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.
- 1 Group I: dsDNA viruses
- 2 Pleolipoviruses
- 3 Group II: ssDNA viruses
- 3.1 Taxonomy
- 3.2 Classification
- 3.3 Host range
- 3.4 Molecular biology
- 3.5 Recently classified viruses
- 3.6 Smacoviridae
- 3.7 Unassigned species
- 4 Satellite viruses
- 5 Phylogenetic relationships
- 6 Bacteriophage evolution
- 7 NCLDVs
- 8 References
- 9 Further reading
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. This proposal has yet to be ratified by the ICTV. Four genera are recognised that have not yet been assigned a family.
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 ~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.
The virophages are a group of viruses that infect other viruses.
A virus with a novel method of genome packing infecting species of the genus Sulfolobus has been described. As this virus does not resemble any known virus it has been classified into a new family, the Portogloboviridae.
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, Guttaviridae and Turriviridae 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 Plasmaviridae infect species of the class Mollicutes.
Species of the family Pandoraviridae infect amoebae.
Species of the genus Rhizidiovirus infect stramenopiles. These are the only known dsDNA viruses that infect stramenopiles.
Species of the genus Salterprovirus and Sphaerolipoviridae infect species of the Euryarchaeota.
- Order Caudovirales
- Order Herpesvirales
- Order Ligamenvirales
- 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 Lavidaviridae
- Family Marseilleviridae
- Family Mimiviridae
- Family Nudiviridae
- Family Nimaviridae
- Family Pandoraviridae
- 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 Sphaerolipoviridae
- Family Tectiviridae
- Family Turriviridae
- Unassigned genera
- Unassigned species
- Abalone shriveling syndrome-associated virus
- Bandicoot papillomatosis carcinomatosis virus
- Lentille virus
- Leptopilina boulardi filamentous virus
- Metallosphaera turreted icosahedral virus
- Methanosarcina spherical virus
- Mollivirus sibericum virus
- Orpheovirus IHUMI-LCC2
- Phaeocystis globosa virus
- Family Lavidaviridae
- Ace Lake Mavirus virophage
- Dishui Lake virophage 1
- 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
A group of double stranded DNA viruses have been found in fish that appear to be related to the herpesviruses.
Another group of viruses that infect fish has been described.
A group known as the pleolipoviruses, although having a similar genome organisation, differ in having either single or double stranded DNA genomes. Within the double stranded forms have runs of single stranded DNA. These viruses have been placed in the family Pleolipoviridae. 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. 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:
- Genus: Alphapleolipovirus
- Genus: Betapleolipovirus
- Genus: Gammapleolipovirus
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 most DNA viruses contained double-stranded DNA. Recent work, however, has shown that single-stranded DNA viruses can be highly abundant in seawater, freshwater, sediments, terrestrial and extreme environments, as well as 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 have to be created to accommodate them.
Families in this group have been assigned on the basis of the nature of the genome (circular or linear) and the host range. Eleven families are currently recognised.
- Family Anelloviridae
- Family Bacilladnavirus
- Family Bidnaviridae
- Family Circoviridae
- Family Geminiviridae
- Family Genomoviridae
- Family Inoviridae
- Family Microviridae
- Family Nanoviridae
- Family Parvoviridae
- Family Smacoviridae
- Family Spiraviridae
A division of the circular single stranded viruses into four types has been proposed. 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.
All known eukaryotic ssDNA viruses also form icosahedral capsids. With the exception of the family Bidnaviridae, all eukaryotic ssDNA viruses encode homologous rolling-circle replication initiation proteins with characteristic N-terminal endonuclease domains and C-terminal superfamily three helicase domains. A name for this group of viruses has been proposed - circular Rep-encoding single-strand (CRESS) DNA viruses.
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. The name Cruciviridae has been proposed for this group.
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. Members of the Spiraviridae infect archaea. Members of the Genomoviridae infect fungi.
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. Another member of this genus—megabat bufavius 1—has been reported from bats. The human viruses have since been renamed Primate protoparvovirus and been placed in the genus Protoparvovirus.
Another proposed genus is Pecovirus. These are similar in organisation to the Smacovirus but share little sequence similarity.
The most recently introduced family of ssDNA viruses is the Genomoviridae (the family name is an acronym derived from geminivirus-like, no movement protein).
The genus name Gemycircularvirus stands for Gemini-like myco-infecting circular virus. the type species of the genus Gemycircularvirus - Sclerotinia sclerotiorum hypovirulence associated DNA virus 1 - is currently the only cultivated member of the family. The rest of genomoviruses are uncultivated and have been discovered using metagenomics techniques.
- Human isolates
A isolate from this group has also been identified in a child with encephalitis.
Viruses from this group have also been isolated from the blood of HIV+ve patients.
- Animal isolates
Another virus from this group has been isolated from mosquitoes.
Ten new circular viruses have been isolated from dragonfly larvae. 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.
- Plants and fungi
Three viruses in this group have been isolated from plants.
A virus — Cassava associated circular DNA virus — that has some similarity to Sclerotinia sclerotiorum hypovirulence associated DNA virus 1 has been isolated. This virus has been placed in the Gemycircularviridae.
Some of this group of viruses may infect fungi.
A new family, the Smacoviridae, has been created for a number of single-stranded DNA viruses isolated from the faeces of various mammals. 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.
A number of additional single stranded DNA viruses have been described but are as yet unclassified.
Viruses in this group have been isolated from other cases of encephalitis, diarrhoea and sewage.
Two viruses have been isolated from human faeces — circo-like virus Brazil hs1 and hs2 — with genome lengths of 2526 and 2533 nucleotides respectively. 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. 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. 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. 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. Another virus of this group has been reported again from pigs. A virus from this group has been isolated from turkey faeces. Another ten viruses from this group have been isolated from pig faeces. Viruses that appear to belong to this group have been isolated from other mammals including cows, rodents, bats, badgers and foxes.
Another virus in this group has been isolated from birds.
Fur seal feces-associated circular DNA virus was isolated from the faeces of a fur seal (Arctocephalus forsteri) in New Zealand. The genome has 2 main open reading frames and is 2925 nucleotides in length. Another virus - porcine stool associated virus 4 - 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) 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) and CynNCXV has some similarity to the rodent stool associated virus (RodSCV M-45).
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.
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 ICTV to date. Their closest relations appear to be the Brevidensoviruses (family Parvoviridae).
A virus — Acheta domesticus volvovirus - has been isolated from the house cricket (Acheta domesticus). 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. The genomes in this genus are ~2.5 nucleotides in length and encode 4 open reading frames.
A virus has been isolated from the mud flat snail (Amphibola crenata). This virus has a single stranded circular genome of 2351 nucleotides that encoded 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 plasmids. The larger open reading frame (955 nucleotides) has no homology to any currently known protein.
An unusual — and as yet unnamed — virus has been isolated from the flatworm 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.
Several viruses — baminivirus, nepavirus and niminivirus — related to geminvirus have also been reported.
A new virus with a three part single stranded genome has been reported. 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 . 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.
A virus — Boiling Springs Lake virus — appears to have evolved by a recombination event between a DNA virus (circovirus) and an RNA virus (tombusvirus). 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.
A virus - FLIP (Flavobacterium-infecting, lipid-containing phage) - has been isolated from a lake. 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.
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 begomoviruses. 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 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. 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. 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 ~Pangaea. The alphaherpesvirinae separated from the branch leading to the betaherpesvirinae and gammaherpesvirinae about to . The avian herpes viruses diverged from the branch leading to the mammalian species. 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.and underwent subsequent evolution on the supercontinent
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. Another paper has also suggested that herpesviruses originated among the bacteriophages.
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. A second paper has suggested an evolutionary relationship between these two groups of viruses.
Large DNA viruses
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.
Several studies have suggested that the family Ascoviridae evolved from the Iridoviridae. A study of the Iridoviruses suggests that the Iridoviridae, Ascoviridae and Marseilleviridae are related with Ascoviruses most closely related to Iridoviruses.
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.
Some of the relations among the large viruses have been established. Mimiviruses are distantly related to Phycodnaviridae. Pandoraviruses share a common ancestor with Coccolithoviruses within the family Phycodnaviridae. 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).
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.
It has been suggested that at least some of the giant viruses may originate from mitochondria.
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.
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.
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).
The polyoma and papillomaviruses appear to have evolved from single-stranded DNA viruses and ultimately from plasmids.
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.
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.
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. 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.
The ancestor of the geminiviruses probably infected dicots.
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.
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).
Since 1959 ~6300 prokaryote viruses have been described morphologically, including ~6200 bacterial and ~100 archaeal viruses. 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 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. 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.
Tailed phages originated in the early Precambrian, long before eukaryotes and their viruses. The ancestral tailed phage had an icosahedral head of about 60 nanometers 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 lipids, 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 concatemers.
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.
A possible evolutionary pathway using vesicles rather than a protein coat has been described in the archaeal plasmid pR1SE.
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 genes having been gained from multiple sources. It has been proposed that the ancestor of NCLDVs has evolved from large, virus-like DNA transposons of the Polinton/Maverick family. 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.
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 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.
- Colson P, de Lamballerie X, Fournous G, Raoult D (2012). "Reclassification of giant viruses composing a fourth domain of life in the new order Megavirales". Intervirology. 55 (5): 321–32. doi:10.1159/000336562. PMID 22508375.
- 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 (December 2013). ""Megavirales", a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses". Archives of Virology. 158 (12): 2517–21. doi:10.1007/s00705-013-1768-6. PMC . PMID 23812617.
- Simoliūnas E, Kaliniene L, Truncaitė L, Zajančkauskaitė A, Staniulis J, Kaupinis A, Ger M, Valius M, Meškys R (2013). "Klebsiella phage vB_KleM-RaK2 - a giant singleton virus of the family Myoviridae". PLOS One. 8 (4): e60717. Bibcode:2013PLoSO...860717S. doi:10.1371/journal.pone.0060717. PMC . PMID 23593293.
- Liu Y, Ishino S, Ishino Y, Pehau-Arnaudet G, Krupovic M, Prangishvili D (July 2017). "A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea". Journal of Virology. 91 (13): e00589–17. doi:10.1128/JVI.00589-17. PMC . PMID 28424284.
- 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
- Aswad A, Katzourakis A (July 2017). "A novel viral lineage distantly related to herpesviruses discovered within fish genome sequence data". Virus Evolution. 3 (2): vex016. doi:10.1093/ve/vex016. PMID 28798873.
- Dill JA, Camus AC, Leary JH, Ng TF (May 2018). "Microscopic and Molecular Evidence of the First Elasmobranch Adomavirus, the Cause of Skin Disease in a Giant Guitarfish, Rhynchobatus djiddensis". mBio. 9 (3): e00185–18. doi:10.1128/mBio.00185-18. PMC . PMID 29764943.
- Pietilä MK, Atanasova NS, Manole V, Liljeroos L, Butcher SJ, Oksanen HM, Bamford DH (May 2012). "Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea". Journal of Virology. 86 (9): 5067–79. doi:10.1128/JVI.06915-11. PMC . PMID 22357279.
- Sencilo A, Paulin L, Kellner S, Helm M, Roine E (July 2012). "Related haloarchaeal pleomorphic viruses contain different genome types". Nucleic Acids Research. 40 (12): 5523–34. doi:10.1093/nar/gks215. PMC . PMID 22396526.
- Pietilä MK, Roine E, Sencilo A, Bamford DH, Oksanen HM (January 2016). "Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes". Archives of Virology. 161 (1): 249–56. doi:10.1007/s00705-015-2613-x. PMID 26459284.
- International Committee on Taxonomy of Viruses, Virus Taxonomy: 2017 Release, Excel(xlsx)-Datei ICTV 2017 Master Species #32
- Ying Liu et al.: 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
- Sinshemer RL (1959). "Purification and properties of bacteriophage φX174". Journal of Molecular Biology. 1: 37–IN5. doi:10.1016/S0022-2836(59)80005-X.
- Sinshemer RL (1959). "A single-stranded deoxyribonucleic acid from bacteriophage φX174". Journal of Molecular Biology. 1: 43–IN6. doi:10.1016/S0022-2836(59)80006-1.
- Labonté JM, Suttle CA (November 2013). "Previously unknown and highly divergent ssDNA viruses populate the oceans". The ISME Journal. 7 (11): 2169–77. doi:10.1038/ismej.2013.110. PMC . PMID 23842650.
- Desnues C, Rodriguez-Brito B, Rayhawk S, Kelley S, Tran T, Haynes M, Liu H, Furlan M, Wegley L, Chau B, Ruan Y, Hall D, Angly FE, Edwards RA, Li L, Thurber RV, Reid RP, Siefert J, Souza V, Valentine DL, Swan BK, Breitbart M, Rohwer F (March 2008). "Biodiversity and biogeography of phages in modern stromatolites and thrombolites". Nature. 452 (7185): 340–3. Bibcode:2008Natur.452..340D. doi:10.1038/nature06735. PMID 18311127.
- Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H, Mahaffy JM, Mueller JE, Nulton J, Olson R, Parsons R, Rayhawk S, Suttle CA, Rohwer F (November 2006). "The marine viromes of four oceanic regions". PLoS Biology. 4 (11): e368. doi:10.1371/journal.pbio.0040368. PMC . PMID 17090214.
- Roux S, Krupovic M, Poulet A, Debroas D, Enault F (2012). "Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads". PLOS One. 7 (7): e40418. Bibcode:2012PLoSO...740418R. doi:10.1371/journal.pone.0040418. PMC . PMID 22808158.
- Rosario K, Duffy S, Breitbart M (October 2009). "Diverse circovirus-like genome architectures revealed by environmental metagenomics". The Journal of General Virology. 90 (Pt 10): 2418–24. doi:10.1099/vir.0.012955-0. PMID 19570956.
- Krupovic M (2013) Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses. Current Opinion in Virology 3: 578–586
- Rosario K, Duffy S, Breitbart M (October 2012). "A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics". Archives of Virology. 157 (10): 1851–71. doi:10.1007/s00705-012-1391-y. PMID 22760663.
- Diemer GS, Stedman KM (June 2012). "A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses". Biology Direct. 7: 13. doi:10.1186/1745-6150-7-13. PMC . PMID 22515485.
- Quaiser A, Krupovic M, Dufresne A, Francez AJ, Roux S (July 2016). "Sphagnum-dominated peatlands". Virus Evolution. 2 (2): vew025. doi: . PMC . PMID 29492276.
- Phan TG, Vo NP, Bonkoungou IJ, Kapoor A, Barro N, O'Ryan M, Kapusinszky B, Wang C, Delwart E (October 2012). "Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus". Journal of Virology. 86 (20): 11024–30. doi:10.1128/JVI.01427-12. PMC . PMID 22855485.
- 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 (April 2016). "Divergent bufavirus harboured in megabats represents a new lineage of parvoviruses". Scientific Reports. 6: 24257. Bibcode:2016NatSR...624257S. doi:10.1038/srep24257. PMC . PMID 27113297.
- "ICTV Official Taxonomy: Updates since the 8th Report". ICTV Official Taxonomy. ICTV Official Taxonomy. Retrieved 11 June 2014.
- Cotmore SF, Agbandje-McKenna M, Chiorini JA, Mukha DV, Pintel DJ, Qiu J, Soderlund-Venermo M, Tattersall P, Tijssen P, Gatherer D, Davison AJ (May 2014). "The family Parvoviridae". Archives of Virology. 159 (5): 1239–47. doi:10.1007/s00705-013-1914-1. PMC . PMID 24212889.
- Krupovic M, Ghabrial SA, Jiang D, Varsani A (September 2016). "Genomoviridae: a new family of widespread single-stranded DNA viruses". Archives of Virology. 161 (9): 2633–43. doi:10.1007/s00705-016-2943-3. PMID 27343045.
- Varsani A, Krupovic M (January 2017). "Genomoviridae". Virus Evolution. 3 (1): vew037. doi:10.1093/ve/vew037. PMC . PMID 28458911.
- Rosario K, Dayaram A, Marinov M, Ware J, Kraberger S, Stainton D, Breitbart M, Varsani A (December 2012). "Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta)". The Journal of General Virology. 93 (Pt 12): 2668–81. doi:10.1099/vir.0.045948-0. PMID 22915694.
- Yu X, Li B, Fu Y, Jiang D, Ghabrial SA, Li G, Peng Y, Xie J, Cheng J, Huang J, Yi X (May 2010). "A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus". Proceedings of the National Academy of Sciences of the United States of America. 107 (18): 8387–92. Bibcode:2010PNAS..107.8387Y. doi:10.1073/pnas.0913535107. PMC . PMID 20404139.
- Nakasu EY, Melo FL, Michereff-Filho M, Nagata T, Ribeiro BM, Ribeiro SG, Lacorte C, Inoue-Nagata AK (September 2017). "Discovery of two small circular ssDNA viruses associated with the whitefly Bemisia tabaci". Archives of Virology. 162 (9): 2835–2838. doi:10.1007/s00705-017-3425-y. PMID 28567489.
- Lamberto I, Gunst K, Müller H, Zur Hausen H, de Villiers EM (August 2014). "Mycovirus-like DNA virus sequences from cattle serum and human brain and serum samples from multiple sclerosis patients". Genome Announcements. 2 (4): e00848–14. doi:10.1128/genomeA.00848-14. PMC . PMID 25169858.
- Zhou C, Zhang S, Gong Q, Hao A (November 2015). "A novel gemycircularvirus in an unexplained case of child encephalitis". Virology Journal. 12: 197. doi:10.1186/s12985-015-0431-0. PMC . PMID 26596706.
- Uch R, Fournier PE, Robert C, Blanc-Tailleur C, Galicher V, Barre R, Jordier F, de Micco P, Raoult D, Biagini P (November 2015). "Divergent Gemycircularvirus in HIV-Positive Blood, France". Emerging Infectious Diseases. 21 (11): 2096–8. doi:10.3201/eid2111.150486. PMC . PMID 26488181.
- Li W, Gu Y, Shen Q, Yang S, Wang X, Wan Y, Zhang W (October 2015). "A novel gemycircularvirus from experimental rats". Virus Genes. 51 (2): 302–5. doi:10.1007/s11262-015-1238-1. PMID 26303898.
- Dayaram A, Galatowitsch M, Harding JS, Argüello-Astorga GR, Varsani A (March 2014). "Novel circular DNA viruses identified in Procordulia grayi and Xanthocnemis zealandica larvae using metagenomic approaches". Infection, Genetics and Evolution. 22: 134–41. doi:10.1016/j.meegid.2014.01.013. PMID 24462907.
- Dayaram A, Potter KA, Pailes R, Marinov M, Rosenstein DD, Varsani A (March 2015). "Identification of diverse circular single-stranded DNA viruses in adult dragonflies and damselflies (Insecta: Odonata) of Arizona and Oklahoma, USA". Infection, Genetics and Evolution. 30: 278–287. doi:10.1016/j.meegid.2014.12.037. PMID 25577985.
- Male MF, Kami V, Kraberger S, Varsani A (October 2015). "Genome Sequences of Poaceae-Associated Gemycircularviruses from the Pacific Ocean Island of Tonga". Genome Announcements. 3 (5): e01144–15. doi:10.1128/genomeA.01144-15. PMC . PMID 26472826.
- Dayaram A, Opong A, Jäschke A, Hadfield J, Baschiera M, Dobson RC, Offei SK, Shepherd DN, Martin DP, Varsani A (June 2012). "Molecular characterisation of a novel cassava associated circular ssDNA virus". Virus Research. 166 (1-2): 130–5. doi:10.1016/j.virusres.2012.03.009. PMID 22465471.
- Sikorski A, Massaro M, Kraberger S, Young LM, Smalley D, Martin DP, Varsani A (November 2013). "Novel myco-like DNA viruses discovered in the faecal matter of various animals". Virus Research. 177 (2): 209–16. doi:10.1016/j.virusres.2013.08.008. PMID 23994297.
- Varsani A, Krupovic M (July 2018). "Smacoviridae: a new family of animal-associated single-stranded DNA viruses". Archives of Virology. 163 (7): 2005–2015. doi:10.1007/s00705-018-3820-z. PMID 29572596.
- Phan TG, Mori D, Deng X, Rajindrajith S, Ranawaka U, Fan Ng TF, Bucardo-Rivera F, Orlandi P, Ahmed K, Delwart E (August 2015). "Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage". Virology. 482: 98–104. doi:10.1016/j.virol.2015.03.011. PMC . PMID 25839169.
- Castrignano SB, Nagasse-Sugahara TK, Kisielius JJ, Ueda-Ito M, Brandão PE, Curti SP (December 2013). "Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis". Virus Research. 178 (2): 364–73. doi:10.1016/j.virusres.2013.09.018. PMID 24055464.
- Cheung AK, Ng TF, Lager KM, Alt DP, Delwart EL, Pogranichniy RM (May 2014). "Identification of a novel single-stranded circular DNA virus in pig feces". Genome Announcements. 2 (2): e00347–14. doi:10.1128/genomeA.00347-14. PMID 24786952.
- Cui L, Wu B, Zhu X, Guo X, Ge Y, Zhao K, Qi X, Shi Z, Zhu F, Sun L, Zhou M (November 2017). "Identification and genetic characterization of a novel circular single-stranded DNA virus in a human upper respiratory tract sample". Archives of Virology. 162 (11): 3305–3312. doi:10.1007/s00705-017-3481-3. PMID 28707271.
- Sikorski A, Argüello-Astorga GR, Dayaram A, Dobson RC, Varsani A (January 2013). "Discovery of a novel circular single-stranded DNA virus from porcine faeces". Archives of Virology. 158 (1): 283–9. doi:10.1007/s00705-012-1470-0. PMID 22972681.
- Kim AR, Chung HC, Kim HK, Kim EO, Nguyen VG, Choi MG, Yang HJ, Kim JA, Park BK (February 2014). "Characterization of a complete genome of a circular single-stranded DNA virus from porcine stools in Korea". Virus Genes. 48 (1): 81–8. doi:10.1007/s11262-013-1003-2. PMID 24170425.
- Reuter G, Boros Á, Delwart E, Pankovics P (August 2014). "Novel circular single-stranded DNA virus from turkey faeces". Archives of Virology. 159 (8): 2161–4. doi:10.1007/s00705-014-2025-3. PMID 24562429.
- Cheung AK, Ng TF, Lager KM, Alt DP, Delwart E, Pogranichniy RM (January 2015). "Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces". Archives of Virology. 160 (1): 353–8. doi:10.1007/s00705-014-2234-9. PMID 25248627.
- Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Van Hemert C, Handel CM, Dumbacher JP (September 2015). "Isolation of a Complete Circular Virus Genome Sequence from an Alaskan Black-Capped Chickadee (Poecile atricapillus) Gastrointestinal Tract Sample". Genome Announcements. 3 (5): e01081–15. doi:10.1128/genomeA.01081-15. PMID 26404604.
- Sikorski A, Dayaram A, Varsani A (August 2013). "Identification of a Novel Circular DNA Virus in New Zealand Fur Seal (Arctocephalus forsteri) Fecal Matter". Genome Announcements. 1 (4): e00558–13. doi:10.1128/genomeA.00558-13. PMC . PMID 23929471.
- Cheung AK, Ng TF, Lager KM, Alt DP, Delwart EL, Pogranichniy RM (April 2014). "Unique circovirus-like genome detected in pig feces". Genome Announcements. 2 (2): e00251–14. doi:10.1128/genomeA.00251-14. PMID 24723710.
- Sikorski A, Kearvell J, Elkington S, Dayaram A, Argüello-Astorga GR, Varsani A (July 2013). "Novel ssDNA viruses discovered in yellow-crowned parakeet (Cyanoramphus auriceps) nesting material". Archives of Virology. 158 (7): 1603–7. doi:10.1007/s00705-013-1642-6. PMID 23417396.
- Yoon HS, Price DC, Stepanauskas R, Rajah VD, Sieracki ME, Wilson WH, Yang EC, Duffy S, Bhattacharya D (May 2011). "Single-cell genomics reveals organismal interactions in uncultivated marine protists". Science. 332 (6030): 714–7. Bibcode:2011Sci...332..714Y. doi:10.1126/science.1203163. PMID 21551060.
- Phan TG, Kapusinszky B, Wang C, Rose RK, Lipton HL, Delwart EL (September 2011). "The fecal viral flora of wild rodents". PLoS Pathogens. 7 (9): e1002218. doi:10.1371/journal.ppat.1002218. PMC . PMID 21909269.
- Ng TF, Manire C, Borrowman K, Langer T, Ehrhart L, Breitbart M (March 2009). "Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics". Journal of Virology. 83 (6): 2500–9. doi:10.1128/JVI.01946-08. PMC . PMID 19116258.
- 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
- Tijssen P, Bergoin M (1995). "Densonucleosis viruses constitute an increasingly diversified subfamily among the parvoviruses". Seminars in Virology. 6 (5): 347–355. doi:10.1006/smvy.1995.0041.
- Sukhumsirichart W, Attasart P, Boonsaeng V, Panyim S (March 2006). "Complete nucleotide sequence and genomic organization of hepatopancreatic parvovirus (HPV) of Penaeus monodon". Virology. 346 (2): 266–77. doi:10.1016/j.virol.2005.06.052. PMID 16356523.
- Pham HT, Bergoin M, Tijssen P (March 2013). "Acheta domesticus Volvovirus, a Novel Single-Stranded Circular DNA Virus of the House Cricket". Genome Announcements. 1 (2): e0007913. doi:10.1128/genomeA.00079-13. PMID 23516206.
- Pham HT, Iwao H, Bergoin M, Tijssen P (June 2013). "New Volvovirus Isolates from Acheta domesticus (Japan) and Gryllus assimilis (United States)". Genome Announcements. 1 (3): e00328–13. doi:10.1128/genomeA.00328-13. PMID 23792751.
- Dayaram A, Goldstien S, Zawar-Reza P, Gomez C, Harding JS, Varsani A (May 2013). "Novel ssDNA virus recovered from estuarine Mollusc (Amphibola crenata) whose replication associated protein (Rep) shares similarities with Rep-like sequences of bacterial origin". The Journal of General Virology. 94 (Pt 5): 1104–10. doi:10.1099/vir.0.050088-0. PMID 23364192.
- Wu B, Li Y, Yan H, Ma Y, Luo H, Yuan L, Chen S, Lu S (January 2012). "Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea". BMC Genomics. 13 (1): 15. doi:10.1186/1471-2164-3-15. PMC . PMID 22233149.
- Ng TF, Alavandi S, Varsani A, Burghart S, Breitbart M (September 2013). "Metagenomic identification of a nodavirus and a circular ssDNA virus in semi-purified viral nucleic acids from the hepatopancreas of healthy Farfantepenaeus duorarum shrimp". Diseases of Aquatic Organisms. 105 (3): 237–42. doi:10.3354/dao02628. PMID 23999707.
- Pham HT, Yu Q, Boisvert M, Van HT, Bergoin M, Tijssen P (January 2014). "A Circo-Like Virus Isolated from Penaeus monodon Shrimps". Genome Announcements. 2 (1): e01172–13. doi:10.1128/genomeA.01172-13. PMC . PMID 24435870.
- Jackson EW, Bistolas KS, Button JB, Hewson I (2016). "Novel Circular Single-Stranded DNA Viruses among an Asteroid, Echinoid and Holothurian (Phylum: Echinodermata)". PLOS One. 11 (11): e0166093. Bibcode:2016PLoSO..1166093J. doi:10.1371/journal.pone.0166093. PMC . PMID 27855181.
- Krenz B, Thompson JR, Fuchs M, Perry KL (July 2012). "Complete genome sequence of a new circular DNA virus from grapevine". Journal of Virology. 86 (14): 7715. doi:10.1128/JVI.00943-12. PMC . PMID 22733880.
- 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 (November 2014). "Preservation of viral genomes in 700-y-old caribou feces from a subarctic ice patch". Proceedings of the National Academy of Sciences of the United States of America. 111 (47): 16842–7. Bibcode:2014PNAS..11116842N. doi:10.1073/pnas.1410429111. PMC . PMID 25349412.
- Gronenborn B, Randles JW, Knierim D, Barrière Q, Vetten HJ, Warthmann N, Cornu D, Sileye T, Winter S, Timchenko T (April 2018). "Analysis of DNAs associated with coconut foliar decay disease implicates a unique single-stranded DNA virus representing a new taxon". Scientific Reports. 8 (1): 5698. Bibcode:2018NatSR...8.5698G. doi:10.1038/s41598-018-23739-y. PMC . PMID 29632309.
- Roux S, Enault F, Bronner G, Vaulot D, Forterre P, Krupovic M (2013). "Chimeric viruses blur the borders between the major groups of eukaryotic single-stranded DNA viruses". Nature Communications. 4: 2700. Bibcode:2013NatCo...4E2700R. doi:10.1038/ncomms3700. PMID 24193254.
- Tomaru Y, Toyoda K, Suzuki H, Nagumo T, Kimura K, Takao Y (November 2013). "New single-stranded DNA virus with a unique genomic structure that infects marine diatom Chaetoceros setoensis". Scientific Reports. 3: 3337. Bibcode:2013NatSR...3E3337T. doi:10.1038/srep03337. PMC . PMID 24275766.
- Laanto E, Mäntynen S, De Colibus L, Marjakangas J, Gillum A, Stuart DI, Ravantti JJ, Huiskonen JT, Sundberg LR (August 2017). "Virus found in a boreal lake links ssDNA and dsDNA viruses". Proceedings of the National Academy of Sciences of the United States of America. 114 (31): 8378–8383. doi:10.1073/pnas.1703834114. PMC . PMID 28716906.
- McGeoch DJ, Rixon FJ, Davison AJ (April 2006). "Topics in herpesvirus genomics and evolution". Virus Research. 117 (1): 90–104. doi:10.1016/j.virusres.2006.01.002. PMID 16490275.
- Davison AJ (June 2010). "Herpesvirus systematics". Veterinary Microbiology. 143 (1): 52–69. doi:10.1016/j.vetmic.2010.02.014. PMC . PMID 20346601.
- Grose C (September 2012). "Pangaea and the Out-of-Africa Model of Varicella-Zoster Virus Evolution and Phylogeography". Journal of Virology. 86 (18): 9558–65. doi:10.1128/JVI.00357-12. PMC . PMID 22761371.
- McGeoch DJ, Cook S, Dolan A, Jamieson FE, Telford EA (March 1995). "Molecular phylogeny and evolutionary timescale for the family of mammalian herpesviruses". Journal of Molecular Biology. 247 (3): 443–58. doi:10.1006/jmbi.1995.0152. PMID 7714900.
- McGeoch DJ, Cook S (April 1994). "Molecular phylogeny of the alphaherpesvirinae subfamily and a proposed evolutionary timescale". Journal of Molecular Biology. 238 (1): 9–22. doi:10.1006/jmbi.1994.1264. PMID 8145260.
- Davison AJ (April 2002). "Evolution of the herpesviruses". Veterinary Microbiology. 86 (1-2): 69–88. doi:10.1016/S0378-1135(01)00492-8. PMID 11888691.
- Koonin EV, Krupovic M, Yutin N (April 2015). "Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses". Annals of the New York Academy of Sciences. 1341: 10–24. Bibcode:2015NYASA1341...10K. doi:10.1111/nyas.12728. PMC . PMID 25727355.
- Baker ML, Jiang W, Rixon FJ, Chiu W (December 2005). "Common ancestry of herpesviruses and tailed DNA bacteriophages". Journal of Virology. 79 (23): 14967–70. doi:10.1128/JVI.79.23.14967-14970.2005. PMC . PMID 16282496.
- Krupovic M, Forterre P, Bamford DH (March 2010). "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 of Molecular Biology. 397 (1): 144–60. doi:10.1016/j.jmb.2010.01.037. PMID 20109464.
- 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 (May 2013). "Snapshot of haloarchaeal tailed virus genomes". RNA Biology. 10 (5): 803–16. doi:10.4161/rna.24045. PMC . PMID 23470522.
- Krupovic M, Bamford DH (December 2008). "Virus evolution: how far does the double beta-barrel viral lineage extend?". Nature Reviews. Microbiology. 6 (12): 941–8. doi:10.1038/nrmicro2033. PMID 19008892.
- Stasiak K, Demattei MV, Federici BA, Bigot Y (December 2000). "Phylogenetic position of the Diadromus pulchellus ascovirus DNA polymerase among viruses with large double-stranded DNA genomes". The Journal of General Virology. 81 (Pt 12): 3059–72. doi:10.1099/0022-1317-81-12-3059. PMID 11086137.
- Stasiak K, Renault S, Demattei MV, Bigot Y, Federici BA (November 2003). "Evidence for the evolution of ascoviruses from iridoviruses". The Journal of General Virology. 84 (Pt 11): 2999–3009. doi:10.1099/vir.0.19290-0. PMID 14573805.
- Federici BA, Bideshi DK, Tan Y, Spears T, Bigot Y (2009). "Ascoviruses: superb manipulators of apoptosis for viral replication and transmission". Current Topics in Microbiology and Immunology. Current Topics in Microbiology and Immunology. 328: 171–96. doi:10.1007/978-3-540-68618-7_5. ISBN 978-3-540-68617-0. PMID 19216438.
- Piégu B, Asgari S, Bideshi D, Federici BA, Bigot Y (March 2015). "Evolutionary relationships of iridoviruses and divergence of ascoviruses from invertebrate iridoviruses in the superfamily Megavirales". Molecular Phylogenetics and Evolution. 84: 44–52. doi:10.1016/j.ympev.2014.12.013. PMID 25562178.
- Chinchar VG, Waltzek TB, Subramaniam K (November 2017). "Ranaviruses and other members of the family Iridoviridae: Their place in the virosphere". Virology. 511: 259–271. doi:10.1016/j.virol.2017.06.007. PMID 28648249.
- Bigot Y, Renault S, Nicolas J, Moundras C, Demattei MV, Samain S, Bideshi DK, Federici BA (July 2009). "Symbiotic virus at the evolutionary intersection of three types of large DNA viruses; iridoviruses, ascoviruses, and ichnoviruses". PLOS One. 4 (7): e6397. Bibcode:2009PLoSO...4.6397B. doi:10.1371/journal.pone.0006397. PMC . PMID 19636425.
- Wilson WH, Van Etten JL, Allen MJ (2009). "The Phycodnaviridae: the story of how tiny giants rule the world". Current Topics in Microbiology and Immunology. Current Topics in Microbiology and Immunology. 328: 1–42. doi:10.1007/978-3-540-68618-7_1. ISBN 978-3-540-68617-0. PMC . PMID 19216434.
- Yutin N, Wolf YI, Koonin EV (October 2014). "Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life". Virology. 466-467: 38–52. doi:10.1016/j.virol.2014.06.032. PMC . PMID 25042053.
- Yutin N, Koonin EV (October 2013). "Pandoraviruses are highly derived phycodnaviruses". Biology Direct. 8: 25. doi:10.1186/1745-6150-8-25. PMID 24148757.
- Prangishvili D, Garrett RA (April 2004). "Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses". Biochemical Society Transactions. 32 (Pt 2): 204–8. doi:10.1042/BST0320204. PMID 15046572.
- Ogata H, Toyoda K, Tomaru Y, Nakayama N, Shirai Y, Claverie JM, Nagasaki K (October 2009). "Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus". Virology Journal. 6 (1): 178. doi:10.1186/1743-422X-6-178. PMC . PMID 19860921.
- Seligmann H (June 2018). "Giant viruses as protein-coated amoeban mitochondria?". Virus Research. 253: 77–86. doi:10.1016/j.virusres.2018.06.004. PMID 29913250.
- Benson SD, Bamford JK, Bamford DH, Burnett RM (September 1999). "Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures". Cell. 98 (6): 825–33. doi:10.1016/S0092-8674(00)81516-0. PMID 10499799.
- Thézé J, Bézier A, Periquet G, Drezen JM, Herniou EA (September 2011). "Paleozoic origin of insect large dsDNA viruses". Proceedings of the National Academy of Sciences of the United States of America. 108 (38): 15931–5. Bibcode:2011PNAS..10815931T. doi:10.1073/pnas.1105580108. PMC . PMID 21911395.
- Wang Y, Jehle JA (July 2009). "Nudiviruses and other large, double-stranded circular DNA viruses of invertebrates: new insights on an old topic". Journal of Invertebrate Pathology. 101 (3): 187–93. doi:10.1016/j.jip.2009.03.013. PMID 19460388.
- Jehle JA, Abd-Alla AM, Wang Y (March 2013). "Phylogeny and evolution of Hytrosaviridae". Journal of Invertebrate Pathology. 112 Suppl: S62–7. doi:10.1016/j.jip.2012.07.015. PMID 22841640.
- Wang Y, Bininda-Emonds OR, van Oers MM, Vlak JM, Jehle JA (June 2011). "The genome of Oryctes rhinoceros nudivirus provides novel insight into the evolution of nuclear arthropod-specific large circular double-stranded DNA viruses". Virus Genes. 42 (3): 444–56. doi:10.1007/s11262-011-0589-5. PMID 21380757.
- Bézier A, Annaheim M, Herbinière J, Wetterwald C, Gyapay G, Bernard-Samain S, Wincker P, Roditi I, Heller M, Belghazi M, Pfister-Wilhem R, Periquet G, Dupuy C, Huguet E, Volkoff AN, Lanzrein B, Drezen JM (February 2009). "Polydnaviruses of braconid wasps derive from an ancestral nudivirus". Science. 323 (5916): 926–30. Bibcode:2009Sci...323..926B. doi:10.1126/science.1166788. PMID 19213916.
- Keller J, Leulliot N, Cambillau C, Campanacci V, Porciero S, Prangishvili D, Forterre P, Cortez D, Quevillon-Cheruel S, van Tilbeurgh H (January 2007). "Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses". Virology Journal. 4: 12. doi:10.1186/1743-422X-4-12. PMC . PMID 17241456.
- Knopf CW (1998). "Evolution of viral DNA-dependent DNA polymerases". Virus Genes. 16 (1): 47–58. doi:10.1023/A:1007997609122. PMID 9562890.
- Villarreal LP, DeFilippis VR (August 2000). "A hypothesis for DNA viruses as the origin of eukaryotic replication proteins". Journal of Virology. 74 (15): 7079–84. doi:10.1128/JVI.74.15.7079-7084.2000. PMC . PMID 10888648.
- Zillig W, Prangishvilli D, Schleper C, Elferink M, Holz I, Albers S, Janekovic D, Götz D (May 1996). "Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea". FEMS Microbiology Reviews. 18 (2-3): 225–36. doi:10.1111/j.1574-6976.1996.tb00239.x. PMID 8639330.
- Shutt TE, Gray MW (February 2006). "Bacteriophage origins of mitochondrial replication and transcription proteins". Trends in Genetics. 22 (2): 90–5. doi:10.1016/j.tig.2005.11.007. PMID 16364493.
- Yutin N, Raoult D, Koonin EV (May 2013). "Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies". Virology Journal. 10: 158. doi:10.1186/1743-422X-10-158. PMC . PMID 23701946.
- Delwart E, Li L (March 2012). "Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes". Virus Research. 164 (1-2): 114–21. doi:10.1016/j.virusres.2011.11.021. PMC . PMID 22155583.
- Ilyina TV, Koonin EV (July 1992). "Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria". Nucleic Acids Research. 20 (13): 3279–85. doi:10.1093/nar/20.13.3279. PMC . PMID 1630899.
- Krupovic M (October 2012). "Recombination between RNA viruses and plasmids might have played a central role in the origin and evolution of small DNA viruses". BioEssays. 34 (10): 867–70. doi:10.1002/bies.201200083. PMID 22886750.
- Krupovic M (October 2013). "Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses". Current Opinion in Virology. 3 (5): 578–86. doi:10.1016/j.coviro.2013.06.010. PMID 23850154.
- Gibbs MJ, Weiller GF (July 1999). "Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus". Proceedings of the National Academy of Sciences of the United States of America. 96 (14): 8022–7. Bibcode:1999PNAS...96.8022G. doi:10.1073/pnas.96.14.8022. PMC . PMID 10393941.
- Meehan BM, Creelan JL, McNulty MS, Todd D (January 1997). "Sequence of porcine circovirus DNA: affinities with plant circoviruses". The Journal of General Virology. 78 ( Pt 1) (Pt 1): 221–7. doi:10.1099/0022-1317-78-1-221. PMID 9010307.
- Niagro FD, Forsthoefel AN, Lawther RP, Kamalanathan L, Ritchie BW, Latimer KS, Lukert PD (1998). "Beak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses". Archives of Virology. 143 (9): 1723–44. doi:10.1007/s007050050412. PMID 9787657.
- Xie Y, Wu P, Liu P, Gong H, Zhou X (August 2010). "Characterization of alphasatellites associated with monopartite begomovirus/betasatellite complexes in Yunnan, China". Virology Journal. 7 (1): 178. doi:10.1186/1743-422X-7-178. PMC . PMID 20678232.
- Krupovic M, Ravantti JJ, Bamford DH (May 2009). "Geminiviruses: a tale of a plasmid becoming a virus". BMC Evolutionary Biology. 9: 112. doi:10.1186/1471-2148-9-112. PMC . PMID 19460138.
- Gronenborn B (February 2004). "Nanoviruses: genome organisation and protein function". Veterinary Microbiology. 98 (2): 103–9. doi:10.1016/j.vetmic.2003.10.015. PMID 14741122.
- Bernardo P, Golden M, Akram M, Nadarajan N, Fernandez E, Granier M, Rebelo AG, Peterschmitt M, Martin DP, Roumagnac P (October 2013). "Identification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implications". Virus Research. 177 (1): 35–45. doi:10.1016/j.virusres.2013.07.006. PMID 23886668.
- Belyi VA, Levine AJ, Skalka AM (December 2010). "Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the parvoviridae and circoviridae are more than 40 to 50 million years old". Journal of Virology. 84 (23): 12458–62. doi:10.1128/JVI.01789-10. PMC . PMID 20861255.
- Liu H, Fu Y, Xie J, Cheng J, Ghabrial SA, Li G, Peng Y, Yi X, Jiang D (October 2011). "Widespread endogenization of densoviruses and parvoviruses in animal and human genomes". Journal of Virology. 85 (19): 9863–76. doi:10.1128/JVI.00828-11. PMC . PMID 21795360.
- Krupovic M, Koonin EV (June 2014). "Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses". Scientific Reports. 4: 5347. Bibcode:2014NatSR...4E5347K. doi:10.1038/srep05347. PMC . PMID 24939392.
- Ackermann HW, Prangishvili D (October 2012). "Prokaryote viruses studied by electron microscopy". Archives of Virology. 157 (10): 1843–9. doi:10.1007/s00705-012-1383-y. PMID 22752841.
- Ackermann HW (May 2003). "Bacteriophage observations and evolution". Research in Microbiology. 154 (4): 245–51. doi:10.1016/S0923-2508(03)00067-6. PMID 12798228.
- Ackermann HW (1998). "Tailed bacteriophages: the order caudovirales". Advances in Virus Research. Advances in Virus Research. 51: 135–201. doi:10.1016/S0065-3527(08)60785-X. ISBN 9780120398515. PMID 9891587.
- Erdmann S, Tschitschko B, Zhong L, Raftery MJ, Cavicchioli R (October 2017). "A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells". Nature Microbiology. 2 (10): 1446–1455. doi:10.1038/s41564-017-0009-2. PMID 28827601.
- Iyer LM, Balaji S, Koonin EV, Aravind L (April 2006). "Evolutionary genomics of nucleo-cytoplasmic large DNA viruses". Virus Research. 117 (1): 156–84. doi:10.1016/j.virusres.2006.01.009. PMID 16494962.
- Yutin N, Wolf YI, Raoult D, Koonin EV (December 2009). "Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution". Virology Journal. 6: 223. doi:10.1186/1743-422X-6-223. PMC . PMID 20017929.
- Yutin N, Koonin EV (August 2012). "Hidden evolutionary complexity of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes". Virology Journal. 9: 161. doi:10.1186/1743-422X-9-161. PMC . PMID 22891861.
- Krupovic M, Koonin EV (February 2015). "Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution". Nature Reviews. Microbiology. 13 (2): 105–15. doi:10.1038/nrmicro3389. PMC . PMID 25534808.
- Krupovic M, Bamford DH, Koonin EV (April 2014). "Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses". Biology Direct. 9: 6. doi:10.1186/1745-6150-9-6. PMC . PMID 24773695.
- Pennisi E (July 2013). "Microbiology. Ever-bigger viruses shake tree of life". Science. 341 (6143): 226–7. doi:10.1126/science.341.6143.226. PMID 23868995.
- 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 (March 2014). "Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology". Proceedings of the National Academy of Sciences of the United States of America. 111 (11): 4274–9. Bibcode:2014PNAS..111.4274L. doi:10.1073/pnas.1320670111. PMC . PMID 24591590.
- Andreani J, Aherfi S, Bou Khalil JY, Di Pinto F, Bitam I, Raoult D, Colson P, La Scola B (November 2016). "Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses". Viruses. 8 (11): 300. doi:10.3390/v8110300. PMC . PMID 27827884.
- Fauquent CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005-05-27). "8th Reports of the International Committee on Taxonomy of Viruses". Academic Press. US National Center for Biotechnology Information, National Library for Medicine, National Institutes of Health.
- "ICTV Online (10th) Report Now Available". International Committee on Taxonomy of Viruses.