are the most common virus in fecal samples of both humans and animals with or without signs of diarrhea.Bluetongue virus is an economically important pathogen that infects cattle and sheep. In recent years, progress has been made in determining atomic and subnanometer resolution structures of a number of key viral proteins and virion capsids of several dsRNA viruses, highlighting the significant parallels in the structure and replicative processes of many of these viruses.[2][page needed]
RNA viruses generally have very highmutation rates compared toDNA viruses,[7] because viralRNA polymerases lack theproofreading ability ofDNA polymerases.[8] Thegenetic diversity of RNA viruses is one reason why it is difficult to make effectivevaccines against them.[9] Retroviruses also have a high mutation rate even though their DNA intermediate integrates into the host genome (and is thus subject to host DNA proofreading once integrated), because errors during reverse transcription are embedded into both strands of DNA before integration.[10] Some genes of RNA virus are important to the viral replication cycles and mutations are not tolerated. For example, the region of thehepatitis C virus genome that encodes the core protein ishighly conserved,[11] because it contains an RNA structure involved in aninternal ribosome entry site.[12]
On average, dsRNA viruses show a lower sequence redundancy relative to ssRNA viruses. Contrarily, dsDNA viruses contain the most redundant genome sequences while ssDNA viruses have the least.[13] The sequence complexity of viruses has been shown to be a key characteristic for accurate reference-free viral classification.[13]
There are three distinct groups of RNA viruses depending on their genome and mode of replication:
Numerous RNA viruses are capable ofgenetic recombination when at least two viralgenomes are present in the same host cell.[14] Very rarely viral RNA can recombine with host RNA.[15] RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution amongPicornaviridae ((+)ssRNA), e.g.poliovirus.[16] In theRetroviridae ((+)ssRNA), e.g.HIV, damage in the RNA genome appears to be avoided duringreverse transcription by strand switching, a form of recombination.[17][18][19] Recombination also occurs in theReoviridae (dsRNA), e.g. reovirus;Orthomyxoviridae ((-)ssRNA), e.g.influenza virus;[19] andCoronaviridae ((+)ssRNA), e.g.SARS.[20] Recombination in RNA viruses appears to be an adaptation for coping with genome damage.[14] Recombination can occur infrequently between animal viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans.[20]
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Classification is based principally on the type of genome (double-stranded, negative- or positive-single-strand) and gene number and organization. Currently, there are 5 orders and 47 families of RNA viruses recognized. There are also many unassigned species and genera.
Related to but distinct from the RNA viruses are theviroids and theRNA satellite nucleic acids. These are not currently classified as RNA viruses and are described on their own pages.
A study of several thousand RNA viruses has shown the presence of at least five main taxa: a levivirus and relatives group; a picornavirus supergroup; an alphavirus supergroup plus a flavivirus supergroup; the dsRNA viruses; and the -ve strand viruses.[21] Thelentivirus group appears to be basal to all the remaining RNA viruses. The next major division lies between the picornasupragroup and the remaining viruses. The dsRNA viruses appear to have evolved from a +ve RNA ancestor and the -ve RNA viruses from within the dsRNA viruses. The closest relation to the -ve stranded RNA viruses is theReoviridae.
This is the single largest group of RNA viruses[22] and has been organized by theICTV into the phylaKitrinoviricota,Lenarviricota, andPisuviricota in the kingdomOrthornavirae andrealmRiboviria.[23]
Positive-strand RNA viruses can also be classified based on the RNA-dependent RNA polymerase. Three groups have been recognised:[24]
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.[25] 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 threeclades: the rubi-like, tobamo-like, and tymo-like viruses.[26]
Additional work has identified five groups of positive-stranded RNA viruses containing four, three, three, three, and one order(s), respectively.[27] 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.
The evolution of the picornaviruses based on an analysis of their RNA polymerases andhelicases appears to date to the divergence ofeukaryotes.[28] Their putative ancestors include the bacterial group IIretroelements, the family of HtrAproteases and DNAbacteriophages.
Partitiviruses are related to and may have evolved from a totivirus ancestor.[29]
Hypoviruses and barnaviruses appear to share an ancestry with the potyvirus and sobemovirus lineages respectively.[29]
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 familiesCaliciviridae,Flaviviridae, andPicornaviridae and a second that includes the familiesAlphatetraviridae,Birnaviridae,Cystoviridae,Nodaviridae, andPermutotretraviridae.[30]
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 inarthropods and to have diversified from there.[31]
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 andVirtovirus.[32] A family—Sarthroviridae which includes the genusMacronovirus—has been proposed for the positive sense single stranded RNA satellite viruses that infectarthropods.
There are twelve families and a number of unassigned genera and species recognised in this group.[8]
There are three orders and 34 families recognised in this group. In addition, there are a number of unclassified species and genera.
Satellite viruses
An unclassified astrovirus/hepevirus-like virus has also been described.[34]
This group of viruses has been placed into a single phylum—Negarnaviricota. This phylum has been divided into two subphyla—Haploviricotina andPolyploviricotina. Within the subphylum Haploviricotina four classes are currently recognised:Chunqiuviricetes,Milneviricetes,Monjiviricetes andYunchangviricetes. In the subphylum Polyploviricotina two classes are recognised:Ellioviricetes andInsthoviricetes.
Six classes, eight orders, and thirty families are currently recognized in this group. A number of unassigned species and genera are yet to be classified.[8]
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