Editing RNA virus

{{Short description|Subclass of viruses}}
{{Use dmy dates|date=December 2020}}
{{Update|taxonomy in baltimore sections [ICTV release 2018b→2019]|date=January 2021}}
[[File:18 2014 1695 Fig1 HTML.webp|thumb|Taxonomy and replication strategies of different types of RNA viruses]]
An '''RNA virus''' is a [[virus]] characterized by a ribonucleic acid ([[RNA]]) based [[genome]].<ref>{{cite book |last1=Wagner |first1=Edward K. |last2=Hewlett |first2=Martinez J. |title=Basic virology |url=https://archive.org/details/basicvirology0000wagn |access-date=30 March 2020 |year=1999 |publisher=Blackwell Science, Inc. |location=Malden, MA |isbn=0-632-04299-0 |page=249 }}</ref> The genome can be [[single-stranded]] RNA ([[ssRNA]]) or double-stranded ([[Double-stranded RNA|dsRNA]]).<ref name = Pattonrnav/> Notable human diseases caused by RNA viruses include [[influenza]], [[SARS]], [[MERS]], [[COVID-19]], [[Dengue virus]], [[hepatitis C]], [[hepatitis E]], [[West Nile fever]], [[Ebola virus disease]], [[rabies]], [[polio]], [[mumps]], and [[measles]].

All known RNA viruses, that is viruses that use a homologous RNA-dependent polymerase for replication, are categorized by the [[International Committee on Taxonomy of Viruses]] (ICTV) into the realm ''[[Riboviria]]''.<ref>{{cite journal |title=The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks |journal=Nature Microbiology |date=May 2020 |volume=5 |issue=5 |pages=668–674 |doi=10.1038/s41564-020-0709-x|pmid=32341570 |doi-access=free |author1=International Committee on Taxonomy of Viruses Executive Committee |pmc=7186216 }}</ref>  This includes RNA viruses belonging to ''Group III'', ''Group IV'' or ''Group V'' of the [[Virus classification#Baltimore classification|Baltimore classification]] system as well as ''Group VI. Group VI'' viruses are [[retrovirus]]es, viruses with RNA genetic material that use [[DNA]] intermediates in their [[Viral life cycle|life cycle]] including [[HIV-1]] and [[HIV-2]] which cause [[AIDS]].

The majority of such RNA viruses fall into the kingdom ''[[Orthornavirae]]'' and the rest have a positioning [[Incertae sedis|not yet defined]].<ref name=ortho>TaxoProp [https://ictv.global/taxonomy/taxondetails?taxnode_id=201907198 2019.006G]</ref> The realm does not contain all RNA viruses: ''[[Deltavirus]]'', ''[[Avsunviroidae]]'', and ''[[Pospiviroidae]]'' are taxa of RNA viruses that were mistakenly included in 2019,{{efn|1=This inclusion was due to TaxoProp [https://ictv.global/taxonomy/taxondetails?taxnode_id=201907095 2017.006G], which proposed ''Riboviria''. The confusion might be due to the TaxoProp's reference to a "monophyly of all RNA viruses", improperly termed as it was only demonstrated with RdRP. On the other hand, the proposed definition of ''Riboviria'' did correctly mention RdRP
.}} but corrected in 2020.<ref>TaxoProp [https://ictv.global/taxonomy/taxondetails?taxnode_id=201905347 2019.009G]</ref>

==Characteristics==

===Single-stranded RNA viruses and RNA Sense===
RNA viruses can be further classified according to the sense or polarity of their RNA into [[Negative-sense single-stranded RNA virus|negative-sense]] and [[Positive-sense single-stranded RNA virus|positive-sense]], or ambisense RNA viruses. Positive-sense viral RNA is similar to [[mRNA]] and thus can be immediately [[translation (genetics)|translated]] by the host cell. Negative-sense viral RNA is complementary to mRNA and thus must be converted to positive-sense RNA by an [[RNA-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 be [[Transcription (genetics)|transcribed]] into positive-sense RNA; each [[virion]] 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.<ref>{{cite journal | vauthors = Nguyen M, Haenni AL | title = Expression strategies of ambisense viruses | journal = Virus Research | volume = 93 | issue = 2 | pages = 141–50 | date = June 2003 | pmid = 12782362 | doi = 10.1016/S0168-1702(03)00094-7 }}</ref>

===Double-stranded RNA viruses===
{{Further|Double-stranded RNA viruses}}
[[File:Structure of the reovirus virion.png|thumb|Structure of the reovirus virion]]
The [[Double-stranded RNA viruses|double-stranded (ds)RNA viruses]] represent a diverse group of viruses that vary widely in host range (humans, animals, plants, [[fungi]],{{efn|The majority of fungal viruses are double-stranded RNA viruses. A small number of positive-strand RNA viruses have been described. One report has suggested the possibility of a negative stranded virus.<ref name=Kondo2012>{{cite journal | vauthors = Kondo H, Chiba S, Toyoda K, Suzuki N | title = Evidence for negative-strand RNA virus infection in fungi | journal = Virology | volume = 435 | issue = 2 | pages = 201–09 | date = January 2013 | pmid = 23099204 | doi = 10.1016/j.virol.2012.10.002 | doi-access = free }}</ref>}} and [[bacteria]]), [[genome]] segment number (one to twelve), and [[virion]] organization ([[Capsid#Triangulation number|Triangulation number]], [[capsid]] layers, spikes, turrets, etc.). Members of this group include the [[rotavirus]]es, which are the most common cause of [[gastroenteritis]] in young children, and [[picobirnavirus]]es, 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.<ref name=Pattonrnav>{{cite book |editor = Patton JT | title = Segmented Double-stranded RNA Viruses: Structure and Molecular Biology | publisher = Caister Academic Press | year = 2008 | url=http://www.horizonpress.com/rnav |  isbn = 978-1-904455-21-9}}</ref>{{page needed|date=March 2020}}

===Mutation rates===
RNA viruses generally have very high [[mutation]] rates compared to [[DNA virus]]es,<ref name="SanjuanNebot2010">{{cite journal | vauthors = Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R | title = Viral mutation rates | journal = Journal of Virology | volume = 84 | issue = 19 | pages = 9733–48 | date = October 2010 | pmid = 20660197 | pmc = 2937809 | doi = 10.1128/JVI.00694-10 }}</ref> because viral [[RNA-dependent RNA polymerase|RNA polymerases]] lack the [[Proofreading (biology)|proofreading]] ability of [[DNA polymerase]]s.<ref name=Klein>{{cite book | last1 = Klein | first1 = Donald W. | last2 =Prescott | first2 = Lansing M. | last3 = Harley | first3 = John | name-list-style = vanc |title=Microbiology |publisher=Wm. C. Brown |location=Dubuque, Iowa |year=1993 |isbn=978-0-697-01372-9 }}</ref> The [[genetic diversity]] of RNA viruses is one reason why it is difficult to make effective [[vaccines]] against them.<ref name="pmid3318675">{{cite journal | vauthors = Steinhauer DA, Holland JJ | title = Rapid evolution of RNA viruses | journal = Annual Review of Microbiology | volume = 41 | pages = 409–33 | year = 1987 | pmid = 3318675 | doi = 10.1146/annurev.mi.41.100187.002205 }}</ref> 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.<ref name="pmid20846038">{{cite journal | vauthors = Boutwell CL, Rolland MM, Herbeck JT, Mullins JI, Allen TM | title = Viral evolution and escape during acute HIV-1 infection | journal = The Journal of Infectious Diseases | volume = 202 | issue = Suppl 2 | pages = S309–14 | date = October 2010 | pmid = 20846038 | pmc = 2945609 | doi = 10.1086/655653 }}</ref> Some genes of RNA virus are important to the viral replication cycles and mutations are not tolerated. For example, the region of the [[hepatitis C virus]] genome that encodes the core protein is [[conserved sequence|highly conserved]],<ref name="pmid8058787">{{cite journal | vauthors = Bukh J, Purcell RH, Miller RH | title = Sequence analysis of the core gene of 14 hepatitis C virus genotypes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 91 | issue = 17 | pages = 8239–43 | date = August 1994 | pmid = 8058787 | pmc = 44581 | doi = 10.1073/pnas.91.17.8239 | bibcode = 1994PNAS...91.8239B | doi-access = free }}</ref> because it contains an RNA structure involved in an [[internal ribosome entry site]].<ref name="pmid15448367">{{cite journal | vauthors = Tuplin A, Evans DJ, Simmonds P | title = Detailed mapping of RNA secondary structures in core and NS5B-encoding region sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods | journal = The Journal of General Virology | volume = 85 | issue = Pt 10 | pages = 3037–47 | date = October 2004 | pmid = 15448367 | doi = 10.1099/vir.0.80141-0 | doi-access = free }}</ref>

===Sequence complexity===
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.<ref name=landscape/> The sequence complexity of viruses has been shown to be a key characteristic for accurate reference-free viral classification.<ref name=landscape>{{cite journal |vauthors=Silva JM, Pratas D, Caetano T, Matos D |date=August 2022 |title=The complexity landscape of viral genomes |journal=GigaScience |volume=11 |pages=1–16| doi=10.1093/gigascience/giac079|pmid=35950839|pmc=9366995 }}</ref>

==Replication==
There are three distinct groups of RNA viruses depending on their genome and mode of replication:
* Double-stranded RNA viruses (Group III) contain from one to a dozen different RNA molecules, each coding for one or more viral proteins.
* Positive-sense ssRNA viruses (Group IV) have their genome directly utilized as mRNA, with host [[ribosomes]] [[Translation (biology)|translating]] it into a single protein that is modified by host and viral proteins to form the various proteins needed for replication. One of these includes RNA-dependent RNA polymerase (RNA replicase), which copies the viral RNA to form a double-stranded replicative form.  In turn, this dsRNA directs the formation of new viral RNA.
* Negative-sense ssRNA viruses (Group V) must have their genome copied by an RNA replicase to form positive-sense RNA. This means that the virus must bring along with it the enzyme RNA replicase. The positive-sense RNA molecule then acts as viral mRNA, which is translated into proteins by the host ribosomes.

[[Retrovirus]]es (Group VI) have a single-stranded RNA genome but, in general, are not considered RNA viruses because they use DNA intermediates to replicate. [[Reverse transcriptase]], a viral enzyme that comes from the virus itself after it is uncoated, converts the viral RNA into a complementary strand of DNA, which is copied to produce a double-stranded molecule of viral DNA. After this DNA is integrated into the host genome using the viral enzyme [[integrase]], expression of the encoded genes may lead to the formation of new virions.

==Recombination==

Numerous RNA viruses are capable of [[genetic recombination]] when at least two viral [[genome]]s are present in the same host cell.<ref name = Barr2010>{{cite journal | vauthors = Barr JN, Fearns R | title = How RNA viruses maintain their genome integrity | journal = The Journal of General Virology | volume = 91 | issue = Pt 6 | pages = 1373–87 | date = June 2010 | pmid = 20335491 | doi = 10.1099/vir.0.020818-0 | doi-access = free }}</ref> Very rarely viral RNA can recombine with host RNA.<ref>{{Cite journal|last=Stedman|first=Kenneth M.|date=2015|title=Deep Recombination: RNA and ssDNA Virus Genes in DNA Virus and Host Genomes|journal=Annual Review of Virology|volume=2|issue=1|pages=203–217|doi=10.1146/annurev-virology-100114-055127|issn=2327-0578|pmid=26958913|s2cid=207745438 |doi-access=free}}</ref> RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution among ''[[Picornavirus|Picornaviridae]]'' ([[positive-sense single-stranded RNA virus|(+)ssRNA]]), e.g. [[poliovirus]].<ref name="pmid31540135">{{cite journal | vauthors = Muslin C, Mac Kain A, Bessaud M, Blondel B, Delpeyroux F | title = Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process | journal = Viruses | volume = 11 | issue = 9 | date = September 2019 | pages = 859 | pmid = 31540135 | pmc = 6784155 | doi = 10.3390/v11090859 | doi-access = free }}</ref> In the ''[[retrovirus|Retroviridae]]'' ((+)ssRNA), e.g. [[HIV]], damage in the RNA genome appears to be avoided during [[reverse transcriptase|reverse transcription]] by strand switching, a form of recombination.<ref name="pmid1700865">{{cite journal | vauthors = Hu WS, Temin HM | title = Retroviral recombination and reverse transcription | journal = Science | volume = 250 | issue = 4985 | pages = 1227–33 | date = November 1990 | pmid = 1700865 | doi = 10.1126/science.1700865 | bibcode = 1990Sci...250.1227H }}</ref><ref name="pmid30307534">{{cite journal | vauthors = Rawson JM, Nikolaitchik OA, Keele BF, Pathak VK, Hu WS | title = Recombination is required for efficient HIV-1 replication and the maintenance of viral genome integrity | journal = Nucleic Acids Research | volume = 46 | issue = 20 | pages = 10535–45 | date = November 2018 | pmid = 30307534 | pmc = 6237782 | doi = 10.1093/nar/gky910 }}</ref><ref name = Bernstein2018>{{cite journal | vauthors = Bernstein H, Bernstein C, Michod RE | title = Sex in microbial pathogens | journal = Infection, Genetics and Evolution | volume = 57 | pages = 8–25 | date = January 2018 | pmid = 29111273 | doi = 10.1016/j.meegid.2017.10.024 | doi-access = free | bibcode = 2018InfGE..57....8B }}</ref> Recombination also occurs in the ''[[Reoviridae]]'' (dsRNA), e.g. reovirus; ''[[Orthomyxoviridae]]'' ((-)ssRNA), e.g. [[influenza virus]];<ref name = Bernstein2018/> and ''[[Coronaviridae]]'' ((+)ssRNA), e.g. [[Severe acute respiratory syndrome|SARS]].<ref name = Su2016>{{cite journal | vauthors = Su S, Wong G, Shi W, Liu J, Lai AC, Zhou J, Liu W, Bi Y, Gao GF | display-authors = 6 | title = Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses | journal = Trends in Microbiology | volume = 24 | issue = 6 | pages = 490–502 | date = June 2016 | pmid = 27012512 | doi = 10.1016/j.tim.2016.03.003 | doi-access = free | pmc = 7125511 }}</ref> Recombination in RNA viruses appears to be an adaptation for coping with genome damage.<ref name = Barr2010/> 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.<ref name = Su2016/>

==Classification==
{{Cleanup section|reason=outdated and redundant with [[riboviria]] article as well as later text; see [[DNA virus]] for a clean integration between ICTV higher-order and Baltimore|date=January 2021}}
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 the [[viroid]]s and the [[Satellite (biology)|RNA satellite viruses]]. 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.<ref name=Wolf2018>{{cite journal | vauthors = Wolf YI, Kazlauskas D, Iranzo J, Lucía-Sanz A, Kuhn JH, Krupovic M, Dolja VV, Koonin EV | title = Origins and Evolution of the Global RNA Virome | journal = mBio | volume = 9 | issue = 6 | date = November 2018 | pmid = 30482837 | pmc = 6282212 | doi = 10.1128/mBio.02329-18 }}</ref> The [[lentivirus]] 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 the [[Reoviridae]].

===[[Positive-strand RNA virus|Positive-strand RNA viruses]]===

This is the single largest group of RNA viruses<ref>{{cite book| vauthors = Francki RI, Fauquet CM, Knudson DL, Brown F |title=Classification and nomenclature of viruses. Fifth report of the International Committee on Taxonomy of Viruses, Archives of Virology (Suppl. 2)|date=1991|publisher=Springer |isbn=978-3-7091-9163-7 }}</ref> and has been organized by the [[International Committee on Taxonomy of Viruses|ICTV]] into the phyla ''[[Kitrinoviricota]]'', ''[[Lenarviricota]]'', and ''[[Pisuviricota]]'' in the kingdom ''[[Orthornavirae]]'' and [[Realm (virology)|realm]] ''[[Riboviria]]''.<ref>{{Cite web |title=Current ICTV Taxonomy Release {{!}} ICTV |url=https://ictv.global/taxonomy |access-date=2023-04-03 |website=ictv.global}}</ref> 

Positive-strand RNA viruses can also be classified based on the RNA-dependent RNA polymerase. Three groups have been recognised:<ref name=Koonin>{{cite journal | vauthors = Koonin EV | title = The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses | journal = The Journal of General Virology | volume = 72 | issue = Pt 9 | pages = 2197–206 | date = September 1991 | pmid = 1895057 | doi = 10.1099/0022-1317-72-9-2197 | doi-access = free }}</ref>

# 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).
# 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).
# 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.<ref name=Rozanov1992>{{cite journal | vauthors = Rozanov MN, Koonin EV, Gorbalenya AE | title = Conservation of the putative methyltransferase domain: a hallmark of the 'Sindbis-like' supergroup of positive-strand RNA viruses | journal = The Journal of General Virology | volume = 73 | issue = Pt 8 | pages = 2129–34 | date = August 1992 | pmid = 1645151 | doi = 10.1099/0022-1317-73-8-2129 | citeseerx = 10.1.1.532.7367 }}</ref> 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.<ref name=Koonin1993>{{cite journal | vauthors = Koonin EV, Dolja VV | title = Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences | journal = Critical Reviews in Biochemistry and Molecular Biology | volume = 28 | issue = 5 | pages = 375–430 | year = 1993 | pmid = 8269709 | doi = 10.3109/10409239309078440 }}</ref>

Additional work has identified five groups of positive-stranded RNA viruses containing four, three, three, three, and one order(s), respectively.<ref name=Ward1993>{{cite journal | vauthors = Ward CW | title = Progress towards a higher taxonomy of viruses | journal = Research in Virology | volume = 144 | issue = 6 | pages = 419–53 | year = 1993 | pmid = 8140287 | doi = 10.1016/S0923-2516(06)80059-2 | pmc = 7135741 }}</ref> 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 [[helicase]]s appears to date to the divergence of [[eukaryote]]s.<ref name=Koonin2008>{{cite journal | vauthors = Koonin EV, Wolf YI, Nagasaki K, Dolja VV | title = The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups | journal = Nature Reviews. Microbiology | volume = 6 | issue = 12 | pages = 925–39 | date = December 2008 | pmid = 18997823 | doi = 10.1038/nrmicro2030 | doi-access = free }}</ref> Their putative ancestors include the bacterial group II [[retroelement]]s, the family of HtrA [[protease]]s and DNA [[bacteriophage]]s.

Partitiviruses are related to and may have evolved from a totivirus ancestor.<ref name=Ghabrial1998>{{cite journal | vauthors = Ghabrial SA  | year = 1998 | title = Origin, adaptation and evolutionary pathways of fungal viruses | journal = Virus Genes | volume = 16 | issue = 1| pages = 119–31 | doi = 10.1023/a:1007966229595 | pmid = 9562896 | pmc = 7089520 }}</ref>

Hypoviruses and barnaviruses appear to share an ancestry with the potyvirus and sobemovirus lineages respectively.<ref name=Ghabrial1998/>

===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 families ''Caliciviridae'', ''Flaviviridae'', and ''Picornaviridae'' and a second that includes the families ''Alphatetraviridae'', ''Birnaviridae'', ''Cystoviridae'', ''Nodaviridae'', and ''Permutotretraviridae''.<ref name=Gibrat2013>{{cite journal | vauthors = Gibrat JF, Mariadassou M, Boudinot P, Delmas B | title = Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods | journal = BMC Evolutionary Biology | volume = 13 | pages = 154 | date = July 2013 | issue = 1 | pmid = 23865988 | pmc = 3724706 | doi = 10.1186/1471-2148-13-154 | doi-access = free | bibcode = 2013BMCEE..13..154G }}</ref>

===Negative strand RNA viruses===
{{Main article|Negative-strand RNA virus}}
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 [[arthropod]]s and to have diversified from there.<ref name=v2015>{{cite journal | vauthors = Li CX, Shi M, Tian JH, Lin XD, Kang YJ, Chen LJ, Qin XC, Xu J, Holmes EC, Zhang YZ | display-authors = 6 | title = Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses | journal = eLife | volume = 4 | date = January 2015 | pmid = 25633976 | pmc = 4384744 | doi = 10.7554/eLife.05378 | doi-access = free }}</ref>

===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]].<ref name=Krupovic2016>{{cite journal | vauthors = Krupovic M, Kuhn JH, Fischer MG | title = A classification system for virophages and satellite viruses | journal = Archives of Virology | volume = 161 | issue = 1 | pages = 233–47 | date = January 2016 | pmid = 26446887 | doi = 10.1007/s00705-015-2622-9 | doi-access = free | hdl = 11858/00-001M-0000-0028-DC34-F | hdl-access = free }}</ref> A family—[[Sarthroviridae]] which includes the genus [[Macronovirus]]—has been proposed for the positive sense single stranded RNA satellite viruses that infect [[arthropod]]s.

==Group III&nbsp;– dsRNA viruses==
{{main|Double-stranded RNA viruses}}
There are twelve families and a number of unassigned genera and species recognised in this group.<ref name=Klein/>
* Family [[Amalgaviridae]]
* Family [[Birnaviridae]]
* Family [[Chrysoviridae]]
* Family [[Cystoviridae]]
* Family [[Endornaviridae]]
* Family [[Hypoviridae]]
* Family [[Megabirnaviridae]]
* Family [[Partitiviridae]]
* Family [[Picobirnaviridae]]
* Family [[Reoviridae]]&nbsp;– includes [[Rotavirus]]
* Family [[Totiviridae]]
* Family [[Quadriviridae]]
* Genus [[Botybirnavirus]]
* Unassigned species
** ''[[Botrytis porri RNA virus 1]]''
** ''[[Circulifer tenellus virus 1]]''
** ''[[Colletotrichum camelliae filamentous virus 1]]''
** ''[[Cucurbit yellows associated virus]]''
** ''[[Sclerotinia sclerotiorum debilitation-associated virus]]''
** ''[[Spissistilus festinus virus 1]]''

==Group IV&nbsp;– positive-sense ssRNA viruses==
{{main|Positive-sense single-stranded RNA virus}}
There are three orders and 34 families recognised in this group. In addition, there are a number of unclassified species and genera.
* Order [[Nidovirales]]
** Family [[Arteriviridae]]
** Family [[Coronaviridae]] – includes [[Human coronavirus]] (common cold viruses [[Human coronavirus 229E|HCoV-229E]], [[Human coronavirus HKU1|HCoV-HKU1]], [[Human coronavirus NL63|HCoV-NL63]], and [[Human coronavirus OC43|HCoV-OC43]]), [[MERS-CoV]], [[SARS-CoV-1]] and [[SARS-CoV-2]]
** Family [[Mesoniviridae]]
** Family [[Roniviridae]]
* Order [[Picornavirales]]
** Family [[Dicistroviridae]]
** Family [[Iflaviridae]]
** Family [[Marnaviridae]]
** Family [[Picornaviridae]] – includes [[Poliovirus]], [[Rhinovirus]] (a common cold virus), [[Hepatitis A]] virus
** Family [[Secoviridae]] includes subfamily [[Comoviridae|Comovirinae]]
** Genus [[Bacillariornavirus]]
** Species [[Kelp fly virus]]
* Order [[Tymovirales]]
** Family [[Alphaflexiviridae]]
** Family [[Betaflexiviridae]]
** Family [[Gammaflexiviridae]]
** Family [[Tymoviridae]]
* Unassigned
** Family [[Alphatetraviridae]]
** Family [[Alvernaviridae]]
** Family [[Astroviridae]]
** Family [[Barnavirus|Barnaviridae]]
** Family [[Benyviridae]]
** Family [[Botourmiaviridae]]
** Family [[Bromoviridae]]
** Family [[Caliciviridae]] – includes [[Norovirus|Norwalk virus]]
** Family [[Carmotetraviridae]]
** Family [[Closteroviridae]]
** Family [[Flaviviridae]] – includes [[Yellow fever]] virus, [[West Nile virus]], [[Hepatitis C virus]], [[Dengue fever]] virus, [[Zika virus]]
** Family [[Fusariviridae]]
** Family [[Hepeviridae]]
** Family [[Hypoviridae]]
** Family [[Leviviridae]]
** Family [[Luteoviridae]] – includes [[Barley yellow dwarf virus]]
** Family [[Polycipiviridae]]
** Family [[Narnaviridae]]
** Family [[Nodaviridae]]
** Family [[Permutotetraviridae]]
** Family [[Potyviridae]]
** Family [[Sarthroviridae]]
** Family [[Statovirus]]
** Family [[Togaviridae]] – includes [[Rubella]] virus, [[Ross River virus]], [[Sindbis virus]], [[Chikungunya virus]]
** Family [[Tombusviridae]]
** Family [[Virgaviridae]]<ref name=Adams2009>{{cite journal | vauthors = Adams MJ, Antoniw JF, Kreuze J | title = Virgaviridae: a new family of rod-shaped plant viruses | journal = Archives of Virology | volume = 154 | issue = 12 | pages = 1967–72 | year = 2009 | pmid = 19862474 | doi = 10.1007/s00705-009-0506-6 | doi-access = free }}</ref>
** Unassigned genera
*** Genus ''[[Blunervirus]]''
*** Genus ''[[Cilevirus]]''
*** Genus ''[[Higrevirus]]''
*** Genus ''[[Idaeovirus]]''
*** Genus ''[[Negevirus]]''
*** Genus ''[[Ourmiavirus]]''
*** Genus ''[[Polemovirus]]''
*** Genus ''[[Sinaivirus]]''
*** Genus ''[[Sobemovirus]]''
** Unassigned species
*** [[Acyrthosiphon pisum virus]]
*** [[Bastrovirus]]
*** [[Blackford virus]]
*** [[Blueberry necrotic ring blotch virus]]
*** [[Cadicistrovirus]]
*** [[Chara australis virus]]
*** [[Extra small virus]]
*** [[Goji berry chlorosis virus]]
*** [[Harmonia axyridis virus 1]]
*** [[Hepelivirus]]
*** [[Jingmen tick virus]]
*** [[Le Blanc virus]]
*** [[Nedicistrovirus]]
*** [[Nesidiocoris tenuis virus 1]]
*** [[Niflavirus]]
*** [[Nylanderia fulva virus 1]]
*** [[Orsay virus]]
*** [[Osedax japonicus RNA virus 1]]
*** [[Picalivirus]]
*** [[Planarian secretory cell nidovirus]]
*** [[Plasmopara halstedii virus]]
*** [[Rosellinia necatrix fusarivirus 1]]
*** [[Santeuil virus]]
*** [[Secalivirus]]
*** [[Solenopsis invicta virus 3]]
*** [[Wuhan large pig roundworm virus]]

Satellite viruses
* Family [[Sarthroviridae]]
* Genus [[Albetovirus]]
* Genus [[Aumaivirus]]
* Genus [[Papanivirus]]
* Genus [[Virtovirus]]
* [[Chronic bee paralysis virus]]

An unclassified astrovirus/hepevirus-like virus has also been described.<ref name=Pankovics2019>Pankovics P, Boros Á, Kiss T, Engelmann P, Reuter G (2019) Genetically highly divergent RNA virus with astrovirus-like (5'-end) and hepevirus-like (3'-end) genome organization in carnivorous birds, European roller (''Coracias garrulus''). Infect Genet Evol</ref>

==Group V&nbsp;– negative-sense ssRNA viruses==
{{main|Negative-sense single-stranded RNA virus}}

With the exception of the [[Hepatitis D virus]], this group of viruses has been placed into a single phylum—[[Negarnaviricota]]. This phylum has been divided into two subphyla—[[Haploviricotina]] and [[Polyploviricotina]]. Within the subphylum Haploviricotina four classes are currently recognised: [[Chunqiuviricetes]], [[Milneviricetes]], [[Monjiviricetes]] and [[Yunchangviricetes]]. In the subphylum Polyploviricotina two classes are recognised: [[Ellioviricetes]] and [[Insthoviricetes]].

Six classes, seven orders and twenty four families are currently recognized in this group. A number of unassigned species and genera are yet to be classified.<ref name="Klein"/>
* Phylum ''[[Negarnaviricota]]''<ref name=ictv>{{cite web|url=https://ictv.global/taxonomy|title=Virus Taxonomy: 2018 Release|access-date=2018-11-13|publisher=[[International Committee on Taxonomy of Viruses]]}}</ref>
** Subphylum ''[[Haploviricotina]]''
*** Class ''[[Chunqiuviricetes]]''
**** Order ''[[Muvirales]]''
***** Family ''[[Qinviridae]]''
*** Class ''[[Milneviricetes]]''
**** Order ''[[Serpentovirales]]''
***** Family ''[[Aspiviridae]]''
*** Class ''[[Monjiviricetes]]''
**** Order ''[[Jingchuvirales]]''
***** Family ''[[Chuviridae]]''
**** Order ''[[Mononegavirales]]''
***** Family ''[[Borna disease|Bornaviridae]]'' – [[Borna disease virus]]
***** Family ''[[Filoviridae]]'' – includes [[Ebola]] virus, [[Marburg virus]]
***** Family ''[[Mymonaviridae]]''
***** Family ''[[Nyamiviridae]]''<ref>{{cite journal | vauthors = Mihindukulasuriya KA, Nguyen NL, Wu G, Huang HV, da Rosa AP, Popov VL, Tesh RB, Wang D | display-authors = 6 | title = Nyamanini and midway viruses define a novel taxon of RNA viruses in the order Mononegavirales | journal = Journal of Virology | volume = 83 | issue = 10 | pages = 5109–16 | date = May 2009 | pmid = 19279111 | pmc = 2682064 | doi = 10.1128/JVI.02667-08 }}</ref>
***** Family ''[[Paramyxoviridae]]'' – includes [[Measles]] virus, [[Mumps virus]], [[Nipah virus]], [[Hendra virus]], and [[Newcastle disease|NDV]]
***** Family ''[[Pneumoviridae]]'' – includes [[Human respiratory syncytial virus|RSV]] and [[Metapneumovirus]]
***** Family ''[[Rhabdoviridae]]'' – includes [[Rabies]] virus
***** Family ''[[Sunviridae]]''
***** Genus [[Anphevirus]]
***** Genus [[Arlivirus]]
***** Genus [[Chengtivirus]]
***** Genus [[Crustavirus]]
***** Genus [[Wastrivirus]]
*** Class ''[[Yunchangviricetes]]''
**** Order ''[[Goujianvirales]]''
***** Family ''[[Yueviridae]]''
** Subphylum ''[[Polyploviricotina]]''
*** Class ''[[Ellioviricetes]]''
**** Order ''[[Bunyavirales]]''
***** Family ''[[Arenaviridae]]'' – includes [[Lassa virus]]
***** Family ''[[Cruliviridae]]''
***** Family ''[[Feraviridae]]''
***** Family ''[[Fimoviridae]]''
***** Family ''[[Hantaviridae]]''
***** Family ''[[Jonviridae]]''
***** Family ''[[Nairoviridae]]''
***** Family ''[[Peribunyaviridae]]''
***** Family ''[[Phasmaviridae]]''
***** Family ''[[Phenuiviridae]]''
***** Family ''[[Tospoviridae]]''
***** Genus ''[[Tilapineviridae]]''
*** Class ''[[Insthoviricetes]]''
**** Order ''[[Articulavirales]]''
***** Family ''[[Amnoonviridae]]''&nbsp;– includes [[Taastrup virus]]
***** Family ''[[Orthomyxoviridae]]''&nbsp;– includes [[Influenza]] viruses
* Unassigned genera:
** Genus ''[[Deltavirus]]'' – includes [[Hepatitis D]] virus (not a true virus, but a [[subviral agent]])

==Gallery==

<gallery class="center">
File:Lassa virus.JPG|[[Lassa virus]] (''[[Arenaviridae]]'')
File:Lymphocytic choriomeningitis virus.jpg|[[Lymphocytic choriomeningitis virus]] (''[[Arenaviridae]]'')
File:Sin Nombre virus Hanta TEM 1137 lores.jpg|[[Hantavirus]] (''[[Bunyaviridae]]'')
File:Marburg virus.jpg|[[Marburg virus]] (''[[Filoviridae]]'')
File:Ebola virions.png|[[Ebola virus]] (''[[Filoviridae]]'')
File:Influenza virus particle 8430 lores.jpg|[[Influenza]] (''[[Orthomyxoviridae]]'')
File:Measles virus.JPG|[[Measles]] (''[[Paramyxoviridae]]'')
File:Mumps virus, negative stained TEM 8758 lores.jpg|[[Mumps virus]] (''[[Paramyxoviridae]]'')
File:Respiratory Syncytial Virus (RSV) EM PHIL 2175 lores.jpg|[[Human respiratory syncytial virus]] (''[[Paramyxoviridae]]'')
File:Parainfluenza virus TEM PHIL 271 lores.jpg|[[Parainfluenza]] (''[[Paramyxoviridae]]'')
File:Rabies Virus EM PHIL 1876.JPG|[[Rabies]] (''[[Rhabdoviridae]]'')
File:Vesicular stomatitis virus (VSV) EM 18 lores.jpg|[[Vesicular stomatitis virus]] (''[[Rhabdoviridae]]'') <!-- Image:Mumps virions, thin sectioned TEM 8757 lores.jpg| [[Parotiditis]] (''[[Paramyxoviridae]]'') --> <!-- Image:Rift Valley fever tissue.jpg|[[Fiebre del Valle del Rift]] (''[[Bunyaviridae]]'') --> <!-- Image:Marburg virus EM PHIL 1873 lores.JPG --> <!-- Image:Lake Victoria marburgvirus.jpg --> <!-- Image:Influenza virus.png --> <!-- Image:Influenza A virus - negative stain image TEM.JPG --> <!-- Image:Influenza A - late passage.jpg --> <!-- Image:Spanish flu virus TEM PHIL 1246 lores.JPG --> <!-- Image:Grippe v2.JPG  --> <!-- Image:EM of influenza virus.jpg --> <!-- Image:Influenza A virus - early passage TEM PHIL 279 lores.jpg --> <!-- Image:A (H5N1) virion, a type of bird flu virus which is a subtype of avian influenza A.jpg --> <!-- Image:H5N1 virions 108,000x.jpg --> <!-- Image:Rabies virus longitudinal.svg --> <!-- Image:Respiratory syncytial virus 01.jpg --> <!-- Image:Ebola Virus TEM PHIL 1832 lores.jpg --> <!-- Image:Sin Nombre hanta virus TEM PHIL 1136 lores.jpg --> <!-- Image:Phocine distemper virus.jpg|[[Distémper de la foca]] (''[[Paramyxoviridae]]'') -->
</gallery>

== See also ==
{{Portal|Viruses}}
* [[Virus classification]]
* [[List of viruses]]
* [[Virus#Replication cycle|Viral replication]]
* [[Sense (molecular biology)|Positive/negative-sense]]
* [[Animal virology|Animal viruses]]
* [[Double-stranded RNA viruses]]
* [[Retrovirus]]
* [[DNA viruses]]
* [[Norovirus cis-acting replication element]]
* [[Viroid]]

==Notes==
{{notelist}}

== References ==
{{Reflist}}

== External links ==
* {{MeshName|RNA+Viruses|3=RNA Viruses}}
* [http://www.horizonpress.com/gateway/animal-viruses.html Animal viruses]

{{Viruses}}
{{Baltimore classification}}
{{Self-replicating organic structures}}
{{Authority control}}

[[Category:RNA viruses| ]]
[[Category:RNA]]