Editing Viroid (section)

{{Short description|Pathogenic small single-stranded circular RNA}}
{{For|a variant of viroids dependent on viruses|Virusoid}}
{{Cs1 config|name-list-style=vanc}}
{{Virusbox
| image = PSTviroid.png
| taxon = Viroid
| subdivision_ranks = Families
| subdivision = *''[[Pospiviroidae]]''
*''[[Avsunviroidae]]''
}}

'''Viroids''' are small single-stranded, [[circular RNA]]s that are infectious pathogens.<ref name="Navarro">{{cite journal |last1=Navarro |first1=Beatriz |last2=Flores |first2=Ricardo |last3=Di Serio |first3=Francesco |title=Advances in Viroid-Host Interactions |journal=Annual Review of Virology |date=29 September 2021 |volume=8 |issue=1 |pages=305–325|doi-access=free |doi=10.1146/annurev-virology-091919-092331 |pmid=34255541 |issn=2327-056X}}</ref><ref>{{cite web |last1=Di Serio |first1=Francesco |last2=Owens |first2=Robert A. |last3=Li |first3=Shi-Fang |last4=Matoušek |first4=Jaroslav |last5=Pallás |first5=Vicente |last6=Randles |first6=John W. |last7=Sano |first7=Teruo |last8=Verhoeven |first8=Jacobus Th. J. |last9=Vidalakis |first9=Georgios |last10=Flores |first10=Ricardo |date=November 2020 |editor-last=Zerbini |editor-first=F. Murilo |editor2-last=Sabanadzovic |editor2-first=Sead |title=Viroids |url=https://talk.ictvonline.org/ictv-reports/ictv_online_report/subviral-agents/w/viroids |access-date=February 3, 2021 |url-status=dead |archive-date=December 2, 2020 |archive-url=https://web.archive.org/web/20201202061614/https://talk.ictvonline.org/ictv-reports/ictv_online_report/subviral-agents/w/viroids}}</ref> Unlike [[virus]]es, they have no protein coating. All known viroids are inhabitants of [[angiosperms]] (flowering plants),<ref>{{cite journal |vauthors=Hadidi A |title=Next-Generation Sequencing and CRISPR/Cas13 Editing in Viroid Research and Molecular Diagnostics |journal=Viruses |volume=11 |issue=2 |pages=120 |date=January 2019 |pmid=30699972 |pmc=6409718 |doi=10.3390/v11020120 |doi-access=free}}</ref> and most cause diseases, whose respective [[Agricultural economics|economic]] importance to humans varies widely.<ref name="pmid32752288">{{cite journal |vauthors=Adkar-Purushothama CR, Perreault JP |title=Impact of Nucleic Acid Sequencing on Viroid Biology |journal=International Journal of Molecular Sciences |volume=21 |issue=15 |date=August 2020 |page=5532 |pmid=32752288 |pmc=7432327 |doi=10.3390/ijms21155532 |url=|doi-access=free }}</ref> A recent [[metatranscriptomics]] study suggests that the host diversity of viroids and viroid-like elements is broader than previously thought and that it would not be limited to plants, encompassing even the [[prokaryotes]].<ref name=Lee>{{cite journal |vauthors=Lee BD, Neri U, Roux S, Wolf YI, Camargo AP, Krupovic M |collaboration=RNA Virus Discovery Consortium; Simmonds P, Kyrpides N, Gophna U, Dolja VV, Koonin EV |title=Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs |journal=Cell |date=2 Feb 2023 |volume=186 |issue=3 |pages=646–661 |doi=10.1016/j.cell.2022.12.039 |pmid=36696902 |pmc=9911046 |biorxiv=10.1101/2022.07.19.500677 }}</ref>

The first discoveries of viroids in the 1970s triggered the historically third major extension of the [[biosphere]]—to include smaller lifelike entities—after the discoveries in 1675 by [[Antonie van Leeuwenhoek]] (of the "subvisible" microorganisms) and  in 1892–1898 by [[Dmitri Iosifovich Ivanovsky]] and [[Martinus Beijerinck]] (of the "submicroscopic" viruses). 
The unique properties of viroids have been recognized by the [[International Committee on Taxonomy of Viruses]],  in creating a new [[order (taxonomic rank)|order]] of [[subviral agents]].<ref>{{cite book | vauthors = King AM, Adams MJ, Carstens EB, Lefkovitz EJ, etal | title = Virus Taxonomy. Ninth Report of the International Committee for Virus Taxonomy. | location = Burlington, Massachusetts, US | publisher = Elsevier Academic Press | date = 2012 | pages = 1221–1259  | isbn = 978-0-12-384685-3  }}</ref>

The first recognized viroid, the pathogenic agent of the [[Potato spindle tuber viroid|potato spindle tuber disease]], was discovered, initially molecularly characterized, and named by [[Theodor Otto Diener]], plant pathologist at the U.S Department of Agriculture's Research Center in Beltsville, Maryland, in 1971.<ref name="pmid5095900">{{cite journal | vauthors = Diener TO | title = Potato spindle tuber "virus". IV. A replicating, low molecular weight RNA | journal = Virology | volume = 45 | issue = 2 | pages = 411–28 | date = August 1971 | pmid = 5095900 | doi = 10.1016/0042-6822(71)90342-4 }}</ref><ref name = "ARS_timeline">{{cite web|url=http://www.ars.usda.gov/is/timeline/viroid.htm |title=ARS Research Timeline – Tracking the Elusive Viroid |date=2006-03-02 |access-date=2007-07-18}}</ref> This viroid is now called potato spindle tuber viroid, abbreviated PSTVd.  The ''[[Citrus exocortis|Citrus exocortis viroid]]'' (CEVd)  was discovered soon thereafter, and together understanding of PSTVd and CEVd shaped the concept of the viroid.<ref name="pmid16078879">{{cite journal |vauthors=Flores R, Hernández C, Martínez de Alba AE, Daròs JA, Di Serio F |title=Viroids and viroid-host interactions |journal=Annual Review of Phytopathology |volume=43 |issue= |pages=117–39 |date=2005 |pmid=16078879 |doi=10.1146/annurev.phyto.43.040204.140243 |url=}}</ref>

Although viroids are composed of nucleic acid, they do not code for any [[protein]].<ref>{{cite journal | vauthors = Tsagris EM, Martínez de Alba AE, Gozmanova M, Kalantidis K | title = Viroids | journal = Cellular Microbiology | volume = 10 | issue = 11 | pages = 2168–79 | date = November 2008 | pmid = 18764915 | doi = 10.1111/j.1462-5822.2008.01231.x | s2cid = 221581424 | doi-access = free }}</ref><ref>{{cite journal| vauthors = Flores R, Di Serio F, Hernández C |title=Viroids: The Noncoding Genomes|journal=Seminars in Virology|date=February 1997|volume=8|issue=1|pages=65–73|doi=10.1006/smvy.1997.0107}}</ref> The viroid's replication mechanism uses [[RNA polymerase II]], a host cell enzyme normally associated with synthesis of [[messenger RNA]] from DNA, which instead catalyzes "[[rolling circle]]" synthesis of new RNA using the viroid's RNA as a template. Viroids are often [[ribozymes]], having [[catalytic]] properties that allow self-cleavage and ligation of unit-size genomes from larger replication intermediates.<ref name="pmid33800543">{{cite journal |vauthors=Moelling K, Broecker F |title=Viroids and the Origin of Life |journal=International Journal of Molecular Sciences |volume=22 |issue=7 |date=March 2021 |page=3476 |pmid=33800543 |pmc=8036462 |doi=10.3390/ijms22073476 |url=|doi-access=free }}</ref>

Diener initially hypothesized in 1989 that viroids may represent "living relics" from the widely assumed, ancient, and non-cellular [[RNA world]], and others have followed this conjecture.<ref name="Diener_1989">{{cite journal |vauthors=Diener TO |date=December 1989 |title=Circular RNAs: relics of precellular evolution? |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=86 |issue=23 |pages=9370–4 |bibcode=1989PNAS...86.9370D |doi=10.1073/pnas.86.23.9370 |pmc=298497 |pmid=2480600 |doi-access=free}}</ref><ref>{{cite journal|last1=Moelling|first1=Karin|last2=Broecker |first2=Felix|date=2021-03-28|title=Viroids and the Origin of Life|journal=International Journal of Molecular Sciences|volume=22|issue=7|pages=3476 |doi=10.3390/ijms22073476|issn=1422-0067 |pmc=8036462|pmid=33800543|doi-access=free}}</ref> Following the discovery of [[retrozyme]]s, it has been proposed that viroids and other viroid-like elements may derive from this newly found class of [[retrotransposon]].<ref name=":3">{{cite journal|last1=Cervera|first1=Amelia |last2=Urbina|first2=Denisse |last3=de la Peña|first3=Marcos|date=2016-06-23 |title=Retrozymes are a unique family of non-autonomous retrotransposons with hammerhead ribozymes that propagate in plants through circular RNAs |journal=Genome Biology|volume=17|issue=1|pages=135 |doi=10.1186/s13059-016-1002-4|issn=1474-760X|pmc=4918200|pmid=27339130 |doi-access=free }}</ref><ref name=":0">{{cite journal |last1=de la Peña|first1=Marcos|last2=Cervera|first2=Amelia|date=2017-08-03|title=Circular RNAs with hammerhead ribozymes encoded in eukaryotic genomes: The enemy at home|journal=RNA Biology |language=en|volume=14|issue=8 |pages=985–991|doi=10.1080/15476286.2017.1321730|issn=1547-6286 |pmc=5680766|pmid=28448743}}</ref><ref name=":1">{{cite journal|last1=Lee|first1=Benjamin D. |last2=Koonin |first2=Eugene V.|date=2022-01-12|title=Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators?|journal=Life|volume=12|issue=1|pages=103 |doi=10.3390/life12010103|pmid=35054497 |pmc=8781251 |bibcode=2022Life...12..103L |issn=2075-1729|doi-access=free}}</ref>

The human pathogen [[hepatitis D virus]] is a subviral agent similar in structure to a viroid, as it is a hybrid particle enclosed by surface proteins from the [[hepatitis B virus]].<ref>{{cite journal | vauthors = Alves C, Branco C, Cunha C | title = Hepatitis delta virus: a peculiar virus | journal = Advances in Virology | volume = 2013 | pages = 560105 | year = 2013 | pmid = 24198831 | pmc = 3807834 | doi = 10.1155/2013/560105 | doi-access = free }}</ref>