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.
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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).
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.
Orders 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 33 families are currently recognised. Four genera are recognised that have not yet been assigned a family. The species Sulfolobus turreted icosahedral virus is so unlike any previously described virus that it will almost certainly be placed in a new family on the next revision of viral families.
Fifteen families are 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.
Bacteriophages belonging to the families Tectiviridae and Corticoviridae have a lipid bilayer inside the icosahedral protein capsid and the membrane surrounds the genome. The crenarchaeal virus Sulfolobus turreted icosahedral virus has a similar structure.
The genomes in this group vary considerably from ~20 kilobases to over 1.2 megabases in length.
Species of the order Caudovirales and of the families Corticoviridae and Tectiviridae infect bacteria.
Species of the order Ligamenvirales and the families Ampullaviridae, Bacilloviridae, Bicaudaviridae, Clavaviridae, Fuselloviridae, Globuloviridae and Guttaviridae infect hyperthermophilic archaea species of the Crenarchaeota.
Species of the order Herpesvirales and of the families Adenoviridae, Asfarviridae, Iridoviridae, Papillomaviridae, Polyomaviridae and Poxviridae infect vertebrates.
Species of the families Ascovirus, Baculovirus, Hytrosaviridae, Iridoviridae and Polydnaviruses and of the genus Nudivirus infect insects.
Species of the families Marseilleviridae, Megaviridae and Mimiviridae and the species Mavirus virophage and Sputnik virophage infect protozoa.
Species of the family Nimaviridae infect crustaceans.
Species of the family Phycodnaviridae and the species Organic Lake virophage infect algae. These are the only known dsDNA viruses that infect plants.
Species of the family Plasmaviridae infect species of the class Mollicutes.
Species of the genus Dinodnavirus infect dinoflagellates. These are the only known viruses that infect dinoflagellates.
Species of the genus Rhizidiovirus infect stramenopiles. These are the only known dsDNA viruses that infect stramenopiles.
Species of the genus Salterprovirus infect infect halophilic archaea species of the Euryarchaeota.
Although bacteriophages were first described in 1927, it was only in 1959 that Sinshemer working with the phage X174 showed that they could possess single stranded DNA genomes.[1][2] Despite this discovery until relatively recently it was believed that the majority of DNA viruses belonged to the double stranded clade. Recent work suggests that this may not be the case with single stranded viruses forming the majority of viruses found in sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats.[3][4] The majority of these viruses have 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 be created for these.
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.
The evolutionary history of this group is currently poorly understood. However the parvoviruses have frequently invaded the germ lines of diverse animal species including mammals, fishes, birds, tunicates, arthropods and flatworms.[5][6] In particular they have been associated with the human genome for ~98 million years.
Families in this group have been assigned on the basis of the nature of the genome (circular or linear) and the host range. Eight families are currently recognised.
The family Parvoviridae all have linear genomes while the other families have circular genomes. The Inoviridae and Microviridae infect bacteria; the Anelloviridae and Circoviridae infect animals (mammals and birds respectively); and the Geminiviridae and Nanoviridae infect plants. In both the Geminiviridae and Nanoviridae the genome is composed of more than a single chromosome. The Bacillariodnaviridae infect diatoms 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.
A number of additional single stranded DNA viruses are known but are as yet unclassified. 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 the Bombyx mori densovirus type 2, 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 ICTV to date.[7] Their closest relations appear to be the Brevidensoviruses (family Parvoviridae).[8]
Another new genus - as yet unnamed - has been proposed.[9] This genus includes the species bovine stool associated circular virus and chimpanzee stool associated circular virus.[10] The closest relations to this genus appear to be the Nanoviridae but further work will be needed to confirm this.
A virus with a circular genome - sea turtle tornovirus 1 - has been isolated from a sea turtle with fibropapillomatosis.[11] 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.
Although ~50 archaeal viruses are known all the DNA viruses infecting archaea, with one known exception, have double stranded genomes. This exception is the Halorubrum pleomorphic virus 1 which has a unique structure and a circular genome.[12]
Most known fungal viruses have either double stranded DNA or RNA genomes. A single stranded DNA fungal virus - Sclerotinia sclerotiorum hypovirulence associated DNA virus 1 - has been described.[13] This virus appears to be related to the Geminiviridae but is distinct from them.
An unusual - and as yet unnamed - virus has been isolated from the flatwom Girardia tigrina.[14] Because of its genome organisation, this virus appears to belong to an entirely new family. It is the first virus to be isolated from a flatworm.
Satellite viruses 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 alphasatellites and the betasatellites - both of which are dependent on begomaviruses. 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.
The asfarviruses, iridoviruses, mimiviruses, phycodnaviruses and poxviruses have been shown to belong to a single group.[15] - the large nuclear and cytoplasmic DNA viruses. These are also abbreviated "NCLDV".[16] This clade can be divided into two groups:
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 factors (4) capping and polyadenylation enzymes (5) the DNA packaging apparatus (6) and structural components of an icosahedral capsid and the viral membrane.
Bacteriophages occur in over 140 bacterial or archaeal genera.[17] They arose repeatedly in different hosts and there are at least 11 separate lines of descent. Over 5100 bacteriophages have been examined in the electron microscope since 1959. Of these at least 4950 phages (96%) have tails. Of the tailed phages 61% have long, noncontractile tails (Siphoviridae). Tailed phages appear to be monophyletic and are the oldest known virus group.
The family Ascoviridae appear to have evolved from the Iridoviridae.[18] The family Polydnaviridae may have evolved from the Ascoviridae. Molecular evidence suggests that the Phycodnaviridae may have evolved from the family Iridoviridae.[19] These four families (Ascoviridae, Iridoviridae, Phycodnaviridae and Polydnaviridae) may form a clade but more work is needed to confirm this.
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).[20]
The nucleocytoplasmic large DNA virus 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.[21]
Based on the analysis of the DNA polymerase the genus Dinodnavirus may be a member of the family Asfarviridae.[22] Further work on this virus will required before a final assignment can be made.
The families Adenoviridae and Tectiviridae appear to be related structurally.[23]
Based on the analysis of the coat protein Sulfolobus turreted icosahedral virus may share a common ancestry with the Tectiviridae.
A protein common to the families Bicaudaviridae, Lipotrixviridae and Rudiviridae and the unclassified virus Sulfolobus turreted icosahedral virus is known suggesting a common origin.[24]
Examination of the pol genes that encode the DNA dependent DNA polymerase in various groups of viruses suggests a number of possible evolutionary relationships.[25] 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.
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.[26] 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[27] and their pol gene resembles that of eukaryotes. The DNA polymerase of mitochondria resembles that of the T odd phages (Myoviridae).[28]
Only a single gene encoding the putative ATPase subunit of the terminase is conserved among all herpesviruses. To a lesser extent this gene is also found also in T4-like bacteriophages suggesting a common ancestor for these two groups of viruses.[29]
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. [30] These two groups of viruses share a distinctive 12-fold arrangement of subunits in the portal complex.
Baculoviruses evolved from with the Nudiviruses 310 million years ago.[31]
Circoviruses may have evolved from a nanovirus.[32]
Given the similarities between the rep proteins of the alphasatellites and the nanoviruses, it is likely that the alphasatellites evolved from the nanoviruses.[33] Further work in this area is needed to clarify this.
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