Editing RNA virus (section)

==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>