DNA virus
Encyclopedia
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.
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 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.
Order
s within this group are defined on the basis of morphology rather than DNA sequence similarity. It is thought that morphology is more conserved in this group than sequence similarity or gene order which is extremely variable. Three orders and 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.
Bacteriophage
s 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 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 vertebrate
s.
Species of the families Ascovirus, Baculovirus, Hytrosaviridae, Iridoviridae and Polydnaviruses and of the genus Nudivirus infect insect
s.
Species of the families Marseilleviridae, Megaviridae and Mimiviridae and the species Mavirus virophage and Sputnik virophage infect protozoa
.
Species of the family Nimaviridae infect crustacean
s.
Species of the family Phycodnaviridae and the species Organic Lake virophage infect algae
. These are the only known dsDNA viruses that infect plant
s.
Species of the family Plasmaviridae infect species of the class Mollicutes
.
Species of the genus Dinodnavirus infect dinoflagellate
s. These are the only known viruses that infect dinoflagellate
s.
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
.
, terrestrial, extreme, metazoan-associated and marine microbial mats. 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 mammal
s, fish
es, bird
s, tunicate
s, arthropod
s and flatworm
s. In particular they have been associated with the human genome for ~98 million years.
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 animal
s (mammal
s and bird
s respectively); and the Geminiviridae and Nanoviridae infect plant
s. In both the Geminiviridae and Nanoviridae the genome is composed of more than a single chromosome. The Bacillariodnaviridae infect diatom
s and have a unique genome: the major chromosome is circular (~6 kilobases in length): the minor chromosome is linear (~1 kilobase in length) and complementary to part of the major chromosome.
to date. Their closest relations appear to be the Brevidensoviruses.
Another new genus - as yet unnamed - has been recognised. 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.
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.
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.
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.
An unusual virus has been isolated from the flatwom Girardia tigrina. Because of its genome organisation, this virus appears to belong to an entirely new family. This virus is the first to be isolated from a flatworm.
s 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.
It is probable that these viruses evolved before the separation of eukaryoyes into the extant crown groups. The ancestral genome was complex with at least 41 genes including (1) the replication machinery (2) up to four RNA polymerase
subunits (3) at least three transcription factor
s (4) capping and polyadenylation enzymes (5) the DNA packaging apparatus (6) and structural components of an icosahedral capsid and the viral membrane.
The families Adenoviridae and Tectiviridae appear to be related structurally.
Based on the genome organisation and DNA replication mechanism it seems that phylogenetic relationships may exist between the rudiviruses and the large eukaryal DNA viruses: poxviruses (Poxviridae), the African swine fever virus (Asfarviridae) and Chlorella viruses (Phycodnaviridae).
The nucleocytoplasmic large DNA virus group (Asfarviridae, Iridoviridae, Marseilleviridae, Mimiviridae, Phycodnaviridae and Poxviridae) along with the families Adenoviridae, the Cortiviridae, the Tectiviridae, 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.
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 possibly 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 posses 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 mammalian herpesviruses (Herpesviridae), fish lymphocystis disease virus (Iridoviridae), insect ascovirus (Ascoviridae) and chlorella virus (Phycoviridae). The pol genes of the T-even bacteriophages (Myoviridae), poxviruses (Poxviridae), African swine fever virus (Ascoviridae), fish herpesvirus (Herpesviridae) and baculoviruses (Baculoviridae) were not clearly resolved. A second study showed that poxvirus, baculovirus and the animal herpesviruses form separate and distinct clades. 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 eukaryote
s. 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.
Nudiviruses are regarded as a sister clade to the Baculoviruses.
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
that has DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
as its genetic material and replicates using a DNA-dependent DNA polymerase
DNA polymerase
A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....
. The nucleic acid
Nucleic acid
Nucleic acids are biological molecules essential for life, and include DNA and RNA . Together with proteins, nucleic acids make up the most important macromolecules; each is found in abundance in all living things, where they function in encoding, transmitting and expressing genetic information...
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
Baltimore classification
The Baltimore classification, developed by David Baltimore, is a virus classification system that groups viruses into families, depending on their type of genome and their method of replication....
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.
Group I: dsDNA viruses
GenomeGenome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
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 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.
Order
Order
-Ordinality:*Collation, the sequencing and ordering of text**Alphabetical order**Lexicographical order*Order of precedence-Philosophy:* Natural order * Implicate and explicate order according to David Bohm-Science and mathematics:...
s within this group are defined on the basis of morphology rather than DNA sequence similarity. It is thought that morphology is more conserved in this group than sequence similarity or gene order which is extremely variable. Three orders and 33 families
Family (biology)
In biological classification, family is* a taxonomic rank. Other well-known ranks are life, domain, kingdom, phylum, class, order, genus, and species, with family fitting between order and genus. As for the other well-known ranks, there is the option of an immediately lower rank, indicated by the...
are currently recognised. Four genera
Genus
In biology, a genus is a low-level taxonomic rank used in the biological classification of living and fossil organisms, which is an example of definition by genus and differentia...
are recognised that have not yet been assigned a family. The species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
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.
Bacteriophage
Bacteriophage
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid...
s belonging to the families Tectiviridae and Corticoviridae have a lipid bilayer inside the icosahedral protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
capsid and the membrane
Membrane
-In biology:* Biological membrane* Cell membrane, a biological type of Membrane ** Inner membrane** Outer membrane * The two fetal membranes** amnion** chorion* Basement membrane* Mucous membrane* Serous 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 bacteriaBacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
.
Species of the order Ligamenvirales and the families Ampullaviridae, Bacilloviridae, Bicaudaviridae, Clavaviridae, Fuselloviridae, Globuloviridae and Guttaviridae infect hyperthermophilic archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
species of the Crenarchaeota
Crenarchaeota
In taxonomy, the Crenarchaeota has been classified as either a phylum of the Archaea kingdom or a kingdom of its own...
.
Species of the order Herpesvirales and of the families Adenoviridae, Asfarviridae, Iridoviridae, Papillomaviridae, Polyomaviridae and Poxviridae infect vertebrate
Vertebrate
Vertebrates are animals that are members of the subphylum Vertebrata . Vertebrates are the largest group of chordates, with currently about 58,000 species described. Vertebrates include the jawless fishes, bony fishes, sharks and rays, amphibians, reptiles, mammals, and birds...
s.
Species of the families Ascovirus, Baculovirus, Hytrosaviridae, Iridoviridae and Polydnaviruses and of the genus Nudivirus infect insect
Insect
Insects are a class of living creatures within the arthropods that have a chitinous exoskeleton, a three-part body , three pairs of jointed legs, compound eyes, and two antennae...
s.
Species of the families Marseilleviridae, Megaviridae and Mimiviridae and the species Mavirus virophage and Sputnik virophage infect protozoa
Protozoa
Protozoa are a diverse group of single-cells eukaryotic organisms, many of which are motile. Throughout history, protozoa have been defined as single-cell protists with animal-like behavior, e.g., movement...
.
Species of the family Nimaviridae infect crustacean
Crustacean
Crustaceans form a very large group of arthropods, usually treated as a subphylum, which includes such familiar animals as crabs, lobsters, crayfish, shrimp, krill and barnacles. The 50,000 described species range in size from Stygotantulus stocki at , to the Japanese spider crab with a leg span...
s.
Species of the family Phycodnaviridae and the species Organic Lake virophage infect algae
Algae
Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms, such as the giant kelps that grow to 65 meters in length. They are photosynthetic like plants, and "simple" because their tissues are not organized into the many...
. These are the only known dsDNA viruses that infect plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
s.
Species of the family Plasmaviridae infect species of the class Mollicutes
Mollicutes
The Mollicutes are a class of bacteria distinguished by the absence of a cell wall. The word "Mollicutes" is derived from the Latin mollis , and cutis . They are parasites of various animals and plants, living on or in the host's cells. Individuals are very small, typically only 0.2–0.3 μm in size...
.
Species of the genus Dinodnavirus infect dinoflagellate
Dinoflagellate
The dinoflagellates are a large group of flagellate protists. Most are marine plankton, but they are common in fresh water habitats as well. Their populations are distributed depending on temperature, salinity, or depth...
s. These are the only known viruses that infect dinoflagellate
Dinoflagellate
The dinoflagellates are a large group of flagellate protists. Most are marine plankton, but they are common in fresh water habitats as well. Their populations are distributed depending on temperature, salinity, or depth...
s.
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
Euryarchaeota
In the taxonomy of microorganisms, the Euryarchaeota are a phylum of the Archaea.The Euryarchaeota include the methanogens, which produce methane and are often found in intestines, the halobacteria, which survive extreme concentrations of salt, and some extremely thermophilic aerobes and anaerobes...
.
Taxonomy
- Order CaudoviralesCaudoviralesThe Caudovirales are an order of viruses also known as the tailed bacteriophages. Under the Baltimore classification scheme, the Caudovirales are group I viruses as they have double stranded DNA genomes, which can be anywhere from 18,000 base pairs to 500,000 base pairs in length...
- Family MyoviridaeMyoviridaeThe Myoviridae is a family of bacteriophages. It has been divided into three subfamiles and a number of genera not yet assigned to a subfamily. There are at least 130 species in this family.-Virology:...
- includes Enterobacteria phage T4Enterobacteria phage T4Enterobacteria phage T4 is a bacteriophage that infects E. coli bacteria. Its DNA is 169–170 kbp long, and is held in an icosahedral head. T4 is a relatively large phage, at approximately 90 nm wide and 200 nm long... - Family PodoviridaePodoviridaeThe Podoviridae are a family of bacteriophages. Unlike the other families of tailed viruses this family has short tails that are non contractile.There are at least 74 species in this family.-Virology:...
- includes Enterobacteria phage T7 - Family SiphoviridaeSiphoviridaeSiphoviridae are a family of double-stranded DNA viruses infecting only bacteria. The characteristic features of this family is the presence of a head and non contractile tail.There are at least 256 species in this family.-Virology:...
- includes Enterobacteria phage λ
- Family Myoviridae
- Order HerpesviralesHerpesviralesThe Herpesvirales is an order of viruses all sharing the same overall morphology.-Virology:All herpes viruses have a capsid structure that consists of a DNA core surrounded by an icosahedral capsid consisting of 12 pentavalent and 150 hexavalent capsomeres...
- Family AlloherpesviridaeAlloherpesviridaeAlloherpesviridae is a family of viruses within the order Herpesvirales. This family includes the species that infect fish and amphibians...
- Family HerpesviridaeHerpesviridaeThe Herpesviridae are a large family of DNA viruses that cause diseases in animals, including humans. The members of this family are also known as herpesviruses. The family name is derived from the Greek word herpein , referring to the latent, recurring infections typical of this group of viruses...
- includes human herpesviruses, Varicella Zoster virus - Family MalacoherpesviridaeMalacoherpesviridaeThe Malacoherpesviridae are a family of DNA viruses that cause diseases in molluscs.The family name Malacoherpesviridae is derived from Greek word 'μαλακός meaning 'soft' and from Greek word 'μαλάκιον meaning 'mollusc....
- Family Alloherpesviridae
- Order LigamenviralesLigamenviralesLigamenvirales is an order of viruses that infect archaea of the kingdom Crenarchaeota and have double stranded DNA genomes.The name is derived from the Latin word ligamen meaning 'string' or 'thread'.-Taxonomy:...
- Family LipothrixviridaeLipothrixviridaeThe Lipothrixviridae family consists of a family of viruses that infect archaea.-Taxonomy:These viruses share characteristics from the Rudiviridae family and both have are filamentous viruses with linear dsDNA genomes that infect thermophilic archaea in the kingdom Crenarchaeota.There are four...
- Family Rudiviridae
- Family Lipothrixviridae
- Unassigned families
- Family Ascoviridae
- Family AdenoviridaeAdenoviridaeAdenoviruses are medium-sized , nonenveloped icosahedral viruses composed of a nucleocapsid and a double-stranded linear DNA genome...
- includes viruses which cause human adenovirus infectionAdenovirus infectionAdenovirus infections most commonly cause illness of the respiratory system; however, depending on the infecting serotype, they may also cause various other illnesses and presentations.-Resultant illnesses and presentations:... - Family AmpullaviridaeAmpullaviridaeAmpullaviridae is a family of viruses that infect archaea. Only one genus in this family has been described. Only one species within this genus is known .-History:...
- Family AsfarviridaeAsfarviridaeAsfarviridae is a family of viruses that primarily infects swine, resulting in an onset of African swine fever. There is a single genus in this family: Asfivirus. The name of this family and genus are derived from the acronym: African swine fever and related viruses...
- includes African swine fever virusAfrican swine fever virusAfrican swine fever virus is the causative agent of African swine fever . ASFV is a large, double-stranded DNA virus which replicates in the cytoplasm of infected cells, and is the only member of the Asfarviridae family. ASFV infects domestic pigs, warthogs and bushpigs, as well as soft ticks ,... - Family BacilloviridaeBacilloviridaeThe Bacilloviridae are a family of double stranded DNA viruses that infect species belonging to the archaeal genera Sulfolobus and Thermoproteus.-Virology:...
- Family Baculoviridae
- Family BicaudaviridaeBicaudaviridaeBicaudaviridae is a family of viruses. This family currently has a single genus . This genus has a two known species - Acidianus two-tailed virus and Sulfolobus virus STSV1.-History:This family was first described in 2005....
- Family ClavaviridaeClavaviridaeClavaviridae is a family of double stranded viruses that archaea. There is one genus in this family . Within this genus only a single species has been described to date.The name is derived from the Latin word clava meaning stick....
- Family Corticoviridae
- Family Fuselloviridae
- Family GlobuloviridaeGlobuloviridaeGlobuloviridae is a family of dsDNA virus, which infects Pyrobaculum and Thermoproteus Archaea.The name is derived from the Latin word globulus meaning a 'small ball'.-Virology:The virons are enveloped and ~100 nanometers in diameter...
- Family Guttaviridae
- Family HytrosaviridaeHytrosaviridaeHytrosaviridae is a family of double stranded DNA viruses that infect infect insects. The name is derived from Hytrosa, sigla from the Greek Hypertrophia for 'hypertrophy' and 'sialoadenitis' for 'salivary gland inflammation.'-Description:...
- Family IridoviridaeIridoviridaeIridoviridae are a family of viruses with double stranded DNA genomes. The name is derived from Iris the Greek goddess of the rainbow. This name was chosen because of the "rainbow like" iridescence observed in heavily infected insects and pelleted samples of invertebrate iridoviruses.-Taxonomy:The...
- Family MarseilleviridaeMarseilleviridaeMarseilleviridae is a family of double stranded DNA viruses. It is a member of the nucleocytoplasmic large DNA viruses clade.-Taxonomy:There is one genus in this family and one species within this genus currently recognised. It was originally grouped with the Mimivirus but subsequent studies...
- Family Megaviridae
- Family MimiviridaeMimiviridaeMimiviridae is a family of double stranded DNA viruses. Viruses in this family belong to the nucleocytoplasmic large DNA virus clade , a group which includes members of families Asfarviridae, Iridoviridae, Phycodnaviridae and Poxviridae and the genus Dinodnavirus.-Taxonomy:Although only a few...
- Family Nimaviridae
- Family PapillomaviridaePapillomaviridaePapillomaviridae is an ancient taxonomic family of non-enveloped DNA viruses, collectively known as papillomaviruses. Several hundred species of papillomaviruses, traditionally referred to as "types", have been identified infecting all carefully inspected birds and mammals, but also a small number...
- Family PhycodnaviridaePhycodnaviridaePhycodnaviruses are large , double stranded DNA viruses that infect marine or freshwater eukaryotic algae...
- Family Plasmaviridae
- Family Polydnaviruses
- Family Polyomaviridae - includes Simian virus 40SV40SV40 is an abbreviation for Simian vacuolating virus 40 or Simian virus 40, a polyomavirus that is found in both monkeys and humans...
, JC virusJC virusThe JC virus or John Cunningham virus is a type of human polyomavirus and is genetically similar to BK virus and SV40. It was discovered in 1971 and named using the two initials of a patient with progressive multifocal leukoencephalopathy...
, BK virusBK virusThe BK virus is a member of the polyomavirus family. Past infection with the BK virus is widespread, but significant consequences of infection are uncommon, with the exception of the immunocompromised and the immunosuppressed.-History:... - Family PoxviridaePoxviridaePoxviruses are viruses that can, as a family, infect both vertebrate and invertebrate animals.Four genera of poxviruses may infect humans: orthopox, parapox, yatapox, molluscipox....
- includes CowpoxCowpoxCowpox is a skin disease caused by a virus known as the Cowpox virus. The pox is related to the vaccinia virus and got its name from the distribution of the disease when dairymaids touched the udders of infected cows. The ailment manifests itself in the form of red blisters and is transmitted by...
virus, smallpoxSmallpoxSmallpox was an infectious disease unique to humans, caused by either of two virus variants, Variola major and Variola minor. The disease is also known by the Latin names Variola or Variola vera, which is a derivative of the Latin varius, meaning "spotted", or varus, meaning "pimple"... - Family Tectiviridae
- Unassigned genera
- DinodnavirusDinodnavirusDinodnavirus is a genus of viruses that infect dinoflagellates. This genus belongs to the clade of nucleocytoplasmic large DNA viruses. The name is derived from 'di' and DNA ....
- NudivirusNudivirusNudiviruses are large and rod-shaped viruses with a circular, double stranded DNA genome. They are related to the baculoviruses and like these infect arthropods, particularly insects . They share 20 core genes with baculoviruses...
- SalterprovirusSalterprovirusThe Salterprovirus is a genus of viruses that infect extremely halophilic archaea. The genus name is derived from salt terminal protein virus, as their linear dsDNA genomes have proteins attached to the 5' termini...
- RhizidiovirusRhizidiovirusThe Rhizidiovirus genus consists of dsDNA viruses that infect stramenopiles.-Virology:The viron is non enveloped, isosahedral with a diameter of 60 nanometers ....
- Dinodnavirus
- Unassigned species
- KIs-VKIs-VKIs-V is a DNA virus isolated from four human cases of acute hepatitis. The genome has a sequence of 9496 bases and 13 potential genes. The virus is 30-50 nanometers in diameter and is enveloped....
- Haloarcula hispanica pleomorphic virus 1
- Haloarcula hispanica SH1 virus
- Mavirus virophageMavirus virophageMavirus virophage is a double stranded DNA virus that infects the marine phagotropic flagellate Cafeteria roenbergensis in the presence of a second virus - Cafeteria roenbergensis virus.The name is derived from Maverick virus....
- Organic Lake virophageOrganic Lake virophageOrganic Lake virophage is a double stranded DNA virophage...
- Sputnik virophageSputnik virophageSputnik virophage is a subviral agent that reproduces in amoeba cells that are already infected by a certain helper virus; Sputnik uses the helper virus's machinery for reproduction and inhibits replication of the helper virus.Viruses like Sputnik that depend on co-infection of the host cell by...
- Sulfolobus turreted icosahedral virusSulfolobus turreted icosahedral virusSulfolobus turreted icosahedral virus is a virus that infects the archaeon Sulfolobus solfataricus.-History:This virus was isolated from a hot spring in the in the Rabbit Creek thermal area which is located in the Midway Geyser Basin of Yellowstone National Park.-Virology:It is an icosahedrally...
- Thermus thermophilus virus P23-77
- KIs-V
Group II: ssDNA viruses
Although bacteriophages were first described in 1927, it was only in 1959 that Sinshemer working with the phage X174 showed that they could posses 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, sedimentSediment
Sediment is naturally occurring material that is broken down by processes of weathering and erosion, and is subsequently transported by the action of fluids such as wind, water, or ice, and/or by the force of gravity acting on the particle itself....
, terrestrial, extreme, metazoan-associated and marine microbial mats. 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
DNA polymerase
A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....
.
The evolutionary history of this group is currently poorly understood. However the parvoviruses have frequently invaded the germ lines of diverse animal species including mammal
Mammal
Mammals are members of a class of air-breathing vertebrate animals characterised by the possession of endothermy, hair, three middle ear bones, and mammary glands functional in mothers with young...
s, fish
Fish
Fish are a paraphyletic group of organisms that consist of all gill-bearing aquatic vertebrate animals that lack limbs with digits. Included in this definition are the living hagfish, lampreys, and cartilaginous and bony fish, as well as various extinct related groups...
es, bird
Bird
Birds are feathered, winged, bipedal, endothermic , egg-laying, vertebrate animals. Around 10,000 living species and 188 families makes them the most speciose class of tetrapod vertebrates. They inhabit ecosystems across the globe, from the Arctic to the Antarctic. Extant birds range in size from...
s, tunicate
Tunicate
Tunicates, also known as urochordates, are members of the subphylum Tunicata, previously known as Urochordata, a group of underwater saclike filter feeders with incurrent and excurrent siphons that is classified within the phylum Chordata. While most tunicates live on the ocean floor, others such...
s, arthropod
Arthropod
An arthropod is an invertebrate animal having an exoskeleton , a segmented body, and jointed appendages. Arthropods are members of the phylum Arthropoda , and include the insects, arachnids, crustaceans, and others...
s and flatworm
Flatworm
The flatworms, known in scientific literature as Platyhelminthes or Plathelminthes are a phylum of relatively simple bilaterian, unsegmented, soft-bodied invertebrate animals...
s. 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. 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
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
; the Anelloviridae and Circoviridae infect animal
Animal
Animals are a major group of multicellular, eukaryotic organisms of the kingdom Animalia or Metazoa. Their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later on in their life. Most animals are motile, meaning they can move spontaneously and...
s (mammal
Mammal
Mammals are members of a class of air-breathing vertebrate animals characterised by the possession of endothermy, hair, three middle ear bones, and mammary glands functional in mothers with young...
s and bird
Bird
Birds are feathered, winged, bipedal, endothermic , egg-laying, vertebrate animals. Around 10,000 living species and 188 families makes them the most speciose class of tetrapod vertebrates. They inhabit ecosystems across the globe, from the Arctic to the Antarctic. Extant birds range in size from...
s respectively); and the Geminiviridae and Nanoviridae infect plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
s. In both the Geminiviridae and Nanoviridae the genome is composed of more than a single chromosome. The Bacillariodnaviridae infect diatom
Diatom
Diatoms are a major group of algae, and are one of the most common types of phytoplankton. Most diatoms are unicellular, although they can exist as colonies in the shape of filaments or ribbons , fans , zigzags , or stellate colonies . Diatoms are producers within the food chain...
s and have a unique genome: the major chromosome is circular (~6 kilobases in length): the minor chromosome is linear (~1 kilobase in length) and complementary to part of the major chromosome.
Taxonomy
-
- Family Anelloviridae
- Family BacillariodnaviridaeBacillariodnaviridaeBacillariodnaviridae is a family of single straned DNA viruses that infect diatoms. The family has only a single genus at present - Bacilladnavirus-Description:...
- Family CircoviridaeCircoviridaeThe Circoviridae are a family of viruses. These are small, relatively poorly-studied viruses, with circular, single-stranded DNA genomes of approximately one to four kilobases-Virology:...
- Family GeminiviridaeGeminiviridaeGeminiviruses are plant viruses which have single-stranded circular DNA genomes encoding genes that diverge in both directions from a virion strand origin of replication . According to the Baltimore classification they are considered class II viruses...
- Family InoviridaeInoviridaeThe Inoviridae are a family of filamentous bacteriophages. The name of the family is derived from the Greek word 'nos' meaning 'muscle'.-Virology:...
- Family MicroviridaeMicroviridaeThe Microviridae are a family of bacteriophages with a single stranded DNA genome. The name of this family is derived from the Greek word 'micro' meaning small. This refers to the size of their genomes which are among the smallest of the DNA viruses....
- Family NanoviridaeNanoviridaeThe Nanoviridae are a family of viruses, including the following genera:*Genus Nanovirus; type species: Subterranean clover stunt virus*Genus Babuvirus; type species: Banana bunchy top virus-Virus structure and genome:...
- Family ParvoviridaeParvoviridaeThe Parvoviridae family includes the smallest known viruses, and some of the most environmentally resistant. They were discovered during the 1960s and affect vertebrates and insects...
- includes Parvovirus B19Parvovirus B19The B19 virus, generally referred to as parvovirus B19 or sometimes erythrovirus B19, was the first known human virus in the family of parvoviruses, genus erythrovirus...
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 ICTVICTV
ICTV can stand for*International Committee on Taxonomy of Viruses, a taxonomic organisation and the nomenclature code it produces*ICTV , a content distribution network for delivering the web-media experience through television...
to date. Their closest relations appear to be the Brevidensoviruses.
Another new genus - as yet unnamed - has been recognised. 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.
A virus with a circular genome - sea turtle tornovirus 1
Sea turtle tornovirus 1
Sea turtle tornovirus 1 is a single stranded DNA virus that was isolated from a turtle with fibropapillomatosis in 2009.-Virology:The genome is circular and ~1.8 kilobases in length with a G+C content of ~50%. It has at least three open reading frames and two others may also be present...
- has been isolated from a sea turtle with fibropapillomatosis
Fibropapillomatosis
Fibropapillomatosis is a condition characterized by the presence of fibropapillomas, neoplasms consisting of both the epidermal and dermal skin layers.-In sea turtles:...
. 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.
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.
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.
An unusual virus has been isolated from the flatwom Girardia tigrina. Because of its genome organisation, this virus appears to belong to an entirely new family. This virus is the first to be isolated from a flatworm.
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 alphasatelliteAlphasatellite
Alphasatellites are single stranded viruses that are dependent on another virus for transmission. The genome is a single circular single strand DNA molecule. The first alphasatellites were described in 1999 and were associated with cotton leaf curl disease and Ageratum yellow vein disease...
s 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
Begomovirus
The genus Begomovirus contains more than 200 species and belongs to the taxonomic family Geminiviridae. They are plant viruses that as a group have a very wide host range, infecting dicotyledonous plants...
for transmission. Betasatellites are small linear single stranded DNA viruses that require a begomovirus to replicate.
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
RNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
subunits (3) at least three transcription factor
Transcription factor
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
s (4) capping and polyadenylation enzymes (5) the DNA packaging apparatus (6) and structural components of an icosahedral capsid and the viral membrane.
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.Phylogenetic relationships
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.The families Adenoviridae and Tectiviridae appear to be related structurally.
Based on the genome organisation and DNA replication mechanism it seems that phylogenetic relationships may exist between the rudiviruses and the large eukaryal DNA viruses: poxviruses (Poxviridae), the African swine fever virus (Asfarviridae) and Chlorella viruses (Phycodnaviridae).
The nucleocytoplasmic large DNA virus group (Asfarviridae, Iridoviridae, Marseilleviridae, Mimiviridae, Phycodnaviridae and Poxviridae) along with the families Adenoviridae, the Cortiviridae, the Tectiviridae, 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.
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 possibly suggesting a common origin.
Examination of the pol genes that encode the DNA dependent DNA polymerase
DNA polymerase
A DNA polymerase is an enzyme that helps catalyze in the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best known for their feedback role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand....
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 posses a 3'-5'-exonuclease
Exonuclease
Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3’ or the 5’ end occurs. Its close relative is the endonuclease, which cleaves phosphodiester bonds in the middle ...
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 mammalian herpesviruses (Herpesviridae), fish lymphocystis disease virus (Iridoviridae), insect ascovirus (Ascoviridae) and chlorella virus (Phycoviridae). The pol genes of the T-even bacteriophages (Myoviridae), poxviruses (Poxviridae), African swine fever virus (Ascoviridae), fish herpesvirus (Herpesviridae) and baculoviruses (Baculoviridae) were not clearly resolved. A second study showed that poxvirus, baculovirus and the animal herpesviruses form separate and distinct clades. 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 eukaryote
Eukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
s. 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.
Nudiviruses are regarded as a sister clade to the Baculoviruses.