Editing Viroid (section)

==Viroid-like elements==
"Viroid-like elements" refer to pieces of covalently closed circular (ccc) RNA molecules that do not share the viroid's lifecycle. The category encompasses satellite RNAs (including small plant satRNAs "[[virusoids]]", fungal "[[ambivirus]]", and the much larger [[Hepatitis D|HDV]]-like ''[[Ribozyviria]]'') and "retroviroids". Most of them also carry some type of a [[ribozyme]].<ref name=Lee/>

===Viroid-like satellite RNAs===
Viroid-like [[satellite RNA]]s are infectious circular RNA molecules that depend on a carrier virus to reproduce, being carried in their [[capsid]]s. Like Avsunviroidae, however, they are capable of self-clevage.<ref name=pmid35183574>{{cite journal |last1=Balázs |first1=E |last2=Hegedűs |first2=K |last3=Divéki |first3=Z |title=The unique carnation stunt-associated pararetroviroid. |journal=Virus Research |date=15 April 2022 |volume=312 |pages=198709 |doi=10.1016/j.virusres.2022.198709 |pmid=35183574|s2cid=246987005 }}</ref>

===Ambiviruses===
"Ambiviruses" are mobile genetic elements that were recently (2020s) discovered in [[fungi]]. Their RNA [[genome]]s are circular, circa 5 kb in length. One of at least two open reading frames encodes a viral RNA-directed [[RNA polymerase]], that firmly places "ambiviruses" into [[riboviria]]n kingdom ''[[Orthornavirae]]''; a separate phylum ''[[Ambiviricota]]'' has been established since the 2023 ICTV Virus Taxonomy Release because of the unique features of encoding RNA-directed RNA polymerases but also having divergent [[ribozyme]]s in various combinations in both sense and antisense orientation – the detection of circular forms in both sense orientations suggest that "ambiviruses" use rolling circle replication for propagation.<ref>{{cite journal |last1=Sutela |first1=Suvi |last2=Forgia |first2=Marco |last3=Vainio |first3=Eeva J |last4=Chiapello |first4=Marco |last5=Daghino |first5=Stefania |last6=Vallino |first6=Marta |last7=Martino |first7=Elena |last8=Girlanda |first8=Mariangela |last9=Perotto |first9=Silvia |last10=Turina |first10=Massimo |title=The virome from a collection of endomycorrhizal fungi reveals new viral taxa with unprecedented genome organization |journal=Virus Evolution |date=1 July 2020 |volume=6 |issue=2 |pages=veaa076 |doi=10.1093/ve/veaa076 |pmid=33324490 |pmc=7724248}}</ref><ref>{{cite journal |last1=Chong |first1=Li Chuin |last2=Lauber |first2=Chris |title=Viroid-like RNA-dependent RNA polymerase-encoding ambiviruses are abundant in complex fungi |journal=Frontiers in Microbiology |date=12 May 2023 |volume=14 |doi=10.3389/fmicb.2023.1144003 |doi-access=free |pmid=37275138 |pmc=10237039}}</ref><ref name=":2">{{cite web |title=ICTV Virus Taxonomy: 2023 Release |url=https://ictv.global/taxonomy |publisher=ICTV |access-date=2 May 2024}}</ref>

===Retroviroids===
"Retroviroids", more formally "retroviroid-like elements", are viroid-like circular RNA sequences that are also found with homologous copies in the [[DNA]] genome of the host.<ref name="daros">{{cite journal| vauthors=Daròs JA, Flores R| title=Identification of a retroviroid-like element from plants. | journal=Proceedings of the National Academy of Sciences of the United States of America | year= 1995 | volume= 92 | issue= 15 | pages= 6856–6860 | pmid= 7542779| doi= 10.1073/pnas.92.15.6856| pmc= 41428| bibcode=1995PNAS...92.6856D | doi-access=free }}</ref> The only types found are closely related to the original "carnation small viroid-like RNA" (CarSV).<ref name="pmid11172112">{{cite journal |vauthors=Hegedűs K, Palkovics L, Tóth EK, Dallmann G, Balázs E |title=The DNA form of a retroviroid-like element characterized in cultivated carnation species |journal=The Journal of General Virology |volume=82 |issue=Pt 3 |pages=687–691 |date=March 2001 |pmid=11172112 |doi=10.1099/0022-1317-82-3-687 |url=|doi-access=free }}</ref><ref name="hegedus">{{cite journal| vauthors= Hegedűs K, Dallmann G, Balázs E| title=The DNA form of a retroviroid-like element is involved in recombination events with itself and with the plant genome. | journal=Virology| year= 2004 | volume= 325 | issue= 2 | pages= 277–286 | pmid= 15246267| doi= 10.1016/j.virol.2004.04.035| pmc= | doi-access= free}}</ref> These elements may act as a [[sequence homology|homologous]] substrate upon which [[genetic recombination|recombination]] may occur and are linked to [[DNA repair#Double-strand breaks|double-stranded break repair]].<ref name="hegedus"/><ref name=Truong>{{cite journal | vauthors = Truong LN, Li Y, Shi LZ, Hwang PY, He J, Wang H, Razavian N, Berns MW, Wu X | display-authors = 6 | title = Microhomology-mediated End Joining and Homologous Recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 110 | issue = 19 | pages = 7720–25 | date = May 2013 | pmid = 23610439 | pmc = 3651503 | doi = 10.1073/pnas.1213431110 | bibcode = 2013PNAS..110.7720T | doi-access = free }}</ref>

These elements are dubbed retroviroids as the homologous DNA is generated by [[reverse transcriptase]] that is encoded by [[retrovirus]]es.<ref name="Flores-2014"/><ref>{{cite book | vauthors = Hull R | chapter = Chapter 5: Agents Resembling or Altering Virus Diseases | chapter-url = https://books.google.com/books?id=PYrZAAAAQBAJ&pg=PA199 |title=Plant virology |date= October 2013 |location=London, UK | publisher = Academic Press |isbn=978-0-12-384872-7 |edition=Fifth}}</ref> They are neither true viroids nor viroid-like [[satellite RNA]]s: there is no extracellular form of these elements; instead, they are spread only through pollen or egg-cells.<ref name=pmid35183574/> They appear to co-occur with a [[pararetrovirus]].<ref>{{cite journal |last1=Breit |first1=TM |last2=de Leeuw |first2=WC |last3=van Olst |first3=M |last4=Ensink |first4=WA |last5=van Leeuwen |first5=S |last6=Dekker |first6=RJ |title=Genome Sequence of a New Carnation Small Viroid-Like RNA, CarSV-1. |journal=Microbiology Resource Announcements |date=16 March 2023 |volume=12 |issue=3 |pages=e0121922 |doi=10.1128/mra.01219-22 |pmid=36840552 |pmc=10019309 |doi-access=free}}</ref>

===Obelisks===
{{Main|Obelisk (biology)}}
After applying [[metatranscriptomics]] – the computer-aided search for RNA sequences and their analysis – biologists reported in January 2024 the discovery of "[[Obelisk (life form)|obelisks]]", a new class of viroid-like elements, and "oblins", their related group of proteins, in the [[human microbiome]]. Given that the RNA sequences recovered do not have [[Homology (biology)|homologies]] in any other known life form, the researchers suggest that the obelisks are distinct from viruses, viroids and viroid-like entities, and thus form an entirely new class of organisms.<ref name="SA-20240129">{{cite journal |last=Koumoundouros |first=Tessa |title='Obelisks': Entirely New Class of Life Has Been Found in The Human Digestive System |url=https://www.sciencealert.com/obelisks-entirely-new-class-of-life-has-been-found-in-the-human-digestive-system |date=29 January 2024 |journal=[[ScienceAlert]] |url-status=live |archiveurl=https://archive.today/20240129133614/https://www.sciencealert.com/obelisks-entirely-new-class-of-life-has-been-found-in-the-human-digestive-system |archivedate=29 January 2024 |accessdate=29 January 2024 }}</ref><ref name="BRX-20240121">{{Cite Q|Q124389714 |last1=Zheludev |first1=Ivan N. |last2=Edgar |first2=Robert C. |last3=Lopez-Galiano |first3=Maria Jose |last4=de la Peña |first4=Marcos |last5=Artem |first5=Babaian |last6=Bhatt |first6=Ami S. |last7=Fire |first7=Andrew Z. |author-link6=Ami Bhatt |author-link7=Andrew Fire |doi-access=free |url-status=live |accessdate=29 January 2024}}</ref>