Editing DNA virus (section)

==Baltimore classification==
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===
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>

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>

===Single-stranded DNA 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>

[[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>

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>