Editing RNA virus (section)

==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{{Cleanup section|reason=outdated and redundant with [[riboviria]] article as well as later text; see [[DNA virus]] for a clean integration between ICTV higher-order and Baltimore|date=January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.