Editing RNA virus (section)

===[[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/>