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{{shortShort description|Virus that has DNA as its genetic material}}
{{Use dmy dates|date=April 2017}}
A '''DNA virus''' is a [[virus]] that has [[DNA]] as its [[genetic material]] and replicates using a DNA-dependent [[DNA polymerase]]. The [[nucleic acid]] is usually double-stranded DNA (dsDNA) but may also be single-stranded DNA (ssDNA). DNA viruses belong to either ''Group I'' or ''Group II'' of the [[Baltimore classification]] system for viruses. Single-stranded DNA is usually expanded to double-stranded in infected cells. Although ''Group VII'' viruses such as [[hepatitis B]] contain a DNA [[genome]], they are not considered DNA viruses according to the Baltimore classification, but rather [[reverse transcribing viruses]] because they replicate through an RNA intermediate. Notable diseases like [[smallpox]], [[herpes]], and the [[chickenpox]] are caused by such DNA viruses.
[[File:Cowpox virus.jpg|thumb|upright=1.2|''[[Orthopoxvirus]]'' particles]]
A '''DNA virus''' is a [[virus]] that has a [[genome]] made of [[deoxyribonucleic acid]] (DNA) that is replicated by a [[DNA polymerase]]. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and those that have one strand of DNA in their genome, called single-stranded DNA (ssDNA) viruses. dsDNA viruses primarily belong to two [[Realm (virology)|realms]]: ''[[Duplodnaviria]]'' and ''[[Varidnaviria]]'', and ssDNA viruses are almost exclusively assigned to the realm ''[[Monodnaviria]]'', which also includes some dsDNA viruses. Additionally, many DNA viruses are unassigned to higher taxa. Reverse transcribing viruses, which have a DNA genome that is replicated through an RNA intermediate by a [[reverse transcriptase]], are classified into the kingdom ''[[Pararnavirae]]'' in the realm ''[[Riboviria]]''.
 
DNA viruses are ubiquitous worldwide, especially in marine environments where they form an important part of marine ecosystems, and infect both [[prokaryote]]s and [[eukaryote]]s. They appear to have multiple origins, as viruses in ''Monodnaviria'' appear to have emerged from archaeal and bacterial [[plasmid]]s on multiple occasions, though the origins of ''Duplodnaviria'' and ''Varidnaviria'' are less clear.
==Group I: dsDNA viruses==
[[File:Hhv6 genome2.png|thumb|450px|alt=HHV-6 genome|Genome of ''[[human herpesvirus-6]]'', a member of the family [[Herpesviridae]]]]
[[Genome]] organization within this group varies considerably. Some have circular genomes (''Baculoviridae'', ''Papovaviridae'' and ''Polydnaviridae'') while others have linear genomes (''Adenoviridae'', ''Herpesviridae'' and some phages). Some families have circularly permuted linear genomes ([[phage T4]] and some ''Iridoviridae''). Others have linear genomes with covalently closed ends (''Poxviridae'' and ''Phycodnaviridae'').
 
Prominent disease-causing DNA viruses include [[Herpesvirales|herpesviruses]], [[Papillomaviridae|papillomaviruses]], and [[Poxviridae|poxviruses]].
A virus infecting [[archaea]] was first described in 1974. Several others have been described since: most have head-tail morphologies and linear double-stranded DNA genomes. Other morphologies have also been described: spindle shaped, rod shaped, filamentous, icosahedral and spherical. Additional morphological types may exist.
 
==Baltimore classification==
[[Order (biology)|Order]]s within this group are defined on the basis of morphology rather than DNA sequence similarity. It is thought that morphology is more conserved in this group than sequence similarity or gene order which is extremely variable. Three orders and 31 [[family (biology)|families]] are currently recognised. A fourth order—[[Megavirales]]—for the nucleocytoplasmic large DNA viruses has been proposed.<ref name=Colson2012 /><ref name="Colson2013">{{cite journal | vauthors = Colson P, De Lamballerie X, Yutin N, Asgari S, Bigot Y, Bideshi DK, Cheng XW, Federici BA, Van Etten JL, Koonin EV, La Scola B, Raoult D | title = "Megavirales", a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses | journal = Archives of Virology | volume = 158 | issue = 12 | pages = 2517–2521 | date = December 2013 | pmid = 23812617 | pmc = 4066373 | doi = 10.1007/s00705-013-1768-6 }}</ref> This proposal has yet to be ratified by the [[International Committee on Taxonomy of Viruses|ICTV]]. Four [[genus|genera]] are recognised that have not yet been assigned a family.
The [[Baltimore classification]] system is used to group viruses together based on their manner of [[messenger RNA]] (mRNA) synthesis and is often used alongside standard virus taxonomy, which is based on evolutionary history. DNA viruses constitute two Baltimore groups: Group I: double-stranded DNA viruses, and Group II: single-stranded DNA viruses. While Baltimore classification is chiefly based on [[Transcription (biology)|transcription]] of mRNA, viruses in each Baltimore group also typically share their manner of replication. Viruses in a Baltimore group do not necessarily share genetic relation or morphology.<ref name=lostroh11 >[[#lostroh|Lostroh 2019]], pp.&nbsp;11–13</ref>
 
===<span class="anchor" id="Group I: dsDNA viruses"></span>Double-stranded DNA viruses===
Fifteen families are [[viral envelope|enveloped]]. These include all three families in the order ''Herpesvirales'' and the following families: ''Ascoviridae'', ''Ampullaviridae'', ''Asfarviridae'', ''Baculoviridae'', ''Fuselloviridae'', ''Globuloviridae'', ''Guttaviridae'', ''Hytrosaviridae'', ''Iridoviridae'', ''Lipothrixviridae'', ''Nimaviridae'' and ''Poxviridae''.
The first Baltimore group of DNA viruses are those that have a double-stranded DNA genome. All dsDNA viruses have their mRNA synthesized in a three-step process. First, a [[transcription preinitiation complex]] binds to the DNA upstream of the site where transcription begins, allowing for the recruitment of a host [[RNA polymerase]]. Second, once the RNA polymerase is recruited, it uses the negative strand as a template for synthesizing mRNA strands. Third, the RNA polymerase terminates transcription upon reaching a specific signal, such as a [[polyadenylation]] site.<ref name=dsdna >{{cite web|title=dsDNA templated transcription|url=https://viralzone.expasy.org/1942|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref><ref name=rampersad66 >[[#rampersad|Rampersad 2018]], p.&nbsp;66</ref><ref name=fermin36 >[[#fermin|Fermin 2018]], pp.&nbsp;36–40</ref>
 
dsDNA viruses make use of several mechanisms to replicate their genome. Bidirectional replication, in which two replication forks are established at a replication origin site and move in opposite directions of each other, is widely used.<ref name=bidi >{{cite web|title=dsDNA bidirectional replication|url=https://viralzone.expasy.org/1939|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref> A rolling circle mechanism that produces linear strands while progressing in a loop around the circular genome is also common.<ref name=dsdnarcr >{{cite web|title=dsDNA rolling circle replication|url=https://viralzone.expasy.org/2676|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref><ref>{{cite journal |vauthors=Bernstein H, Bernstein C |date=5 July 1973 |title=Circular and branched circular concatenates as possible intermediates in bacteriophage T4 DNA replication |journal=J Mol Biol |volume=77 |issue=3 |pages=355–361 |doi=10.1016/0022-2836(73)90443-9 |pmid=4580243}}</ref> Some dsDNA viruses use a strand displacement method whereby one strand is synthesized from a template strand, and a complementary strand is then synthesized from the prior synthesized strand, forming a dsDNA genome.<ref name=displace >{{cite web|title=DNA strand displacement replication|url=https://viralzone.expasy.org/1940|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref> Lastly, some dsDNA viruses are replicated as part of a process called [[replicative transposition]] whereby a viral genome in a host cell's DNA is replicated to another part of a host genome.<ref name=reptrans>{{cite web|title=Replicative transposition|url=https://viralzone.expasy.org/4017|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref>
[[Bacteriophage]]s (viruses infecting [[bacteria]]) belonging to the families ''Tectiviridae'' and ''Corticoviridae'' have a lipid bilayer [[membrane]] inside the icosahedral [[protein]] [[capsid]] and the membrane surrounds the genome. The crenarchaeal virus ''Sulfolobus turreted icosahedral virus'' has a similar structure.
 
dsDNA viruses can be subdivided between those that replicate in the [[cell nucleus]], and as such are relatively dependent on host cell machinery for transcription and replication, and those that replicate in the [[cytoplasm]], in which case they have evolved or acquired their own means of executing transcription and replication.<ref name=cann122 >[[#cann|Cann 2015]], pp.&nbsp;122–127</ref> dsDNA viruses are also commonly divided between tailed dsDNA viruses, referring to members of the realm ''Duplodnaviria'', usually the tailed bacteriophages of the order ''Caudovirales'', and tailless or non-tailed dsDNA viruses of the realm ''Varidnaviria''.<ref name=duplo >{{cite web|vauthors=Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini M, Kuhn JH|title=Create a megataxonomic framework, filling all principal/primary taxonomic ranks, for dsDNA viruses encoding HK97-type major capsid proteins|url=https://ictv.global/ictv/proposals/2019.004G.zip|website=International Committee on Taxonomy of Viruses|access-date=24 September 2020|language=en|format=docx|date=18 October 2019}}</ref><ref name=vari >{{cite web|vauthors=Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini M, Kuhn JH|title=Create a megataxonomic framework, filling all principal taxonomic ranks, for DNA viruses encoding vertical jelly roll-type major capsid proteins|url=https://ictv.global/ictv/proposals/2019.003G.zip|website=International Committee on Taxonomy of Viruses|access-date=24 September 2020|language=en|format=docx|date=18 October 2019}}</ref>
The genomes in this group vary considerably from ~10 kilobases to over 2.5 megabases in length. The largest bacteriophage known is Klebsiella Phage vB_KleM-RaK2 which has a genome of 346 kilobases.<ref name="Simoliūnas2013">{{cite journal | vauthors = Simoliūnas E, Kaliniene L, Truncaitė L, Zajančkauskaitė A, Staniulis J, Kaupinis A, Ger M, Valius M, Meškys R | title = Klebsiella phage vB_KleM-RaK2 – a giant singleton virus of the family Myoviridae | journal = PLOS ONE | volume = 8 | issue = 4 | pages = e60717 | year = 2013 | pmid = 23593293 | pmc = 3622015 | doi = 10.1371/journal.pone.0060717 | bibcode = 2013PLoSO...860717S }}</ref>
 
===Single-stranded DNA viruses===
The virophages are a group of viruses that infect other viruses.
[[File:Canines_Parvovirus.jpg|thumb|The [[canine parvovirus]] is an ssDNA virus.]]
The second Baltimore group of DNA viruses are those that have a single-stranded DNA genome. ssDNA viruses have the same manner of transcription as dsDNA viruses. However, because the genome is single-stranded, it is first made into a double-stranded form by a [[DNA polymerase]] upon entering a host cell. mRNA is then synthesized from the double-stranded form. The double-stranded form of ssDNA viruses may be produced either directly after entry into a cell or as a consequence of replication of the viral genome.<ref name=ssdna >{{cite web|title=ssDNA Rolling circle|url=https://viralzone.expasy.org/1941|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref><ref name=hairpin >{{cite web|title=Rolling hairpin replication|url=https://viralzone.expasy.org/2656|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref> Eukaryotic ssDNA viruses are replicated in the nucleus.<ref name=cann122 /><ref name=fermin40 >[[#fermin|Fermin 2018]], pp.&nbsp;40–41</ref>
 
Most ssDNA viruses contain circular genomes that are replicated via rolling circle replication (RCR). ssDNA RCR is initiated by an [[endonuclease]] that bonds to and cleaves the positive strand, allowing a DNA polymerase to use the negative strand as a template for replication. Replication progresses in a loop around the genome by means of extending the 3'-end of the positive strand, displacing the prior positive strand, and the endonuclease cleaves the positive strand again to create a standalone genome that is [[Ligation (molecular biology)|ligated]] into a circular loop. The new ssDNA may be packaged into virions or replicated by a DNA polymerase to form a double-stranded form for transcription or continuation of the replication cycle.<ref name=ssdna /><ref name=rampersad61 >[[#rampersad|Rampersad 2018]], pp.&nbsp;61–62</ref>
A virus with a novel method of genome packing infecting species of the genus ''[[Sulfolobus]]'' has been described.<ref name=Liu2016>{{cite journal | vauthors = Liu Y, Ishino S, Ishino Y, Pehau-Arnaudet G, Krupovic M, Prangishvili D | title = A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea | journal = Journal of Virology | volume = 91 | issue = 13 | pages = e00589–17 | date = July 2017 | pmid = 28424284 | pmc = 5469268 | doi = 10.1128/JVI.00589-17 }}</ref> As this virus does not resemble any known virus it has been classified into a new family, the ''[[Portogloboviridae]]''.
 
[[Parvovirus]]es contain linear ssDNA genomes that are replicated via [[rolling hairpin replication]] (RHR), which is similar to RCR. Parvovirus genomes have [[Stem-loop|hairpin loops]] at each end of the genome that repeatedly unfold and refold during replication to change the direction of DNA synthesis to move back and forth along the genome, producing numerous copies of the genome in a continuous process. Individual genomes are then excised from this molecule by the viral endonuclease. For parvoviruses, either the [[Sense (molecular biology)|positive or negative sense]] strand may be packaged into capsids, varying from virus to virus.<ref name=rampersad61 /><ref>{{cite book |vauthors=Kerr J, Cotmore S, Bloom ME |date=25 November 2005 |title=Parvoviruses |publisher=CRC Press |pages=171–185 |isbn=9781444114782}}</ref>
Another ''[[Sulfolobus]]'' infecting virus—Sulfolobus ellipsoid virus 1—has been described.<ref name=Wang2017>Wang H, Guo Z, Feng H, Chen Y, Chen X, Li Z, Hernández-Ascencio W, Dai X, Zhang Z, Zheng X, Mora-López M, Fu Y, Zhang C, Zhu P, Huang L (2017) A novel Sulfolobus virus with an exceptional capsid architecture. J Virol</ref> This enveloped virus has a unique capsid and may be classified into a new taxon.
 
Nearly all ssDNA viruses have positive sense genomes, but a few exceptions and peculiarities exist. The family ''[[Anelloviridae]]'' is the only ssDNA family whose members have negative sense genomes, which are circular.<ref name=fermin40 /> Parvoviruses, as previously mentioned, may package either the positive or negative sense strand into virions.<ref name=hairpin /> Lastly, [[Bidensovirus|bidnavirus]]es package both the positive and negative linear strands.<ref name=fermin40 /><ref name=bidna >{{cite web|title=Bidnaviridae|url=https://viralzone.expasy.org/2957|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref>
===Host range===
Species of the order ''Caudovirales'' and of the families ''Corticoviridae'' and ''Tectiviridae'' infect [[bacteria]].
 
==ICTV classification==
Species of the order ''Ligamenvirales'' and the families ''Ampullaviridae'', ''Bicaudaviridae'', ''Clavaviridae'', ''Fuselloviridae'', ''Globuloviridae'', ''Guttaviridae'' , ''Tristromaviridae'' and ''Turriviridae'' infect hyperthermophilic [[archaea]] species of the ''[[Crenarchaeota]]''.
The [[International Committee on Taxonomy of Viruses]] (ICTV) oversees virus taxonomy and organizes viruses at the basal level at the rank of realm. Virus realms correspond to the rank of [[Domain (biology)|domain]] used for cellular life but differ in that viruses within a realm do not necessarily share [[common ancestry]], nor do the realms share common ancestry with each other. As such, each virus realm represents at least one instance of viruses coming into existence. Within each realm, viruses are grouped together based on shared characteristics that are [[highly conserved]] over time.<ref name=exec >{{cite journal|author=International Committee on Taxonomy of Viruses Executive Committee|date=May 2020|title=The New Scope of Virus Taxonomy: Partitioning the Virosphere Into 15 Hierarchical Ranks|journal=Nat Microbiol|volume=5|issue=5|pages=668–674|doi=10.1038/s41564-020-0709-x|pmc=7186216|pmid=32341570}}</ref> Three DNA virus realms are recognized: ''Duplodnaviria'', ''Monodnaviria'', and ''Varidnaviria''.
 
===''Duplodnaviria''===
Species of the order ''Herpesvirales'' and of the families ''Adenoviridae'', ''Asfarviridae'', ''Iridoviridae'', ''Papillomaviridae'', ''Polyomaviridae'' and ''Poxviridae'' infect [[vertebrate]]s.
[[File:Duplodnaviria virion morphology.jpg|thumb|Illustrated sample of ''Duplodnaviria'' virions]]
''[[Duplodnaviria]]'' contains dsDNA viruses that encode a major capsid protein (MCP) that has the HK97 fold. Viruses in the realm also share a number of other characteristics involving the capsid and capsid assembly, including an icosahedral capsid shape and a terminase enzyme that packages viral DNA into the capsid during assembly. Two groups of viruses are included in the realm: tailed bacteriophages, which infect prokaryotes and are assigned to the order ''[[Caudovirales]]'', and herpesviruses, which infect animals and are assigned to the order ''[[Herpesvirales]]''.<ref name=duplo />
 
''Duplodnaviria'' is a very ancient realm, perhaps predating the [[last universal common ancestor]] (LUCA) of cellular life. Its origins not known, nor whether it is monophyletic or polyphyletic. A characteristic feature is the HK97-fold found in the MCP of all members, which is found outside the realm only in [[encapsulin]]s, a type of nanocompartment found in bacteria: this relation is not fully understood.<ref name=duplo /><ref name=krupovic >{{cite journal|vauthors=Krupovic M, Koonin EV|date=21 March 2017|title=Multiple origins of viral capsid proteins from cellular ancestors|journal=Proc Natl Acad Sci U S A|volume=114|issue=12|pages=E2401–E2410|doi=10.1073/pnas.1621061114|pmc=5373398|pmid=28265094|bibcode=2017PNAS..114E2401K |doi-access=free}}</ref><ref name=luca >{{cite journal|last1=Krupovic|first1=M|last2=Dolja|first2=VV|last3=Koonin|first3=EV|title=The LUCA and its complex virome.|journal=Nat Rev Microbiol|date=14 July 2020|volume=18|issue=11|pages=661–670|doi=10.1038/s41579-020-0408-x|pmid=32665595|s2cid=220516514|url=https://bpp.oregonstate.edu/sites/agscid7/files/bpp/attachments/lucavirome2020.pdf |archive-url=https://web.archive.org/web/20201027183841/https://bpp.oregonstate.edu/sites/agscid7/files/bpp/attachments/lucavirome2020.pdf |archive-date=2020-10-27 |url-status=live|access-date=24 September 2020}}</ref>
Species of the families ''Ascovirus'', ''Baculovirus'', ''Hytrosaviridae'', ''Iridoviridae'' and ''Polydnaviruses'' and of the genus ''Nudivirus'' infect [[insect]]s.
 
The relation between caudoviruses and herpesviruses is also uncertain: they may share a common ancestor or herpesviruses may be a divergent clade from the realm ''Caudovirales''. A common trait among duplodnaviruses is that they cause latent infections without replication while still being able to replicate in the future.<ref>{{cite journal|vauthors=Weidner-Glunde M, Kruminis-Kaszkiel E, Savanagoudar M|date=February 2020|title=Herpesviral Latency—Common Themes|journal=Pathogens|volume=9|issue=2|pages=125|doi=10.3390/pathogens9020125|pmc=7167855|pmid=32075270|doi-access=free}}</ref><ref>{{cite web|title=Virus latency|url=https://viralzone.expasy.org/3970|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref> Tailed bacteriophages are ubiquitous worldwide,<ref>{{cite journal|vauthors=Andrade-Martínez JS, Moreno-Gallego JL, Reyes A|date=August 2019|title=Defining a Core Genome for the Herpesvirales and Exploring their Evolutionary Relationship with the Caudovirales|journal=Sci Rep|volume=9|issue=1|pages=11342 |doi=10.1038/s41598-019-47742-z|pmc=6683198|pmid=31383901|bibcode=2019NatSR...911342A}}</ref> important in marine ecology,<ref>{{cite journal|vauthors=Wilhelm SW, Suttle CA|date=October 1999|title=Viruses and Nutrient Cycles in the Sea: Viruses play critical roles in the structure and function of aquatic food webs|journal=BioScience|volume=49|issue=10|pages=781–788|doi=10.2307/1313569|jstor=1313569|doi-access=free}}</ref> and the subject of much research.<ref>{{cite journal|vauthors=Keen EC|date=January 2015|title=A century of phage research: Bacteriophages and the shaping of modern biology|journal=BioEssays|volume=37|issue=1|pages=6–9|doi=10.1002/bies.201400152|pmc=4418462|pmid=25521633}}</ref> Herpesviruses are known to cause a variety of epithelial diseases, including [[herpes simplex]], [[chickenpox]] and [[shingles]], and [[Kaposi's sarcoma]].<ref>{{cite journal|vauthors=Kukhanova MK, Korovina AN, Kochetkov SN|date=December 2014|title=Human herpes simplex virus: life cycle and development of inhibitors|journal=Biochemistry (Mosc)|volume=79|issue=13|pages=1635–1652|doi=10.1134/S0006297914130124|pmid=25749169|s2cid=7414402}}</ref><ref>{{cite journal|vauthors=Gershon AA, Breuer J, Cohen JI, Cohrs RJ, Gershon MD, Gilden D, Grose C, Hambleton S, Kennedy PG, Oxman MN, Seward JF, Yamanishi K|date=2 July 2015|title=Varicella zoster virus infection|journal=Nat Rev Dis Primers|volume=1|pages=15016|doi=10.1038/nrdp.2015.16|pmc=5381807|pmid=27188665}}</ref><ref>{{cite journal|vauthors=O'Leary JJ, Kennedy MM, McGee JO|date=February 1997|title=Kaposi's sarcoma associated herpes virus (KSHV/HHV 8): epidemiology, molecular biology and tissue distribution|journal=Mol Pathol|volume=50|issue=1|pages=4–8|doi=10.1136/mp.50.1.4|pmc=379571|pmid=9208806}}</ref>
Species of the family ''Mimiviridae'' and the species ''Marseillevirus'', ''Megavirus'', ''Mavirus virophage'' and ''Sputnik virophage'' infect [[protozoa]].
 
===''Monodnaviria''===
Species of the family ''Nimaviridae'' infect [[crustacean]]s.
''[[Monodnaviria]]'' contains ssDNA viruses that encode an [[endonuclease]] of the HUH superfamily that initiates [[rolling circle replication]] and all other viruses descended from such viruses. The prototypical members of the realm are called CRESS-DNA viruses and have circular ssDNA genomes. ssDNA viruses with linear genomes are descended from them, and in turn some dsDNA viruses with circular genomes are descended from linear ssDNA viruses.<ref name=mono />
 
Viruses in ''Monodnaviria'' appear to have emerged on multiple occasions from archaeal and bacterial [[plasmid]]s, a type of extra-chromosomal DNA molecule that self-replicates inside its host. The kingdom ''Shotokuvirae'' in the realm likely emerged from recombination events that merged the DNA of these plasmids and complementary DNA encoding the capsid proteins of RNA viruses.<ref name=mono /><ref>{{cite journal|vauthors=Kazlauskas D, Varsani A, Koonin EV, Krupovic M|date=31 July 2019|title=Multiple Origins of Prokaryotic and Eukaryotic Single-Stranded DNA Viruses From Bacterial and Archaeal Plasmids|journal=Nat Commun|volume=10|issue=1|pages=3425|doi=10.1038/s41467-019-11433-0|pmc=6668415|pmid=31366885|bibcode=2019NatCo..10.3425K}}</ref>
Species of the family ''Phycodnaviridae'' and the species ''Organic Lake virophage'' infect [[algae]]. These are the only known dsDNA viruses that infect [[plant]]s.
 
CRESS-DNA viruses include three kingdoms that infect prokaryotes: ''[[Loebvirae]]'', ''[[Sangervirae]]'', and ''[[Trapavirae]]''. The kingdom ''[[Shotokuvirae]]'' contains eukaryotic CRESS-DNA viruses and the atypical members of ''Monodnaviria''.<ref name=mono /> Eukaryotic monodnaviruses are associated with many diseases, and they include [[papillomavirus]]es and [[polyomavirus]]es, which cause many cancers,<ref>{{cite web|title=Papillomaviridae|url=https://viralzone.expasy.org/5|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref><ref>{{cite web|title=Polyomaviridae|url=https://viralzone.expasy.org/148|website=ViralZone|publisher=Swiss Institute of Bioinformatics|access-date=24 September 2020}}</ref> and [[geminivirus]]es, which infect many economically important crops.<ref>{{cite journal|vauthors=Malathi VG, Renuka Devi P|date=March 2019|title=ssDNA Viruses: Key Players in Global Virome|journal=Virusdisease|volume=30|issue=1|pages=3–12|doi=10.1007/s13337-019-00519-4|pmc=6517461|pmid=31143827}}</ref>
Species of the family ''Plasmaviridae'' infect species of the class ''[[Mollicutes]]''.
 
===''Varidnaviria''===
Species of the family ''Pandoraviridae'' infect [[amoeba]]e.
[[File:2w0c_monomer.png|thumb|A [[ribbon diagram]] of the MCP of ''[[Pseudoalteromonas virus PM2]]'', with the two jelly roll folds colored in red and blue]]
''[[Varidnaviria]]'' contains DNA viruses that encode MCPs that have a [[jelly roll fold]] folded structure in which the jelly roll (JR) fold is perpendicular to the surface of the viral capsid. Many members also share a variety of other characteristics, including a minor capsid protein that has a single JR fold, an ATPase that packages the genome during capsid assembly, and a common [[DNA polymerase]]. Two kingdoms are recognized: ''[[Helvetiavirae]]'', whose members have MCPs with a single vertical JR fold, and ''[[Bamfordvirae]]'', whose members have MCPs with two vertical JR folds.<ref name=vari />
 
Varidnaviria is either monophyletic or polyphyletic and may predate the LUCA. The kingdom ''Bamfordvirae'' is likely derived from the other kingdom ''Helvetiavirae'' via [[Fusion gene|fusion]] of two MCPs to have an MCP with two jelly roll folds instead of one. The single jelly roll (SJR) fold MCPs of ''Helvetiavirae'' show a relation to a group of proteins that contain SJR folds, including the [[Cupin superfamily]] and [[nucleoplasmin]]s.<ref name=vari /><ref name=krupovic /><ref name=luca />
Species of the genus ''Dinodnavirus'' infect [[dinoflagellate]]s. These are the only known viruses that infect [[dinoflagellate]]s.
 
Marine viruses in ''Varidnaviria'' are ubiquitous worldwide and, like tailed bacteriophages, play an important role in marine ecology.<ref>{{cite journal|vauthors=Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM, Chang WK, VanInsberghe D, Elsherbini J, Sharma RS, Cutler MB, Kelly L, Polz MF|date=1 February 2018|title=A Major Lineage of Non-Tailed dsDNA Viruses as Unrecognized Killers of Marine Bacteria|journal=Nature|volume=554|issue=7690|pages=118–122|doi=10.1038/nature25474|pmid=29364876|bibcode=2018Natur.554..118K|s2cid=4462007}}</ref> Most identified eukaryotic DNA viruses belong to the realm.<ref name=krupovic2015 >{{cite journal|vauthors=Krupovic M, Koonin EV|date=February 2015|title=Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution|journal=Nat Rev Microbiol|volume=13|issue=2|pages=105–115|doi=10.1038/nrmicro3389|pmc=5898198|pmid=25534808}}</ref> Notable disease-causing viruses in ''Varidnaviria'' include [[adenovirus]]es, [[poxvirus]]es, and the [[African swine fever virus]].<ref name=ictv >{{cite web|url=https://ictv.global/taxonomy|title=Virus Taxonomy: 2019 Release|website=International Committee on Taxonomy of Viruses|access-date=24 September 2020}}</ref> Poxviruses have been highly prominent in the history of modern medicine, especially ''Variola virus'', which caused [[smallpox]].<ref>{{cite journal|vauthors=Meyer H, Ehmann R, Smith GL|date=February 2020|title=Smallpox in the Post-Eradication Era|journal=Viruses|volume=12|issue=2|pages=138|doi=10.3390/v12020138|pmc=7077202|pmid=31991671|doi-access=free}}</ref> Many varidnaviruses can become endogenized in their host's genome; a peculiar example are [[virophage]]s, which after infecting a host, can protect the host against [[giant virus]]es.<ref name=krupovic2015 />
Species of the genus ''Rhizidiovirus'' infect [[stramenopile]]s. These are the only known dsDNA viruses that infect stramenopiles.
 
===Baltimore classification===
Species of the genus ''Salterprovirus'' and ''Sphaerolipoviridae'' infect species of the ''[[Euryarchaeota]]''.
dsDNA viruses are classified into three realms and include many taxa that are unassigned to a realm:
* All viruses in ''Duplodnaviria'' are dsDNA viruses.<ref name=duplo />
* In ''Monodnaviria'', members of the class ''[[Papovaviricetes]]'' are dsDNA viruses.<ref name=mono >{{cite web|vauthors=Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, Zerbini M, Kuhn JH|title=Create a megataxonomic framework, filling all principal taxonomic ranks, for ssDNA viruses|url=https://ictv.global/ictv/proposals/2019.005G.zip|website=International Committee on Taxonomy of Viruses|access-date=24 September 2020|language=en|format=docx|date=18 October 2019}}</ref>
* All viruses in ''Varidnaviria'' are dsDNA viruses.<ref name=vari />
* The following taxa that are unassigned to a realm exclusively contain dsDNA viruses:<ref name=vari />
** Orders: ''[[Ligamenvirales]]''
** Families: ''[[Ampullaviridae]]'', ''[[Baculoviridae]]'', ''[[Bicaudaviridae]]'', ''[[Clavaviridae]]'', ''[[Fuselloviridae]]'', ''[[Globuloviridae]]'', ''[[Guttaviridae]]'', ''[[Halspiviridae]]'', ''[[Hytrosaviridae]]'', ''[[Nimaviridae]]'', ''[[Nudiviridae]]'', ''[[Ovaliviridae]]'', ''[[Plasmaviridae]]'', ''[[Polydnaviridae]]'', ''[[Portogloboviridae]]'', ''[[Thaspiviridae]]'', ''[[Tristromaviridae]]''
** Genera: ''[[Dinodnavirus]]'', ''[[Rhizidiovirus]]''
 
ssDNA viruses are classified into one realm and include several families that are unassigned to a realm:
===Taxonomy===
* In ''Monodnaviria'', all members except viruses in ''Papovaviricetes'' are ssDNA viruses.<ref name=mono />
* The unassigned families ''[[Anelloviridae]]'' and ''[[Spiraviridae]]'' are ssDNA virus families.<ref name=mono />
* Viruses in the family ''[[Finnlakeviridae]]'' contain ssDNA genomes. ''Finnlakeviridae'' is unassigned to a realm but is a proposed member of ''Varidnaviria''.<ref name=vari />
 
==References==
The classification of DNA viruses has undergone a revision by the International Committee on the Taxonomy of Viruses in 2020.
{{Reflist}}
 
Three realms are recognised: [[Duplodnaviria]], [[Monodnaviria]] and [[Varidnaviria]]. The Duplodnaviria contain several types of double stranded DNA viruses. The Monodnaviria all the single stranded viruses. The Varidnaviria are a taxon of viruses united by the presence of use of vertically-folded jelly roll capsid.
 
Within the Duplodnaviria one kingdom ([[Heunggongvirae]]) and two phlya ([[Peploviricota]], [[Uroviricota]]) are recognised. The phylum Peploviricota has one order - ''[[Herpesvirales]]''. The phylum Uroviricota has one order - ''[[Caudovirales]]''.
 
Within the Monodnaviria four kingdoms ([[Loebvirae]], [[Sangervirae]], [[Shotokuvirae]] and [[Trapavirae]]) are recognised.
 
Within the Varidnaviria two kingdoms ([[Bamfordvirae]], [[Helvetiavirae]]) are recognised.
 
 
 
* Order ''[[Caudovirales]]''
** Family ''[[Myoviridae]]''{{snd}}includes [[Enterobacteria phage T4]]
** Family ''[[Podoviridae]]''{{snd}}includes [[Enterobacteria phage T7]]
** Family ''[[Siphoviridae]]''{{snd}}includes [[Enterobacteria phage lambda|Enterobacteria phage &lambda;]]
* Order ''[[Herpesvirales]]''
** Family ''[[Alloherpesviridae]]''
** Family ''[[Herpesviridae]]''{{snd}}includes human herpesviruses, [[chicken pox|Varicella Zoster]] virus
** Family ''[[Malacoherpesviridae]]''
*Order ''[[Ligamenvirales]]''
**Family ''[[Lipothrixviridae]]''
**Family ''[[Rudiviridae]]''
* Unassigned families
** Family ''[[Adenoviridae]]''{{snd}}includes viruses which cause human [[adenovirus infection]]
** Family ''[[Ampullaviridae]]''
** Family ''[[Ascoviridae]]''
** Family ''[[Asfarviridae]]''{{snd}}includes [[African swine fever virus]]
** Family ''[[Baculoviridae]]''
** Family ''[[Bicaudaviridae]]''
** Family ''[[Clavaviridae]]''
** Family ''[[Corticoviridae]]''
** Family ''[[Fuselloviridae]]''
** Family ''[[Globuloviridae]]''
** Family ''[[Guttaviridae]]''
** Family ''[[Hytrosaviridae]]''
** Family ''[[Iridoviridae]]''
** Family ''[[Lavidaviridae]]''
** Family ''[[Marseilleviridae]]''
** Family ''[[Mimiviridae]]''
** Family ''[[Whispovirus|Nimaviridae]]''
** Family ''[[Nudiviridae]]''
** Family ''[[Pandoraviridae]]''
** Family ''[[Papillomaviridae]]''
** Family ''[[Phycodnaviridae]]''
** Family ''[[Plasmaviridae]]''
** Family ''[[Polydnaviruses]]''
** Family ''[[Polyomaviridae]]''{{snd}}includes [[SV40|Simian virus 40]], [[JC virus]], [[BK virus]]
** Family ''[[Poxviridae]]''{{snd}}includes [[Cowpox]] virus, [[smallpox]]
** Family ''[[Sphaerolipoviridae]]''
** Family ''[[Tectiviridae]]''
** Family ''[[Alphalipothrixvirus|Tristromaviridae]]''
** Family ''[[Turriviridae]]''
* Unassigned genera
** ''[[Dinodnavirus]]''
** ''[[Salterprovirus]]''
** ''[[Rhizidiovirus]]''
* Unassigned species
** ''[[Abalone shriveling syndrome-associated virus]]''
** ''[[Apis mellifera filamentous virus]]''
** ''[[Bandicoot papillomatosis carcinomatosis virus]]''
** ''[[Cedratvirus]]''
** ''[[Kaumoebavirus]]''
** ''[[KIs-V]]''
** ''[[Lentille virus]]''
** ''[[Leptopilina boulardi filamentous virus]]''
** ''[[Megavirus]]''
** ''[[Metallosphaera turreted icosahedral virus]]''
** ''[[Methanosarcina spherical virus]]''
** ''[[Mollivirus|Mollivirus sibericum virus]]''
** ''[[Orpheovirus IHUMI-LCC2]]''
** ''[[Phaeocystis globosa virus]]''
** ''[[Pithovirus]]''
 
===Virophages===
 
* Class ''[[Maveriviricetes]]''
** Order ''[[Priklausovirales]]''
*** Family ''[[Lavidaviridae]]''
**** ''[[Ace Lake Mavirus virophage]]''
**** ''[[Dishui Lake virophage 1]]''
**** ''[[Guarani virophage]]''
**** ''[[Organic Lake virophage]]''
**** ''[[Phaeocystis globosa virus virophage]]''
**** ''[[Rio Negro virophage]]''
**** ''[[Sputnik virophage 2]]''
**** ''[[Yellowstone Lake virophage 1]]''
**** ''[[Yellowstone Lake virophage 2]]''
**** ''[[Yellowstone Lake virophage 3]]''
**** ''[[Yellowstone Lake virophage 4]]''
**** ''[[Yellowstone Lake virophage 5]]''
**** ''[[Yellowstone Lake virophage 6]]''
**** ''[[Yellowstone Lake virophage 7]]''
**** ''[[Zamilon virophage 2]]''
 
===Unclassified viruses===
 
A group of double stranded DNA viruses have been found in fish that appear to be related to the herpesviruses.<ref name=Aswad2017>{{cite journal | vauthors = Aswad A, Katzourakis A | title = A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data | journal = Virus Evolution | volume = 3 | issue = 2 | pages = vex016 | date = July 2017 | pmid = 28798873 | pmc = 5544889 | doi = 10.1093/ve/vex016 }}</ref>
 
Another group of viruses that infect fish has been described.<ref name=Dill2018>{{cite journal | vauthors = Dill JA, Camus AC, Leary JH, Ng TF | title = Microscopic and Molecular Evidence of the First Elasmobranch Adomavirus, the Cause of Skin Disease in a Giant Guitarfish, Rhynchobatus djiddensis | journal = mBio | volume = 9 | issue = 3 | pages = e00185–18 | date = May 2018 | pmid = 29764943 | pmc = 5954223 | doi = 10.1128/mBio.00185-18 }}</ref>
 
===NCLDVs===
{{main|Nucleocytoplasmic large DNA viruses}}
The asfarviruses, iridoviruses, mimiviruses, phycodnaviruses and poxviruses have been shown to belong to a single group,<ref name="Iyer2006"/>—the large nuclear and cytoplasmic DNA viruses. These are also abbreviated "NCLDV".<ref name="pmid20017929">{{cite journal | vauthors = Yutin N, Wolf YI, Raoult D, Koonin EV | title = Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution | journal = Virology Journal | volume = 6 | pages = 223 | date = December 2009 | pmid = 20017929 | pmc = 2806869 | doi = 10.1186/1743-422X-6-223 }}</ref> This clade can be divided into two groups:
 
* the iridoviruses-phycodnaviruses-mimiviruses group. The phycodnaviruses and mimiviruses are sister clades.
* the poxvirus-asfarviruses group.
 
It is probable that these viruses evolved before the separation of eukaryoyes into the extant crown groups. The ancestral genome was complex with at least 41 genes including (1) the replication machinery (2) up to four [[RNA polymerase]] subunits (3) at least three [[transcription factor]]s (4) capping and polyadenylation enzymes (5) the DNA packaging apparatus (6) and structural components of an icosahedral capsid and the viral membrane.
 
The evolution of this group of viruses appears to be complex with genes having been gained from multiple sources.<ref name=Yutin2012/> It has been proposed that the ancestor of NCLDVs has evolved from large, virus-like DNA transposons of the Polinton/Maverick family.<ref>{{cite journal | vauthors = Krupovic M, Koonin EV | title = Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution | journal = Nature Reviews. Microbiology | volume = 13 | issue = 2 | pages = 105–115 | date = February 2015 | pmid = 25534808 | pmc = 5898198 | doi = 10.1038/nrmicro3389 }}</ref> From Polinton/Maverick transposons NCLDVs might have inherited the key components required for virion morphogenesis, including the major and minor capsid proteins, maturation protease and genome packaging ATPase.<ref>{{cite journal | vauthors = Krupovic M, Bamford DH, Koonin EV | title = Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses | journal = Biology Direct | volume = 9 | pages = 6 | date = April 2014 | pmid = 24773695 | pmc = 4028283 | doi = 10.1186/1745-6150-9-6 }}</ref>
 
Another group of large viruses—the [[Pandoraviridae]]—has been described. Two species—[[Pandoravirus salinus]] and [[Pandoravirus dulcis]]—have been recognized. These were isolated from [[Chile]] and [[Australia]] respectively. These viruses are about one [[micrometre|micrometer]] in diameter making them one of the largest viruses discovered so far. Their gene complement is larger than any other known virus to date. At present they appear to be unrelated to any other species of virus.<ref>{{cite journal | vauthors = Pennisi E | title = Microbiology. Ever-bigger viruses shake tree of life | journal = Science | volume = 341 | issue = 6143 | pages = 226–227 | date = July 2013 | pmid = 23868995 | doi = 10.1126/science.341.6143.226 }}</ref>
 
An even larger genus, [[Pithovirus]], has since been discovered, measuring about 1.5&nbsp;µm in length.<ref>{{cite journal | vauthors = Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C, Claverie JM | title = Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 11 | pages = 4274–4279 | date = March 2014 | pmid = 24591590 | pmc = 3964051 | doi = 10.1073/pnas.1320670111 | bibcode = 2014PNAS..111.4274L }}</ref> Another virus—Cedratvirus—may be related this group.<ref name=Andreani2016>{{cite journal | vauthors = Andreani J, Aherfi S, Bou Khalil JY, Di Pinto F, Bitam I, Raoult D, Colson P, La Scola B | title = Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses | journal = Viruses | volume = 8 | issue = 11 | pages = 300 | date = November 2016 | pmid = 27827884 | pmc = 5127014 | doi = 10.3390/v8110300 }}</ref>
 
==Pleolipoviruses==
A group known as the pleolipoviruses, although having a similar genome organisation, differ in having either single or double stranded DNA genomes.<ref name=Pietila2012/> Within the double stranded forms have runs of single stranded DNA.<ref>{{cite journal | vauthors = Sencilo A, Paulin L, Kellner S, Helm M, Roine E | title = Related haloarchaeal pleomorphic viruses contain different genome types | journal = Nucleic Acids Research | volume = 40 | issue = 12 | pages = 5523–5534 | date = July 2012 | pmid = 22396526 | pmc = 3384331 | doi = 10.1093/nar/gks215 }}</ref> These viruses have been placed in the family ''[[Pleolipoviridae]]''.<ref name="Pietilä2016">{{cite journal | vauthors = Pietilä MK, Roine E, Sencilo A, Bamford DH, Oksanen HM | title = Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes | journal = Archives of Virology | volume = 161 | issue = 1 | pages = 249–256 | date = January 2016 | pmid = 26459284 | doi = 10.1007/s00705-015-2613-x | doi-access = free }}</ref> This family has been divided in three genera: [[Alphapleolipovirus]], [[Betapleolipovirus]] and [[Gammapleolipovirus]].
 
These viruses are nonlytic and form virions characterized by a lipid vesicle enclosing the genome.<ref name="Pietila2012">{{cite journal | vauthors = Pietilä MK, Atanasova NS, Manole V, Liljeroos L, Butcher SJ, Oksanen HM, Bamford DH | title = Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea | journal = Journal of Virology | volume = 86 | issue = 9 | pages = 5067–5079 | date = May 2012 | pmid = 22357279 | pmc = 3347350 | doi = 10.1128/JVI.06915-11 }}</ref> They do not have nucleoproteins. The lipids in the viral membrane are unselectively acquired from host cell membranes. The virions contain two to three major [[structural proteins]], which either are embedded in the membrane or form spikes distributed randomly on the external membrane surface.
 
This group includes the following viruses:<ref name="ICTV_2017">International Committee on Taxonomy of Viruses, [https://talk.ictvonline.org/taxonomy/ ''Virus Taxonomy: 2017 Release''], [https://talk.ictvonline.org/files/master-species-lists/m/msl/7185/download Excel(xlsx)-Datei] ''ICTV 2017 Master Species #32''</ref>
*Genus: Alphapleolipovirus
**[[Haloarcula hispanica pleomorphic virus 1]] (Haloarcula virus HHPV1)
**[[Haloarcula hispanica pleomorphic virus 2]] (Haloarcula virus HHPV2)
**[[Halorubrum pleomorphic virus 1]]
**[[Halorubrum pleomorphic virus 2]]
**[[Halorubrum pleomorphic virus 6]]
*Genus: Betapleolipovirus
**[[Halogeometricum pleomorphic virus 1]] (Halogeometricum virus HGPV1)
**[[Halorubrum pleomorphic virus 3]] (Halorubrum virus HRPV3)
**[[SNJ2]] <ref>Ying Liu et al.: [https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.13204 Identification and characterization of SNJ2, the first temperate pleolipovirus integrating into the genome of the SNJ1‐lysogenic archaeal strain], in: Molecular Microbiology, 30 August 2015,
[[doi:10.1111/mmi.13204]]</ref>
 
*Genus: Gammapleolipovirus
**[[Haloarcula virus His2]]
 
==Group II: ssDNA viruses==
[[File:Genome map of the bacteriophage ΦX174 showing overlapping genes.svg|thumb|300px|Genome of bacteriophage ΦX174, a single-stranded DNA virus]]
 
Although [[bacteriophage]]s were first described in 1927, it was only in 1959 that Sinshemer working with phage [[Phi X 174]] showed that they could possess single-stranded DNA genomes.<ref name=Sinshemer1959a/><ref name=Sinshemer1959b/> Despite this discovery, until relatively recently it was believed that most DNA viruses contained [[double-stranded DNA]]. Recent work, however, has shown that single-stranded DNA viruses can be highly abundant in [[seawater]], [[freshwater]], [[sediment]]s, terrestrial and extreme environments, as well as [[metazoa]]n-associated and marine [[microbial mat]]s.<ref name="Labonte 2013">{{cite journal | vauthors = Labonté JM, Suttle CA | title = Previously unknown and highly divergent ssDNA viruses populate the oceans | journal = The ISME Journal | volume = 7 | issue = 11 | pages = 2169–2177 | date = November 2013 | pmid = 23842650 | pmc = 3806263 | doi = 10.1038/ismej.2013.110 }}</ref><ref name=Desnues2008/><ref name=Angly/> Many of these "environmental" viruses belong to the family ''[[Microviridae]]''.<ref>{{cite journal | vauthors = Roux S, Krupovic M, Poulet A, Debroas D, Enault F | title = Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads | journal = PLOS ONE | volume = 7 | issue = 7 | pages = e40418 | year = 2012 | pmid = 22808158 | pmc = 3394797 | doi = 10.1371/journal.pone.0040418 | bibcode = 2012PLoSO...740418R }}</ref> However, the vast majority has yet to be classified and assigned to genera and higher taxa. Because most of these viruses do not appear to be related, or are only distantly related to known viruses, additional taxa will have to be created to accommodate them.
 
;Archaea
 
Although ~50 archaeal viruses are known, all but two have double stranded genomes. These two viruses have been placed in the families ''[[Pleolipoviridae]]'' and ''[[Spiraviridae]]''
 
===Taxonomy===
 
The taxonomy of DNA viruses was significantly revised in 2020. All the single stranded DNA viruses have been placed in a single realm - Monodnaviria. Within this realm four kingdoms (Loebvirae, Sangervirae, Shotokuvirae and Trapavirae) are recognised.
 
 
 
* Family ''[[Anelloviridae]]''
* Family ''[[Bacilladnavirus|Bacilladnaviridae]]''
* Family ''[[Bidnaviridae]]''
* Family ''[[Circoviridae]]''
* Family ''[[Geminiviridae]]''
* Family ''[[Genomoviridae]]''
* Family ''[[Inoviridae]]''
* Family ''[[Microviridae]]''
* Family ''[[Nanoviridae]]''
* Family ''[[Parvoviridae]]''
* Family ''[[Smacoviridae]]''
* Family ''[[Spiraviridae]]''
 
===Classification===
A division of the circular single stranded viruses into four types has been proposed.<ref name=Rosario2009/> This division seems likely to reflect their phylogenetic relationships.
 
Type I genomes are characterized by a small circular DNA genome (approximately 2-kb), with the Rep protein and the major open reading frame (ORF) in opposite orientations. This type is characteristic of the circoviruses, geminiviruses and nanoviruses.
 
Type II genomes have the unique feature of two separate Rep ORFs.
 
Type III genomes contain two major ORFs in the same orientation. This arrangement is typical of the anelloviruses.
 
Type IV genomes have the largest genomes of nearly 4-kb, with up to eight ORFs. This type of genome is found in the Inoviridae and the Microviridae.
 
Given the variety of single stranded viruses that have been described this scheme—if it is accepted by the ICTV—will need to be extended.
 
====CRESS DNA viruses====
 
All known eukaryotic ssDNA viruses have icosahedral capsids. With the exception of the family ''Bidnaviridae'' and ''Anelloviridae'', all eukaryotic ssDNA viruses encode homologous rolling-circle replication initiation proteins with characteristic N-terminal endonuclease domains and C-terminal superfamily three helicase domains.<ref name=Krupovic2013>Krupovic M (2013) "Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses". ''Current Opinion in Virology'' 3: 578–586</ref> A name for this group of viruses has been proposed—circular Rep-encoding single-strand (CRESS) DNA viruses.<ref>{{cite journal|authorlink3=Mya Breitbart | vauthors = Rosario K, Duffy S, Breitbart M | s2cid = 15651172 | title = A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics | journal = Archives of Virology | volume = 157 | issue = 10 | pages = 1851–1871 | date = October 2012 | pmid = 22760663 | doi = 10.1007/s00705-012-1391-y }}</ref> It has been proposed that CRESS-DNA viruses have evolved from bacterial plasmids, from which they inherited the Rep genes.<ref>{{cite journal |last1=Kazlauskas |first1=Darius |last2=Varsani |first2=Arvind |last3=Koonin |first3=Eugene V. |last4=Krupovic |first4=Mart |title=Multiple origins of prokaryotic and eukaryotic single-stranded DNA viruses from bacterial&nbsp;and archaeal plasmids |journal=Nature Communications |date=2019 |volume=10 |issue=1 |page=3425 |doi=10.1038/s41467-019-11433-0 |pmid=31366885 |pmc=6668415 }}</ref>
 
====Cruciviridae====
 
A group of ssDNA viruses whose Rep proteins show homology to ssDNA viruses from the families Geminiviridae, Circoviridae, and Nanoviridae, while their coat protein is related to those of ssRNA viruses from the family Tombusviridae and unclassified oomycete-infecting viruses.<ref name=Diemer2012/> The name Cruciviridae has been proposed for this group.<ref name=Quaiser2016>{{cite journal | vauthors = Quaiser A, Krupovic M, Dufresne A, Francez AJ, Roux S | title = Sphagnum-dominated peatlands | journal = Virus Evolution | volume = 2 | issue = 2 | pages = vew025 | date = July 2016 | pmid = 29492276 | pmc = 5822885 | doi = 10.1093/ve/vew025 | doi-access = free }}</ref>
 
===Host range===
The families ''Bidnaviridae'' and ''Parvoviridae'' have linear genomes while the other families have circular genomes. The ''Bidnaviridae'' have a two part genome and infect invertebrates. The ''Inoviridae'' and ''Microviridae'' infect [[bacteria]]; the ''Anelloviridae'' and ''Circoviridae'' infect [[animal]]s ([[mammal]]s and [[bird]]s respectively); and the ''Geminiviridae'' and ''Nanoviridae'' infect [[plant]]s. In both the ''Geminiviridae'' and ''Nanoviridae'' the genome is composed of more than a single chromosome. The ''Bacillariodnaviridae'' infect [[diatom]]s and have a unique genome: the major chromosome is circular (~6 kilobases in length): the minor chromosome is linear (~1 kilobase in length) and complementary to part of the major chromosome. Members of the ''Spiraviridae'' infect archaea. Members of the ''Genomoviridae'' infect fungi.
 
===Molecular biology===
All viruses in this group require formation of a replicative form—a double stranded DNA intermediate—for genome replication. This is normally created from the viral DNA with the assistance of the host's own [[DNA polymerase]].
 
===Recently classified viruses===
 
In the 9th edition of the viral taxonomy of the ICTV (published 2011) the Bombyx mori densovirus type 2 was placed in a new family—the ''[[Bidnaviridae]]'' on the basis of its genome structure and replication mechanism. This is currently the only member of this family but it seems likely that other species will be allocated to this family in the near future.
 
A new genus—[[Bufavirus]]—was proposed on the basis of the isolation of two new viruses from human stool.<ref name=Phan2012/> Another member of this genus—megabat bufavius 1—has been reported from bats.<ref name=Sasaki2016>{{cite journal | vauthors = Sasaki M, Gonzalez G, Wada Y, Setiyono A, Handharyani E, Rahmadani I, Taha S, Adiani S, Latief M, Kholilullah ZA, Subangkit M, Kobayashi S, Nakamura I, Kimura T, Orba Y, Ito K, Sawa H | title = Divergent bufavirus harboured in megabats represents a new lineage of parvoviruses | journal = Scientific Reports | volume = 6 | pages = 24257 | date = April 2016 | pmid = 27113297 | pmc = 4845017 | doi = 10.1038/srep24257 | bibcode = 2016NatSR...624257S }}</ref> The human viruses have since been renamed [[Primate protoparvovirus]] and been placed in the genus [[Protoparvovirus]].<ref name=ICTV>{{cite web|title=ICTV Official Taxonomy: Updates since the 8th Report|url=http://talk.ictvonline.org/files/ictv_official_taxonomy_updates_since_the_8th_report/m/vertebrate-official/4844.aspx|website=ICTV Official Taxonomy|publisher=ICTV |access-date=11 June 2014}}</ref><ref>{{cite journal | vauthors = Cotmore SF, Agbandje-McKenna M, Chiorini JA, Mukha DV, Pintel DJ, Qiu J, Soderlund-Venermo M, Tattersall P, Tijssen P, Gatherer D, Davison AJ | title = The family Parvoviridae | journal = Archives of Virology | volume = 159 | issue = 5 | pages = 1239–1247 | date = May 2014 | pmid = 24212889 | pmc = 4013247 | doi = 10.1007/s00705-013-1914-1 }}</ref>
 
Another proposed genus is [[Pecovirus]]. These are similar in organisation to the Smacovirus but share little sequence similarity.
 
;''[[Genomoviridae]]''
 
The most recently introduced family of ssDNA viruses is the ''Genomoviridae'' (the family name is an acronym derived from ''ge''minivirus-like, ''no mo''vement protein).<ref name=Genomo>{{cite journal | vauthors = Krupovic M, Ghabrial SA, Jiang D, Varsani A | title = Genomoviridae: a new family of widespread single-stranded DNA viruses | journal = Archives of Virology | volume = 161 | issue = 9 | pages = 2633–2643 | date = September 2016 | pmid = 27343045 | doi = 10.1007/s00705-016-2943-3 | doi-access = free }}</ref>
 
The family includes 9 genera, namely ''[[Gemycircularvirus]]'', ''[[Gemyduguivirus]]'', ''[[Gemygorvirus]]'', ''[[Gemykibivirus]]'', ''[[Gemykolovirus]]'', ''[[Gemykrogvirus]]'', ''[[Gemykroznavirus]]'', ''[[Gemytondvirus]]'' and ''[[Gemyvongvirus]]''.<ref name=Genomo2>{{cite journal | vauthors = Varsani A, Krupovic M | title = Genomoviridae | journal = Virus Evolution | volume = 3 | issue = 1 | pages = vew037 | date = January 2017 | pmid = 28458911 | pmc = 5399927 | doi = 10.1093/ve/vew037 }}</ref>
 
The genus name ''Gemycircularvirus'' stands for Gemini-like myco-infecting circular virus.<ref>{{cite journal | vauthors = Rosario K, Dayaram A, Marinov M, Ware J, Kraberger S, Stainton D, Breitbart M, Varsani A | s2cid = 10814923 | title = Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta) | journal = The Journal of General Virology | volume = 93 | issue = Pt 12 | pages = 2668–2681 | date = December 2012 | pmid = 22915694 | doi = 10.1099/vir.0.045948-0 | doi-access = free }}</ref><ref name=Yu2010/> the type species of the genus ''Gemycircularvirus''—[[Sclerotinia sclerotiorum hypovirulence associated DNA virus 1]]—is currently the only cultivated member of the family.<ref name=Genomo/> The rest of genomoviruses are uncultivated and have been discovered using metagenomics techniques.<ref name=Genomo2/>
 
Another genus has been proposed—''[[Gemybolavirus]]''.<ref name=Nakasu2017>{{cite journal | vauthors = Nakasu EY, Melo FL, Michereff-Filho M, Nagata T, Ribeiro BM, Ribeiro SG, Lacorte C, Inoue-Nagata AK | s2cid = 8448827 | title = Discovery of two small circular ssDNA viruses associated with the whitefly Bemisia tabaci | journal = Archives of Virology | volume = 162 | issue = 9 | pages = 2835–2838 | date = September 2017 | pmid = 28567489 | doi = 10.1007/s00705-017-3425-y }}</ref>
 
;Human isolates
 
Isolates from this group have also been isolated from the cerebrospinal fluid and brains of patients with [[multiple sclerosis]].<ref name=Lamberto2014>{{cite journal | vauthors = Lamberto I, Gunst K, Müller H, Zur Hausen H, de Villiers EM | title = Mycovirus-like DNA virus sequences from cattle serum and human brain and serum samples from multiple sclerosis patients | journal = Genome Announcements | volume = 2 | issue = 4 | pages = e00848–14 | date = August 2014 | pmid = 25169858 | pmc = 4148726 | doi = 10.1128/genomeA.00848-14 }}</ref>
 
An isolate from this group has also been identified in a child with encephalitis.<ref name=Zhou2015>{{cite journal | vauthors = Zhou C, Zhang S, Gong Q, Hao A | title = A novel gemycircularvirus in an unexplained case of child encephalitis | journal = Virology Journal | volume = 12 | pages = 197 | date = November 2015 | pmid = 26596706 | pmc = 4657213 | doi = 10.1186/s12985-015-0431-0 }}</ref>
 
Viruses from this group have also been isolated from the blood of HIV+ve patients.<ref name=Uch2015>{{cite journal | vauthors = Uch R, Fournier PE, Robert C, Blanc-Tailleur C, Galicher V, Barre R, Jordier F, de Micco P, Raoult D, Biagini P | title = Divergent Gemycircularvirus in HIV-Positive Blood, France | journal = Emerging Infectious Diseases | volume = 21 | issue = 11 | pages = 2096–2098 | date = November 2015 | pmid = 26488181 | pmc = 4622245 | doi = 10.3201/eid2111.150486 }}</ref>
 
;Animal isolates
 
[[Ostrich faecal associated ssDNA virus]] has been placed in the genus [[Gemytondvirus]]. [[Rabbit faecal associated ssDNA virus]] has been placed in the genus [[Gemykroznavirus]].
 
Another virus from this group has been isolated from mosquitoes.<ref name=Li2015>{{cite journal | vauthors = Li W, Gu Y, Shen Q, Yang S, Wang X, Wan Y, Zhang W | s2cid = 5614832 | title = A novel gemycircularvirus from experimental rats | journal = Virus Genes | volume = 51 | issue = 2 | pages = 302–305 | date = October 2015 | pmid = 26303898 | doi = 10.1007/s11262-015-1238-1 }}</ref>
 
Ten new circular viruses have been isolated from [[dragonfly]] larvae.<ref name=Dayaram2014>{{cite journal | vauthors = Dayaram A, Galatowitsch M, Harding JS, Argüello-Astorga GR, Varsani A | title = Novel circular DNA viruses identified in Procordulia grayi and Xanthocnemis zealandica larvae using metagenomic approaches | journal = Infection, Genetics and Evolution | volume = 22 | pages = 134–141 | date = March 2014 | pmid = 24462907 | doi = 10.1016/j.meegid.2014.01.013 }}</ref> The genomes range from 1628 to 2668 nucleotides in length. These dragonfly viruses have since been placed in the Gemycircularviridae.
 
Additional viruses from this group have been reported from dragonflies and damselflies.<ref name=Dayaram2015>{{cite journal | vauthors = Dayaram A, Potter KA, Pailes R, Marinov M, Rosenstein DD, Varsani A | title = Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA | journal = Infection, Genetics and Evolution | volume = 30 | issue = | pages = 278–287 | date = March 2015 | pmid = 25577985 | doi = 10.1016/j.meegid.2014.12.037 }}</ref>
 
;Plants and fungi
 
Three viruses in this group have been isolated from plants.<ref name=Male2015>{{cite journal | vauthors = Male MF, Kami V, Kraberger S, Varsani A | title = Genome Sequences of Poaceae-Associated Gemycircularviruses from the Pacific Ocean Island of Tonga | journal = Genome Announcements | volume = 3 | issue = 5 | pages = e01144–15 | date = October 2015 | pmid = 26472826 | pmc = 4611678 | doi = 10.1128/genomeA.01144-15 }}</ref>
 
A virus—[[Cassava associated circular DNA virus]]—that has some similarity to Sclerotinia sclerotiorum hypovirulence associated DNA virus 1 has been isolated.<ref name=Dayaram2012/> This virus has been placed in the Gemycircularviridae.
 
Some of this group of viruses may infect fungi.<ref name=Sikorski2013_VirusRes/>
 
===''[[Smacoviridae]]''===
 
A new family, the ''[[Smacoviridae]]'', has been created for a number of single-stranded DNA viruses isolated from the faeces of various mammals.<ref name=Varsani2018>{{cite journal | vauthors = Varsani A, Krupovic M | s2cid = 4227007 | title = Smacoviridae: a new family of animal-associated single-stranded DNA viruses | journal = Archives of Virology | volume = 163 | issue = 7 | pages = 2005–2015 | date = July 2018 | pmid = 29572596 | doi = 10.1007/s00705-018-3820-z }}</ref> Smacoviruses have circular genomes of ~2.5 kilobases and have a Rep protein and capsid protein encoded in opposite orientations. 43 species have been included in this family which includes six genera—''[[Bovismacovirus]]'', ''[[Cosmacovirus]]'', ''[[Dragsmacovirus]]'', ''[[Drosmacovirus]]'', ''[[Huchismacovirus]]'' and ''[[Porprismacovirus]]''.
 
===Unassigned species===
 
A number of additional single stranded DNA viruses have been described but are as yet unclassified.
 
====Human isolates====
Viruses in this group have been isolated from other cases of encephalitis, diarrhoea and sewage.<ref name=Phan2015>{{cite journal | vauthors = Phan TG, Mori D, Deng X, Rajindrajith S, Ranawaka U, Fan Ng TF, Bucardo-Rivera F, Orlandi P, Ahmed K, Delwart E | title = Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage | journal = Virology | volume = 482 | pages = 98–104 | date = August 2015 | pmid = 25839169 | pmc = 4461510 | doi = 10.1016/j.virol.2015.03.011 }}</ref>
 
Two viruses have been isolated from human faeces—circo-like virus Brazil hs1 and hs2—with genome lengths of 2526 and 2533 nucleotides respectively.<ref name=Castrignano2013>{{cite journal | vauthors = Castrignano SB, Nagasse-Sugahara TK, Kisielius JJ, Ueda-Ito M, Brandão PE, Curti SP | title = Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis | journal = Virus Research | volume = 178 | issue = 2 | pages = 364–373 | date = December 2013 | pmid = 24055464 | doi = 10.1016/j.virusres.2013.09.018 }}</ref> These viruses have four open reading frames. These viruses appear to be related to three viruses previously isolated from waste water, a bat and from a rodent.<ref>{{cite journal | vauthors = Cheung AK, Ng TF, Lager KM, Alt DP, Delwart EL, Pogranichniy RM | title = Identification of a novel single-stranded circular DNA virus in pig feces | journal = Genome Announcements | volume = 2 | issue = 2 | pages = e00347–14 | date = May 2014 | pmid = 24786952 | pmc = 4007987 | doi = 10.1128/genomeA.00347-14 }}</ref>
This appears to belong to a novel group.
 
A novel species of virus—human respiratory-associated PSCV-5-like virus—has been isolated from the respiratory tract.<ref name=Cui2017>{{cite journal | vauthors = Cui L, Wu B, Zhu X, Guo X, Ge Y, Zhao K, Qi X, Shi Z, Zhu F, Sun L, Zhou M | s2cid = 9239411 | title = Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample | journal = Archives of Virology | volume = 162 | issue = 11 | pages = 3305–3312 | date = November 2017 | pmid = 28707271 | doi = 10.1007/s00705-017-3481-3 }}</ref> The virus is approximately 3 kilobases in length and has two open reading frames—one encoding the coat protein and the other the DNA replicase. The significance—if any—of this virus for human disease is unknown presently.
 
====Animal viruses – vertebrates====
An unrelated group of ssDNA viruses, also discovered using viral metagenomics, includes the species [[bovine stool associated circular virus]] and [[chimpanzee stool associated circular virus]].<ref name=Blinkova2010/> The closest relations to this genus appear to be the ''Nanoviridae'' but further work will be needed to confirm this. Another isolate that appears to be related to these viruses has been isolated from pig faeces in New Zealand.<ref name=Sikorski2012/> This isolate also appears to be related to the [[pig stool-associated single-stranded DNA virus]]. This virus has two large open reading frames one encoding the capsid gene and the other the Rep gene. These are bidirectionally transcribed and separated by intergenic regions. Another virus of this group has been reported again from pigs.<ref name=Kim2013>{{cite journal | vauthors = Kim AR, Chung HC, Kim HK, Kim EO, Nguyen VG, Choi MG, Yang HJ, Kim JA, Park BK | s2cid = 3024397 | title = Characterization of a complete genome of a circular single-stranded DNA virus from porcine stools in Korea | journal = Virus Genes | volume = 48 | issue = 1 | pages = 81–88 | date = February 2014 | pmid = 24170425 | doi = 10.1007/s11262-013-1003-2 }}</ref> A virus from this group has been isolated from turkey faeces.<ref name=Reuter2014>{{cite journal | vauthors = Reuter G, Boros Á, Delwart E, Pankovics P | s2cid = 17899724 | title = Novel circular single-stranded DNA virus from turkey faeces | journal = Archives of Virology | volume = 159 | issue = 8 | pages = 2161–2164 | date = August 2014 | pmid = 24562429 | doi = 10.1007/s00705-014-2025-3 }}</ref> Another ten viruses from this group have been isolated from pig faeces.<ref name=Cheung2014B>{{cite journal | vauthors = Cheung AK, Ng TF, Lager KM, Alt DP, Delwart E, Pogranichniy RM | s2cid = 586115 | title = Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces | journal = Archives of Virology | volume = 160 | issue = 1 | pages = 353–358 | date = January 2015 | pmid = 25248627 | doi = 10.1007/s00705-014-2234-9 }}</ref> Viruses that appear to belong to this group have been isolated from other mammals including cows, rodents, bats, badgers and foxes.<ref name=Sikorski2013_VirusRes/>
 
Another virus in this group has been isolated from birds.<ref name=Hanna2015>{{cite journal | vauthors = Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Van Hemert C, Handel CM, Dumbacher JP | title = Isolation of a Complete Circular Virus Genome Sequence from an Alaskan Black-Capped Chickadee (Poecile atricapillus) Gastrointestinal Tract Sample | journal = Genome Announcements | volume = 3 | issue = 5 | pages = e01081–15 | date = September 2015 | pmid = 26404604 | pmc = 4582580 | doi = 10.1128/genomeA.01081-15 }}</ref>
 
[[Fur seal feces-associated circular DNA virus]] was isolated from the faeces of a fur seal (''[[Arctocephalus forsteri]]'') in [[New Zealand]].<ref name=Sikorski2013_GenomeAnnounc/> The genome has 2 main open reading frames and is 2925 nucleotides in length. Another virus—[[porcine stool associated virus 4]]<ref name="CheungNg2014">{{cite journal | vauthors = Cheung AK, Ng TF, Lager KM, Alt DP, Delwart EL, Pogranichniy RM | title = Unique circovirus-like genome detected in pig feces | journal = Genome Announcements | volume = 2 | issue = 2 | pages = e00251–14 | date = April 2014 | pmid = 24723710 | pmc = 3983299 | doi = 10.1128/genomeA.00251-14 }}</ref>—has been isolated. It appears to be related to the fur seal virus.
Two viruses have been described from the nesting material yellow crowned parakeet (''[[Cyanoramphus auriceps]]'')—[[Cyanoramphus nest-associated circular X virus]] (2308 nt) and [[Cyanoramphus nest-associated circular K virus]] (2087 nt)<ref name=Sikorski2013_ArchVirol/> Both viruses have two bidirectional open reading frames. Within these are the rolling-circle replication motifs I, II, III and the helicase motifs Walker A and Walker B. There is also a conserved nonanucleotide motif required for rolling-circle replication. CynNCKV has some similarity to the [[picobiliphyte nano-like virus]] (Picobiliphyte M5584-5)<ref name=Yoon2011>{{cite journal | vauthors = Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, Yang EC, Duffy S, Bhattacharya D | title = Single-cell genomics reveals organismal interactions in uncultivated marine protists | journal = Science | volume = 332 | issue = 6030 | pages = 714–717 | date = May 2011 | pmid = 21551060 | doi = 10.1126/science.1203163 | bibcode = 2011Sci...332..714Y | s2cid = 34343205 }}</ref> and CynNCXV has some similarity to the [[rodent stool associated virus]] (RodSCV M-45).<ref name=Phan2011>{{cite journal | vauthors = Phan TG, Kapusinszky B, Wang C, Rose RK, Lipton HL, Delwart EL | title = The fecal viral flora of wild rodents | journal = PLOS Pathogens | volume = 7 | issue = 9 | pages = e1002218 | date = September 2011 | pmid = 21909269 | pmc = 3164639 | doi = 10.1371/journal.ppat.1002218 }}</ref>
 
A virus with a [[circular genome]]—[[sea turtle tornovirus 1]]—has been isolated from a sea turtle with [[fibropapillomatosis]].<ref name=Ng2009/> It is sufficiently unrelated to any other known virus that it may belong to a new family. The closest relations seem to be the ''Gyrovirinae''. The proposed genus name for this virus is [[Tornovirus]].
 
Another faecal virus—[[feline stool-associated circular DNA virus]]—has been described.<ref name=Takano2018>Takano T, Yanai Y, Hiramatsu K, Doki T, Hohdatsu T (2018) Novel single-stranded, circular DNA virus identified in cats in Japan. Arch Virol {{doi|10.1007/s00705-018-4020-6}}</ref>
 
====Animal viruses – invertebrates====
Among these are the parvovirus-like viruses. These have linear single-stranded DNA genomes but unlike the parvoviruses the genome is bipartate. This group includes [[Hepatopancreatic parvo-like virus]] and [[Lymphoidal parvo-like virus]]. A new family [[Bidensoviridae]] has been proposed for this group but this proposal has not been ratified by the [[International Committee on Taxonomy of Viruses|ICTV]] to date.<ref name=Tijssen1995/> Their closest relations appear to be the ''[[Brevidensoviruses]]'' (family Parvoviridae).<ref name=Sukhumsirichart2006/>
 
A virus—[[Acheta domesticus volvovirus]]—has been isolated from the house cricket (''[[Acheta domesticus]]'').<ref name=Pham2013>{{cite journal | vauthors = Pham HT, Bergoin M, Tijssen P | title = Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket | journal = Genome Announcements | volume = 1 | issue = 2 | pages = e0007913 | date = March 2013 | pmid = 23516206 | pmc = 3623006 | doi = 10.1128/genomeA.00079-13 }}</ref> The genome is circular, has four open reading frames and is 2,517 nucleotides in length. It appears to be unrelated to previously described species. The genus name [[Volvovirus]] has been proposed for these species.<ref name=Pham2013B>{{cite journal | vauthors = Pham HT, Iwao H, Bergoin M, Tijssen P | title = New Volvovirus Isolates from Acheta domesticus (Japan) and Gryllus assimilis (United States) | journal = Genome Announcements | volume = 1 | issue = 3 | pages = e00328–13 | date = June 2013 | pmid = 23792751 | pmc = 3675518 | doi = 10.1128/genomeA.00328-13 }}</ref> The genomes in this genus are ~2.5 nucleotides in length and encode 4 open reading frames.
 
Two new viruses have been isolated from the [[copepod]]s ''[[Acartia tonsa]]'' and ''[[Labidocera aestiva]]''—[[Acartia tonsa copepod circo-like virus]] and [[Labidocera aestiva copepod circo-like virus]] respectively.
 
A virus has been isolated from the mud flat snail (''[[Amphibola crenata]]'').<ref name=Dayaram2013/> This virus has a single stranded circular genome of 2351 nucleotides that encodes 2 open reading frames that are oriented in opposite directions. The smaller open reading frame (874 nucleotides) encodes a protein with similarities to the ''Rep'' (replication) proteins of circoviruses and [[plasmid]]s. The larger open reading frame (955 nucleotides) has no homology to any currently known protein.<ref name=Dayaram2013/>
 
An unusual—and as yet unnamed—virus has been isolated from the flatworm ''[[Girardia tigrina]]''.<ref name=Rebrikov2002/> Because of its genome organization, this virus appears to belong to an entirely new family. It is the first virus to be isolated from a [[flatworm]].
 
From the [[hepatopancreas]] of the shrimp (''[[Farfantepenaeus duorarum]]'') a circular single stranded DNA virus has been isolated.<ref name=Ng2013>{{cite journal | vauthors = Ng TF, Alavandi S, Varsani A, Burghart S, Breitbart M | title = Metagenomic identification of a nodavirus and a circular ssDNA virus in semi-purified viral nucleic acids from the hepatopancreas of healthy Farfantepenaeus duorarum shrimp | journal = Diseases of Aquatic Organisms | volume = 105 | issue = 3 | pages = 237–242 | date = September 2013 | pmid = 23999707 | doi = 10.3354/dao02628 | url = https://ir.canterbury.ac.nz/bitstream/10092/8461/1/12646318_Ng%202013.pdf }}</ref> This virus does not appear to cause disease in the shrimp.
 
A circo-like virus has been isolated from the shrimp (''[[Penaeus monodon]]'').<ref name=Pham2014>{{cite journal | vauthors = Pham HT, Yu Q, Boisvert M, Van HT, Bergoin M, Tijssen P | title = A Circo-Like Virus Isolated from Penaeus monodon Shrimps | journal = Genome Announcements | volume = 2 | issue = 1 | pages = e01172–13 | date = January 2014 | pmid = 24435870 | pmc = 3894284 | doi = 10.1128/genomeA.01172-13 }}</ref> The 1,777-nucleotide genome is circular and single stranded. It has some similarity to the circoviruses and cycloviruses.
 
Ten viruses have been isolated from [[echinoderm]]s.<ref>{{cite journal | vauthors = Jackson EW, Bistolas KS, Button JB, Hewson I | title = Novel Circular Single-Stranded DNA Viruses among an Asteroid, Echinoid and Holothurian (Phylum: Echinodermata) | journal = PLOS ONE | volume = 11 | issue = 11 | pages = e0166093 | year = 2016 | pmid = 27855181 | pmc = 5113903 | doi = 10.1371/journal.pone.0166093 | bibcode = 2016PLoSO..1166093J }}</ref> All appear to belong to as yet undescribed genera.
 
A filamentous virus—[[Apis mellifera filamentous virus]]—has been described.<ref name=Gauthier2015>Gauthier L, Cornman S, Hartmann U, Cousserans F, Evans JD, de Miranda JR, Neumann P (2015) "The Apis mellifera filamentous virus genome". ''Viruses'' 7(7):3798–3815</ref> It appears to be unrelated to other DNA viruses.
 
====Plants====
A circular single stranded DNA virus has been isolated from a grapevine.<ref name=Krenz2012/> This species may be related to the family Geminiviridae but differs from this family in a number of important respects including genome size.
 
Several viruses—baminivirus, nepavirus and niminivirus—related to geminvirus have also been reported.<ref name=Sikorski2013_VirusRes />
 
A virus—[[Ancient caribou feces associated virus]]—has been cloned from 700-y-old caribou faeces.<ref name=Ng2014>{{cite journal | vauthors = Ng TF, Chen LF, Zhou Y, Shapiro B, Stiller M, Heintzman PD, Varsani A, Kondov NO, Wong W, Deng X, Andrews TD, Moorman BJ, Meulendyk T, MacKay G, Gilbertson RL, Delwart E | title = Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 47 | pages = 16842–16847 | date = November 2014 | pmid = 25349412 | pmc = 4250163 | doi = 10.1073/pnas.1410429111 | bibcode = 2014PNAS..11116842N }}</ref>
 
A new virus with a three part single stranded genome has been reported.<ref name=Gronenborn2018>{{cite journal | vauthors = Gronenborn B, Randles JW, Knierim D, Barrière Q, Vetten HJ, Warthmann N, Cornu D, Sileye T, Winter S, Timchenko T | title = Analysis of DNAs associated with coconut foliar decay disease implicates a unique single-stranded DNA virus representing a new taxon | journal = Scientific Reports | volume = 8 | issue = 1 | pages = 5698 | date = April 2018 | pmid = 29632309 | pmc = 5890292 | doi = 10.1038/s41598-018-23739-y | bibcode = 2018NatSR...8.5698G }}</ref> This seems likely to be a member of a new family of viruses.
 
====Marine and other====
More than 600 single-stranded DNA viral genomes were identified in ssDNA purified from seawater.<ref name="Labonte 2013"/> These fell into 129 genetically distinct groups that had no recognizable similarity to each other or to other virus sequences, and thus many likely represent new families of viruses. Of the 129 groups, eleven were much more abundant than the others, and although their hosts have yet to be identified, they are likely to be eukaryotic phytoplankton, zooplankton and bacteria.{{citation needed|date=June 2018}}
 
A virus—[[Boiling Springs Lake virus]]—appears to have evolved by a recombination event between a DNA virus (circovirus) and an [[RNA virus]] (tombusvirus).<ref name=Diemer2012>{{cite journal | vauthors = Diemer GS, Stedman KM | title = A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses | journal = Biology Direct | volume = 7 | pages = 13 | date = June 2012 | pmid = 22515485 | pmc = 3372434 | doi = 10.1186/1745-6150-7-13 }}</ref> The genome is circular and encodes two proteins—a Rep protein and a capsid protein.
 
Further reports of viruses that appear to have evolved from recombination events between ssRNA and ssDNA viruses have been made.<ref name=Roux2013>{{cite journal | vauthors = Roux S, Enault F, Bronner G, Vaulot D, Forterre P, Krupovic M | title = Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses | journal = Nature Communications | volume = 4 | pages = 2700 | year = 2013 | pmid = 24193254 | doi = 10.1038/ncomms3700 | bibcode = 2013NatCo...4.2700R | doi-access = free }}</ref>
 
A new virus has been isolated from the diatom ''[[Chaetoceros setoensis]]''.<ref name=Tomaru2013>{{cite journal | vauthors = Tomaru Y, Toyoda K, Suzuki H, Nagumo T, Kimura K, Takao Y | title = New single-stranded DNA virus with a unique genomic structure that infects marine diatom Chaetoceros setoensis | journal = Scientific Reports | volume = 3 | pages = 3337 | date = November 2013 | pmid = 24275766 | pmc = 3840382 | doi = 10.1038/srep03337 | bibcode = 2013NatSR...3E3337T }}</ref> It has a single stranded DNA genome and does not appear to be a member of any previously described group.
 
A virus—FLIP (Flavobacterium-infecting, lipid-containing phage)—has been isolated from a lake.<ref name=Laanto2017>{{cite journal | vauthors = Laanto E, Mäntynen S, De Colibus L, Marjakangas J, Gillum A, Stuart DI, Ravantti JJ, Huiskonen JT, Sundberg LR | title = Virus found in a boreal lake links ssDNA and dsDNA viruses | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 114 | issue = 31 | pages = 8378–8383 | date = August 2017 | pmid = 28716906 | pmc = 5547622 | doi = 10.1073/pnas.1703834114 }}</ref> This virus has a circular ssDNA genome (9,174 nucleotides) and an internal lipid membrane enclosed in an icosahedral capsid. The capsid organisation is he capsid organization pseudo T = 21 ''dextro''. The major capsid protein has two β-barrels. The capsid organisation is similar to bacteriophage PM2—a double stranded bacterial virus.{{citation needed|date=June 2018}}
 
==Satellite viruses==
[[Satellite virus]]es are small viruses with either RNA or DNA as their genomic material that require another virus to replicate. There are two types of DNA satellite viruses—the [[alphasatellite]]s and the [[betasatellite]]s—both of which are dependent on [[begomovirus]]es. At present satellite viruses are not classified into genera or higher taxa.
 
Alphasatellites are small circular single strand DNA viruses that require a begomovirus for transmission. Betasatellites are small linear single stranded DNA viruses that require a begomovirus to replicate.
 
==Phylogenetic relationships==
===Introduction===
 
Phylogenetic relationships between these families are difficult to determine. The genomes differ significantly in size and organisation. Most studies that have attempted to determine these relationships are based either on some of the more conserved proteins—DNA polymerase and others—or on common structural features. In general most of the proposed relationships are tentative and have not yet been used by the ICTV in their classification.
 
===ds DNA viruses===
====Herpesviruses and caudoviruses====
While determining the phylogenetic relations between the various known clades of viruses is difficult, on a number of grounds the herpesviruses and caudoviruses appear to be related.
 
While the three families in the order Herpesvirales are clearly related on morphological grounds, it has proven difficult to determine the dates of divergence between them because of the lack of gene conservation.<ref name=McGeoch2006/> On morphological grounds they appear to be related to the bacteriophages—specifically the Caudoviruses.
 
The branching order among the herpesviruses suggests that ''Alloherpesviridae'' is the basal clade and that ''Herpesviridae'' and ''Malacoherpesviridae'' are sister clades.<ref name="Davison2010">{{cite journal | vauthors = Davison AJ | title = Herpesvirus systematics | journal = Veterinary Microbiology | volume = 143 | issue = 1 | pages = 52–69 | date = June 2010 | pmid = 20346601 | pmc = 2995426 | doi = 10.1016/j.vetmic.2010.02.014 }}</ref> Given the phylogenetic distances between vertebrates and molluscs this suggests that herpesviruses were initially fish viruses and that they have evolved with their hosts to infect other vertebrates.
 
The vertebrate herpesviruses initially evolved ~{{Ma|400}} and underwent subsequent evolution on the supercontinent [[Pangaea]].<ref name=Grose2012/> The alphaherpesvirinae separated from the branch leading to the betaherpesvirinae and gammaherpesvirinae about {{Ma|180}} to {{Ma|220}}.<ref name=McGeoch1995/> The avian herpes viruses diverged from the branch leading to the mammalian species.<ref name=McGeoch1994/> The mammalian species divided into two branches—the Simplexvirus and Varicellovirus genera. This latter divergence appears to have occurred around the time of the mammalian radiation.
 
Several dsDNA bacteriophages and the herpesviruses encode a powerful ATP driven DNA translocating machine that encapsidates a viral genome into a preformed capsid shell or prohead. The critical components of the packaging machine are the packaging enzyme (terminase) which acts as the motor and the portal protein that forms the unique DNA entrance vertex of prohead. The terminase complex consists of a recognition subunit (small terminase) and an endonuclease/translocase subunit (large terminase) and cuts viral genome concatemers. It forms a motor complex containing five large terminase subunits. The terminase-viral DNA complex docks on the portal vertex. The pentameric motor processively translocates DNA until the head shell is full with one viral genome. The motor cuts the DNA again and dissociates from the full head, allowing head-finishing proteins to assemble on the portal, sealing the portal, and constructing a platform for tail attachment. Only a single gene encoding the putative ATPase subunit of the [[terminase]] (''UL15'') is conserved among all herpesviruses. To a lesser extent this gene is also found in [[T4-like]] [[bacteriophages]] suggesting a common ancestor for these two groups of viruses.<ref name=Davison2002/> Another paper has also suggested that herpesviruses originated among the bacteriophages.<ref name="Koonin2015">{{cite journal | vauthors = Koonin EV, Krupovic M, Yutin N | title = Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses | journal = Annals of the New York Academy of Sciences | volume = 1341 | issue = 1 | pages = 10–24 | date = April 2015 | pmid = 25727355 | pmc = 4405056 | doi = 10.1111/nyas.12728 | bibcode = 2015NYASA1341...10K }}</ref>
 
A common origin for the herpesviruses and the caudoviruses has been suggested on the basis of parallels in their capsid assembly pathways and similarities between their portal complexes, through which DNA enters the capsid.<ref name=Baker2005/> These two groups of viruses share a distinctive 12-fold arrangement of subunits in the portal complex. A second paper has suggested an evolutionary relationship between these two groups of viruses.<ref name="Koonin2015"/>
 
It seems likely that the tailed viruses infecting the archaea are also related to the tailed viruses infecting bacteria.<ref name=Krupovic2010>{{cite journal | vauthors = Krupovic M, Forterre P, Bamford DH | title = Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria | journal = Journal of Molecular Biology | volume = 397 | issue = 1 | pages = 144–160 | date = March 2010 | pmid = 20109464 | doi = 10.1016/j.jmb.2010.01.037 }}</ref><ref name="Senčilo2013">{{cite journal | vauthors = Senčilo A, Jacobs-Sera D, Russell DA, Ko CC, Bowman CA, Atanasova NS, Österlund E, Oksanen HM, Bamford DH, Hatfull GF, Roine E, Hendrix RW | title = Snapshot of haloarchaeal tailed virus genomes | journal = RNA Biology | volume = 10 | issue = 5 | pages = 803–816 | date = May 2013 | pmid = 23470522 | pmc = 3737338 | doi = 10.4161/rna.24045 }}</ref>
 
A study involving 600 herpes genomes and 2000 caudoviral genomes suggested that an evolutionary relationship exists between these order.<ref name=Andrade-Martínez2019>Andrade-Martínez JS, Moreno-Gallego JL, Reyes A (2019) "Defining a core genome for the Herpesvirales and exploring their evolutionary relationship with the Caudovirales". ''Sci Rep'' 9(1):11342</ref>
 
====Large DNA viruses====
The NCLDV group (''Asfarviridae'', ''Iridoviridae'', ''Marseilleviridae'', ''Mimiviridae'', ''Phycodnaviridae'' and ''Poxviridae'') along with three other families (''Adenoviridae'', ''Cortiviridae'' and ''Tectiviridae'') and the phage Sulfolobus turreted icosahedral virus and the satellite virus Sputnik all possess double β-barrel major capsid proteins suggesting a common origin.<ref>{{cite journal | vauthors = Krupovic M, Bamford DH | s2cid = 31542714 | title = Virus evolution: how far does the double beta-barrel viral lineage extend? | journal = Nature Reviews. Microbiology | volume = 6 | issue = 12 | pages = 941–948 | date = December 2008 | pmid = 19008892 | doi = 10.1038/nrmicro2033 }}</ref>
 
Several studies have suggested that the family ''Ascoviridae'' evolved from the ''Iridoviridae''.<ref name=Stasiak2000>{{cite journal | vauthors = Stasiak K, Demattei MV, Federici BA, Bigot Y | title = Phylogenetic position of the Diadromus pulchellus ascovirus DNA polymerase among viruses with large double-stranded DNA genomes | journal = The Journal of General Virology | volume = 81 | issue = Pt 12 | pages = 3059–3072 | date = December 2000 | pmid = 11086137 | doi = 10.1099/0022-1317-81-12-3059 | doi-access = free }}</ref><ref name=Stasiak2003>{{cite journal | vauthors = Stasiak K, Renault S, Demattei MV, Bigot Y, Federici BA | title = Evidence for the evolution of ascoviruses from iridoviruses | journal = The Journal of General Virology | volume = 84 | issue = Pt 11 | pages = 2999–3009 | date = November 2003 | pmid = 14573805 | doi = 10.1099/vir.0.19290-0 | doi-access = free }}</ref><ref name=Federici2009/><ref name=Piégu2015>{{cite journal | vauthors = Piégu B, Asgari S, Bideshi D, Federici BA, Bigot Y | title = Evolutionary relationships of iridoviruses and divergence of ascoviruses from invertebrate iridoviruses in the superfamily Megavirales | journal = Molecular Phylogenetics and Evolution | volume = 84 | pages = 44–52 | date = March 2015 | pmid = 25562178 | doi = 10.1016/j.ympev.2014.12.013 }}</ref> A study of the Iridoviruses suggests that the Iridoviridae, Ascoviridae and Marseilleviridae are related with Ascoviruses most closely related to Iridoviruses.<ref name=Chinchar2017>{{cite journal | vauthors = Chinchar VG, Waltzek TB, Subramaniam K | title = Ranaviruses and other members of the family Iridoviridae: Their place in the virosphere | journal = Virology | volume = 511 | pages = 259–271 | date = November 2017 | pmid = 28648249 | doi = 10.1016/j.virol.2017.06.007 | doi-access = free }}</ref>
 
The family ''Polydnaviridae'' may have evolved from the ''Ascoviridae''.<ref name=Bigot2009>{{cite journal | vauthors = Bigot Y, Renault S, Nicolas J, Moundras C, Demattei MV, Samain S, Bideshi DK, Federici BA | title = Symbiotic virus at the evolutionary intersection of three types of large DNA viruses; iridoviruses, ascoviruses, and ichnoviruses | journal = PLOS ONE | volume = 4 | issue = 7 | pages = e6397 | date = July 2009 | pmid = 19636425 | pmc = 2712680 | doi = 10.1371/journal.pone.0006397 | bibcode = 2009PLoSO...4.6397B }}</ref> Molecular evidence suggests that the ''Phycodnaviridae'' may have evolved from the family ''Iridoviridae''.<ref name=Wilson2009/> These four families (''Ascoviridae'', ''Iridoviridae'', ''Phycodnaviridae'' and ''Polydnaviridae'') may form a clade but more work is needed to confirm this.
 
Some of the relations among the large viruses have been established.<ref name=Yutin2014>{{cite journal | vauthors = Yutin N, Wolf YI, Koonin EV | title = Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life | journal = Virology | volume = 466-467 | pages = 38–52 | date = October 2014 | pmid = 25042053 | pmc = 4325995 | doi = 10.1016/j.virol.2014.06.032 }}</ref> Mimiviruses are distantly related to Phycodnaviridae. Pandoraviruses share a common ancestor with Coccolithoviruses within the family Phycodnaviridae.<ref name="YutinKoonin2013">{{cite journal | vauthors = Yutin N, Koonin EV | title = Pandoraviruses are highly derived phycodnaviruses | journal = Biology Direct | volume = 8 | pages = 25 | date = October 2013 | pmid = 24148757 | pmc = 3924356 | doi = 10.1186/1745-6150-8-25 }}</ref> Pithoviruses are related to Iridoviridae and Marseilleviridae.
 
Based on the genome organisation and DNA replication mechanism it seems that phylogenetic relationships may exist between the rudiviruses (''Rudiviridae'') and the large eukaryal DNA viruses: the African swine fever virus (''Asfarviridae''), Chlorella viruses (''Phycodnaviridae'') and poxviruses (''Poxviridae'').<ref name=Prangishvili2004/>
 
Based on the analysis of the DNA polymerase the genus ''Dinodnavirus'' may be a member of the family ''Asfarviridae''.<ref name=Ogata2009/> Further work on this virus will required before a final assignment can be made.
 
It has been suggested that at least some of the giant viruses may originate from mitochondria.<ref name=Seligmann2018>{{cite journal | vauthors = Seligmann H | title = Giant viruses as protein-coated amoeban mitochondria? | journal = Virus Research | volume = 253 | pages = 77–86 | date = June 2018 | pmid = 29913250 | doi = 10.1016/j.virusres.2018.06.004 }}</ref>
 
====Other viruses====
Based on the analysis of the coat protein, ''Sulfolobus turreted icosahedral virus'' may share a common ancestry with the ''Tectiviridae''.
 
The families ''Adenoviridae'' and ''Tectiviridae'' appear to be related structurally.<ref name=Benson1999/>
 
Baculoviruses evolved from the nudiviruses {{ma|310}}.<ref name=Theze2011/><ref name=Wang2009>{{cite journal | vauthors = Wang Y, Jehle JA | title = Nudiviruses and other large, double-stranded circular DNA viruses of invertebrates: new insights on an old topic | journal = Journal of Invertebrate Pathology | volume = 101 | issue = 3 | pages = 187–193 | date = July 2009 | pmid = 19460388 | doi = 10.1016/j.jip.2009.03.013 }}</ref>
 
The ''Hytrosaviridae'' are related to the baculoviruses and to a lesser extent the nudiviruses suggesting they may have evolved from the baculoviruses.<ref name=Jehle2012/>
 
The ''Nimaviridae'' may be related to nudiviruses and baculoviruses.<ref name=Wang2011/>
 
The Nudiviruses seem to be related to the polydnaviruses.<ref name=Bezier2009/>
 
A protein common to the families ''Bicaudaviridae'', ''Lipotrixviridae'' and ''Rudiviridae'' and the unclassified virus Sulfolobus turreted icosahedral virus is known suggesting a common origin.<ref name=Keller2007/>
 
Examination of the ''pol'' genes that encode the DNA dependent [[DNA polymerase]] in various groups of viruses suggests a number of possible evolutionary relationships.<ref name=Knopf1998/> All know viral DNA polymerases belong to the DNA ''pol'' families A and B. All possess a 3'–5'-[[exonuclease]] domain with three sequence motifs Exo I, Exo II and Exo III. The families A and B are distinguishable with family A Pol sharing 9 distinct consensus sequences and only two of them are convincingly homologous to sequence motif B of family B. The putative sequence motifs A, B, and C of the polymerase domain are located near the C-terminus in family A Pol and more central in family B Pol.{{citation needed|date=June 2018}}
 
Phylogenetic analysis of these genes places the adenoviruses (''Adenoviridae''), bacteriophages (''Caudovirales'') and the plant and fungal linear plasmids into a single clade. A second clade includes the alpha- and delta-like viral Pol from insect ascovirus (''Ascoviridae''), mammalian herpesviruses (''Herpesviridae''), fish lymphocystis disease virus (''Iridoviridae'') and chlorella virus (''Phycoviridae''). The ''pol'' genes of the African swine fever virus (''Asfarviridae''), baculoviruses (''Baculoviridae''), fish herpesvirus (''Herpesviridae''), [[T-even bacteriophages]] (''Myoviridae'') and poxviruses (''Poxviridae'') were not clearly resolved. A second study showed that poxvirus, baculovirus and the animal herpesviruses form separate and distinct clades.<ref name=Villarreal2000/> Their relationship to the ''Asfarviridae'' and the ''Myoviridae'' was not examined and remains unclear.
 
The polymerases from the archaea are similar to family B DNA Pols. The T4-like viruses infect both bacteria and archaea<ref name=Zillig1996/> and their ''pol'' gene resembles that of [[eukaryote]]s. The DNA polymerase of [[mitochondria]] resembles that of the T odd phages (''Myoviridae'').<ref name=Shutt2005/>
 
The virophage—[[Mavirus]]—may have evolved from a recombination between a [[transposon]] of the [[Polinton]] (Maverick) family and an unknown virus.<ref name="YutinRaoult2013">{{cite journal | vauthors = Yutin N, Raoult D, Koonin EV | title = Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies | journal = Virology Journal | volume = 10 | pages = 158 | date = May 2013 | pmid = 23701946 | pmc = 3671162 | doi = 10.1186/1743-422X-10-158 }}</ref>
 
The polyoma and papillomaviruses appear to have evolved from single-stranded DNA viruses and ultimately from plasmids.<ref name="Koonin2015"/>
 
===ss DNA viruses===
The evolutionary history of this group is currently poorly understood. An ancient origin for the single stranded circular DNA viruses has been proposed.<ref name=Delwart2012/>
 
Capsid proteins of most icosahedral ssRNA and ssDNA viruses display the same structural fold, the eight-stranded beta-barrel, also known as the [[jelly-roll fold]]. On the other hand, the replication proteins of icosahedral ssDNA viruses belong to the superfamily of rolling-circle replication initiation proteins that are commonly found in prokaryotic plasmids.<ref>{{cite journal | vauthors = Ilyina TV, Koonin EV | title = Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria | journal = Nucleic Acids Research | volume = 20 | issue = 13 | pages = 3279–3285 | date = July 1992 | pmid = 1630899 | pmc = 312478 | doi = 10.1093/nar/20.13.3279 }}</ref> Based on these observations, it has been proposed that small DNA viruses have originated via recombination between RNA viruses and plasmids.<ref>{{cite journal | vauthors = Krupovic M | title = Recombination between RNA viruses and plasmids might have played a central role in the origin and evolution of small DNA viruses | journal = BioEssays | volume = 34 | issue = 10 | pages = 867–870 | date = October 2012 | pmid = 22886750 | doi = 10.1002/bies.201200083 | s2cid = 34180723 }}</ref><ref>{{cite journal | vauthors = Krupovic M | title = Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses | journal = Current Opinion in Virology | volume = 3 | issue = 5 | pages = 578–86 | date = October 2013 | pmid = 23850154 | doi = 10.1016/j.coviro.2013.06.010 }}</ref>
 
Circoviruses may have evolved from a nanovirus.<ref name=Gibbs1999/><ref name=Meehan1997/><ref name=Niagro1998/>
 
Given the similarities between the ''rep'' proteins of the alphasatellites and the nanoviruses, it is likely that the alphasatellites evolved from the nanoviruses.<ref name=Xie2010/> Further work in this area is needed to clarify this.
 
The geminiviruses may have evolved from phytoplasmal plasmids.<ref>{{cite journal | vauthors = Krupovic M, Ravantti JJ, Bamford DH | title = Geminiviruses: a tale of a plasmid becoming a virus | journal = BMC Evolutionary Biology | volume = 9 | pages = 112 | date = May 2009 | pmid = 19460138 | pmc = 2702318 | doi = 10.1186/1471-2148-9-112 }}</ref> The Genomoviridae and the Geminividiae appear to be related.
 
Based on the three-dimensional structure of the Rep proteins the geminiviruses and parvoviruses may be related.<ref name=Gronenborn2004/>
 
The ancestor of the geminiviruses probably infected dicots.<ref name=Bernardo2013>{{cite journal | vauthors = Bernardo P, Golden M, Akram M, Nadarajan N, Fernandez E, Granier M, Rebelo AG, Peterschmitt M, Martin DP, Roumagnac P | title = Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications | journal = Virus Research | volume = 177 | issue = 1 | pages = 35–45 | date = October 2013 | pmid = 23886668 | doi = 10.1016/j.virusres.2013.07.006 | first8 = Anthony G | first11 = Philippe | first5 = Nagaswamy | first9 = Michel | first10 = Darren P | first6 = Emmanuel | first7 = Martine | doi-access = free }}</ref>
 
The [[parvovirus]]es have frequently invaded the germ lines of diverse animal species including [[mammal]]s, [[fish]]es, [[bird]]s, [[tunicate]]s, [[arthropod]]s and [[flatworm]]s.<ref name=Belyi2010/><ref name=Liu2011/> In particular they have been associated with the human genome for ~98 million years.
 
Members of the family [[Bidnaviridae]] have evolved from insect parvoviruses by replacing the typical replication-initiation endonuclease with a protein-primed family B DNA polymerase acquired from large DNA transposons of the Polinton/Maverick family. Some bidnavirus genes were also horizontally acquired from reoviruses (dsRNA genomes) and baculoviruses (dsDNA genomes).<ref>{{cite journal | vauthors = Krupovic M, Koonin EV | title = Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses | journal = Scientific Reports | volume = 4 | pages = 5347 | date = June 2014 | pmid = 24939392 | pmc = 4061559 | doi = 10.1038/srep05347 | bibcode = 2014NatSR...4E5347K }}</ref>
 
Polyomaviruses, papillomaviruses and parvoviruses may have descended from unrelated circular Rep-encoding single-stranded DNA viral ancestors.<ref name="Koonin2015a">Koonin EV, Dolja VV, Krupovic M (2015) "Origins and evolution of viruses of eukaryotes: The ultimate modularity." ''Virology'' 479–80: 2–25</ref>
 
==Bacteriophage evolution==
Since 1959 ~6300 prokaryote viruses have been described morphologically, including ~6200 bacterial and ~100 archaeal viruses.<ref name=Ackermann2012/> Archaeal viruses belong to 15 families and infect members of 16 archaeal genera. These are nearly exclusively hyperthermophiles or extreme halophiles. Tailed archaeal viruses are found only in the [[Euryarchaeota]], whereas most filamentous and pleomorphic archaeal viruses occur in the [[Crenarchaeota]]. Bacterial viruses belong to 10 families and infect members of 179 bacterial genera: most of these are members of the [[Firmicutes]] and γ-[[proteobacteria]].
 
The vast majority (96.3%) are tailed with and only 230 (3.7%) are polyhedral, filamentous or pleomorphic. The family [[Siphoviridae]] is the largest family (>3600 descriptions: 57.3%). The tailed phages appear to be monophyletic and are the oldest known virus group.<ref name=Ackermann2003/> They arose repeatedly in different hosts and there are at least 11 separate lines of descent.
 
All of the known temperate phages employ one of only three different systems for their lysogenic cycle: lambda-like integration/excision, Mu-like transposition or the plasmid-like partitioning of phage N15.
 
A putative course of evolution of these phages has been proposed by Ackermann.<ref name=Ackermann1998/>
 
Tailed phages originated in the early [[Precambrian]], before the [[last universal common ancestor]] (LUCA) during the prebiotic stage known as the [[DNA world]] and were in fact part of the LUCA virome. Bacteriophages arose from nucleic acids that recruited proteins from the LUCA pre-genome.<ref>{{cite journal|vauthors=Krupovic M, Dolja VV, Koonin EV|title=The LUCA and its complex virome.|journal=Nat Rev Microbiol|date=14 July 2020|doi=10.1038/s41579-020-0408-x|pmid=32665595|s2cid=220516514|url=https://bpp.oregonstate.edu/sites/agscid7/files/bpp/attachments/lucavirome2020.pdf|accessdate=16 August 2020}}</ref> The ancestral tailed phage had an icosahedral head of about 60 [[nanometer]]s in diameter and a long non contractile tail with sixfold symmetry. The [[capsid]] contained a single molecule of double stranded DNA of about 50 kilobases. The tail was probably provided with a fixation apparatus. The head and tail were held together by a connector. The viral particle contained no [[lipid]]s, was heavier than its descendant viruses and had a high DNA content proportional to its capsid size (~50%). Most of the genome coded for structural proteins. Morphopoietic genes clustered at one end of the genome, with head genes preceding tail genes. Lytic enzymes were probably coded for. Part of the phage genome was nonessential and possibly bacterial.
 
The virus infected its host from the outside and injected its DNA. Replication involved transcription in several waves and formation of DNA [[concatemer]]s.
 
New phages were released by burst of the infected cell after lysis of host membranes by a [[peptidoglycan hydrolase]]. Capsids were assembled from a starting point, the connector and around a scaffold. They underwent an elaborate maturation process involving protein cleavage and capsid expansion. Heads and tails were assembled separately and joined later. The DNA was cut to size and entered preformed capsids by a headful mechanism.
 
Subsequently, the phages evolved contractile or short tails and elongated heads. Some viruses become temperate by acquiring an [[integrase]]–[[excisionase]] complex, [[plasmid]] parts or [[transposon]]s.
 
A possible evolutionary pathway using vesicles rather than a protein coat has been described in the archaeal plasmid pR1SE.<ref name=Erdmann2017>{{cite journal | vauthors = Erdmann S, Tschitschko B, Zhong L, Raftery MJ, Cavicchioli R | s2cid = 38729395 | title = A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells | journal = Nature Microbiology | volume = 2 | issue = 10 | pages = 1446–1455 | date = October 2017 | pmid = 28827601 | doi = 10.1038/s41564-017-0009-2 }}</ref>
 
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}}
 
== Further reading ==
* {{cite web | vauthors = Fauquent CM, Mayo MA, Maniloff J, Desselberger U, Ball LA |title=8th Reports of the International Committee on Taxonomy of Viruses|url=https://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/fr-fst-g.htm|work=Academic Press|publisher=US National Center for Biotechnology Information, National Library for Medicine, National Institutes of Health|date=2005-05-27}}
* {{cite web |title=ICTV Online (10th) Report Now Available |publisher=International Committee on Taxonomy of Viruses |url=http://www.ictvdb.org/ |access-date=4 February 2017 |archive-url=https://web.archive.org/web/20110510194209/http://www.ictvdb.org/ |archive-date=10 May 2011 |url-status=dead }}
 
===Bibliography===
{{Refbegin}}
* {{cite book|last=Lostroh|first=P.|year=2019|title=Molecular and Cellular Biology of Viruses|url=https://books.google.com/books?id=BcmWDwAAQBAJ&q=baltimore+classification&pg=PT58|publisher=Garland Science|isbn=978-0429664304|access-date=24 September 2020|ref=lostroh}}
* {{cite book|last=Cann|first=A.|date=2015|title=Principles of Molecular Virology|publisher=Elsevier|pages=122–127|isbn=978-0128019559|ref=cann}}
* {{cite book|last=Fermin|first=G.|editor1-last=Tennant |editor1-first=P.|editor2-last=Fermin |editor2-first=G.|editor3-last=Foster |editor3-first=J.|date=2018|title=Viruses: Molecular Biology, Host Interactions and Applications to Biotechnology|chapter-url=https://www.sciencedirect.com/science/article/pii/B9780128112571000024|publisher=Elsevier|location=San Diego, CA|pages=35–46|doi=10.1016/B978-0-12-811257-1.00002-4|isbn= 978-0128112571|s2cid=89706800|access-date=8 December 2020|chapter=Virion Structure, Genome Organization, and Taxonomy of Viruses|ref=fermin}}
* {{cite book |last1=Rampersad |first1=S.|last2=Tennant |first2=P.|editor1-last=Tennant |editor1-first=P.|editor2-last=Fermin |editor2-first=G.|editor3-last=Foster |editor3-first=J. |title=Viruses: Molecular Biology, Host Interactions, and Applications to Biotechnology |date=2018 |publisher=Elsevier |location=San Diego, CA |isbn=978-0128112571 |pages=55–82 |chapter-url=https://www.sciencedirect.com/science/article/pii/B9780128112571000036 |access-date=8 December 2020 |chapter=Replication and Expression Strategies of Viruses|doi=10.1016/B978-0-12-811257-1.00003-6|s2cid=90170103|ref=rampersad}}
{{Refend}}
 
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[[Category:DNA viruses| ]]
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