DNA virus

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 and chickenpox are caused by such DNA viruses.

Group I: dsDNA viruses
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 31 families are currently recognised. A fourth order - Megavirales - for the nucleocytoplasmic large DNA viruses has been proposed. 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 (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.

The genomes in this group vary considerably from ~20 kilobases to over 1.2 megabases in length.

Host range
Species of the order Caudovirales and of the families Corticoviridae and Tectiviridae infect bacteria.

Species of the order Ligamenvirales and the families Ampullaviridae, 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 family Mimiviridae and the species Marseillevirus, Megavirus, 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 halophilic archaea species of the Euryarchaeota.

Taxonomy

 * Order Caudovirales
 * Family Myoviridae - includes Enterobacteria phage T4
 * Family Podoviridae - includes Enterobacteria phage T7
 * Family Siphoviridae - includes Enterobacteria phage &lambda;


 * Order Herpesvirales
 * Family Alloherpesviridae
 * Family Herpesviridae - includes human herpesviruses, Varicella Zoster virus
 * Family Malacoherpesviridae


 * Order Ligamenvirales
 * Family Lipothrixviridae
 * Family Rudiviridae


 * Unassigned families
 * Family Adenoviridae - includes viruses which cause human adenovirus infection
 * Family Ampullaviridae
 * Family Ascoviridae
 * Family Asfarviridae - includes African swine fever virus
 * Family Baculoviridae
 * Family Bicaudaviridae
 * Family Clavaviridae
 * Family Corticoviridae
 * Family Fuselloviridae
 * Family Globuloviridae
 * Family Guttaviridae
 * Family Hytrosaviridae
 * Family Iridoviridae
 * Family Mimiviridae
 * Family Nimaviridae
 * Family Papillomaviridae
 * Family Phycodnaviridae
 * Family Plasmaviridae
 * Family Polydnaviruses
 * Family Polyomaviridae - includes Simian virus 40, JC virus, BK virus
 * Family Poxviridae - includes Cowpox virus, smallpox
 * Family Tectiviridae


 * Unassigned genera
 * Dinodnavirus
 * Nudivirus
 * Salterprovirus
 * Rhizidiovirus


 * Unassigned species
 * Abalone shriveling syndrome-associated virus
 * Bandicoot papillomatosis carcinomatosis virus
 * KIs-V
 * Haloarcula hispanica pleomorphic virus 1
 * Haloarcula hispanica SH1 virus
 * Marseillevirus
 * Mavirus virophage
 * Megavirus
 * Organic Lake virophage
 * Sputnik virophage
 * Sputnik virophage 2
 * Sulfolobus turreted icosahedral virus
 * Thermus aquaticus virus IN93
 * Thermus thermophilus virus P23-77

Group II: ssDNA viruses
Although bacteriophages 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. 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. Many of these "environmental" viruses belong to the family Microviridae. 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 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. The parvoviruses have frequently invaded the germ lines of diverse animal species including mammals, fishes, birds, tunicates, arthropods and flatworms. In particular they have been associated with the human genome for ~98 million years.

Host range
Families in this group have been assigned on the basis of the nature of the genome (circular or linear) and the host range. Nine families are currently recognised.

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 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.

Classification
A division of the circular single stranded viruses into four types has been proposed. This division seems likely reflects 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.

Taxonomy

 * Family Anelloviridae
 * Family Bacillariodnaviridae
 * Family Bidnaviridae
 * Family Circoviridae
 * Family Geminiviridae
 * Family Inoviridae
 * Family Microviridae
 * Family Nanoviridae
 * Family Parvoviridae - includes Parvovirus B19

Unassigned species
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. Their closest relations appear to be the Brevidensoviruses (family Parvoviridae).

In the 9th edition of the viral taxonomy of the ICTV (published in 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.

Another new genus - as yet unnamed - has been proposed. This genus includes the species bovine stool associated circular virus and chimpanzee stool associated circular virus. 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. 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.

A virus with a circular genome - sea turtle tornovirus 1 - has been isolated from a sea turtle with fibropapillomatosis. 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 but two have double stranded genomes. The first archaeal ssDNA virus to be isolated is the Halorubrum pleomorphic virus 1, which has a pleomorphic enveloped virion and a circular genome.

The second single stranded DNA virus infecting Archaea is Aeropyrum coil-shaped virus (ACV). The genome is circular and with 24,893 nucleotides is currently the largest known ssDNA genome. The viron is nonenveloped, hollow, cylindrical and formed from a coiling fiber. The morphology and the genome appear to be unique. ACV has been suggested to represent a new viral family tentatively called "Spiraviridae" (from Latin spira, "a coil").

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. This virus appears to be related to the Geminiviridae but is distinct from them. A genus - Breviviridae - has been proposed for Sclerotinia sclerotiorum hypovirulence associated DNA virus 1 and a European badger fecal virus.

A second virus - Cassava associated circular DNA virus - that has some similarity to Sclerotinia sclerotiorum hypovirulence associated DNA virus 1 has been isolated.

An unusual - and as yet unnamed - virus has been isolated from the flatwom Girardia tigrina. 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.

A circular single stranded DNA virus has been isolated from a grapevine. This species may be related to the family Geminiviridae but differs from this family in a number of important respects including genome size.

A new genus - Bufavirus - has been proposed on the basis of the isolation of two new viruses from human stool. These viruses appear to be related to the Parvoviruses.

Satellite viruses
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.

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
The family Ascoviridae appear to have evolved from the Iridoviridae. The family Polydnaviridae may have evolved from the Ascoviridae. Molecular evidence suggests that the Phycodnaviridae may have evolved from the family Iridoviridae. 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).

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.

Based on the analysis of the DNA polymerase the genus Dinodnavirus may be a member of the family Asfarviridae. Further work on this virus will required before a final assignment can be made.

Baculoviruses evolved from the Nudiviruses.

The Hytrosaviridae are related to the Baculoviruses and to a lesser extent the Nudiviruses suggesting they may have evolved from the Baculoviruses.

The Nimaviridae may be related to Nudiviruses and Baculoviruses.

The Nudiviruses seem to be related to the Polydnaviruses.

The families Adenoviridae and Tectiviridae appear to be related structurally.

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.

Examination of the pol genes that encode the DNA dependent DNA polymerase in various groups of viruses suggests a number of possible evolutionary relationships. 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. 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 and their pol gene resembles that of eukaryotes. The DNA polymerase of mitochondria resembles that of the T odd phages (Myoviridae).

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.

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. These two groups of viruses share a distinctive 12-fold arrangement of subunits in the portal complex.

ss DNA viruses
An ancient origin for the single stranded circular DNA viruses has been proposed.

Circoviruses may have evolved from a nanovirus.

Given the similarities between the rep proteins of the alphasatellites and the nanoviruses, it is likely that the alphasatellites evolved from the nanoviruses. Further work in this area is needed to clarify this.

The geminiviruses may have evolved from phytoplasmal plasmids.

Based on the three-dimensional structure of the Rep proteins the geminiviruses and parvoviruses may be related.

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. Based on these observations, it has been proposed that small DNA viruses have originated via recombination between RNA viruses and plasmids.

Bacteriophage evolution
Bacteriophages occur in over 140 bacterial or archaeal genera. 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.

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.

NCLDVs
The asfarviruses, iridoviruses, mimiviruses, phycodnaviruses and poxviruses have been shown to belong to a single group. - the large nuclear and cytoplasmic DNA viruses. These are also abbreviated "NCLDV". 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 factors (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 gene having been gained from multiple sources.

Additional reading


فيروس دنا Virus d'ADN DNA viry DNA-Virus DNA-viirused Virus ADN Virus à ADN DNA 바이러스 Virus DNA Virus a DNA DNA-virus DNAウイルス Wirusy DNA Vírus DNA Deoxiribovirus ДНК-содержащие вирусы DNA virus DNA-virus 去氧核糖核酸病毒