Circular Rep-encoding SsDNA Viruses
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''Monodnaviria'' is a
realm A realm is a community or territory over which a sovereign rules. The term is commonly used to describe a monarchical or dynastic state. A realm may also be a subdivision within an empire, if it has its own monarch, e.g. the German Empire. Etym ...
of
virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...
es that includes all
single-stranded DNA virus A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and t ...
es that
encode The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims to identify functional elements in the human genome. ENCODE also supports further biomedical research by "generating community resources of genomics data, software ...
an endonuclease of the HUH superfamily that initiates
rolling circle replication Rolling circle replication (RCR) is a process of unidirectional nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA or RNA, such as plasmids, the genomes of bacteriophages, and the circular RNA genom ...
of the circular viral genome. Viruses descended from such viruses are also included in the realm, including certain linear single-stranded DNA (ssDNA) viruses and circular double-stranded DNA (dsDNA) viruses. These atypical members typically replicate through means other than rolling circle replication. ''Monodnaviria'' was established in 2019 and contains four kingdoms: ''
Loebvirae ''Tubulavirales'' is an order of viruses. Taxonomy The following families are recognized: * ''Inoviridae Filamentous bacteriophage is a family of viruses (''Inoviridae'') that infect bacteria. The phages are named for their filamentous sha ...
'', ''
Sangervirae ''Microviridae'' is a family of bacteriophages with a single-stranded DNA genome. The name of this family is derived from the ancient Greek word (), meaning "small". This refers to the size of their genomes, which are among the smallest of the ...
'', ''
Trapavirae ''Pleolipoviridae'' is a family of DNA virus A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, ...
'', and ''
Shotokuvirae ''Shotokuvirae'' is a kingdom of virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bac ...
''. Viruses in the first three kingdoms infect
prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...
s, and viruses in ''Shotokuvirae'' infect
eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...
s and include the atypical members of the realm. Viruses in ''Monodnaviria'' appear to have come into existence independently multiple times from circular
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...
l and
archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...
l
plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...
s that encode the HUH endonuclease. Eukaryotic viruses in the realm appear to have come into existence multiple times via
genetic recombination Genetic recombination (also known as genetic reshuffling) is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryo ...
events that merged deoxyribonucleic acid (DNA) from the aforementioned plasmids with capsid proteins of certain
RNA virus An RNA virus is a virusother than a retrovirusthat has ribonucleic acid (RNA) as its genetic material. The nucleic acid is usually single-stranded RNA ( ssRNA) but it may be double-stranded (dsRNA). Notable human diseases caused by RNA viruses ...
es. Most identified ssDNA viruses belong to ''Monodnaviria''. The prototypic members of the realm are often called CRESS-DNA viruses. CRESS-DNA viruses are associated with a wide range of diseases, including diseases in economically important crops and a variety of diseases in animals. The atypical members of the realm include
papillomavirus ''Papillomaviridae'' is a family of non- enveloped DNA viruses whose members are known as papillomaviruses. Several hundred species of papillomaviruses, traditionally referred to as "types", have been identified infecting all carefully inspected ...
es and
polyomavirus ''Polyomaviridae'' is a family of viruses whose natural hosts are primarily mammals and birds. As of 2020, there are six recognized genera and 117 species, five of which are unassigned to a genus. 14 species are known to infect humans, while othe ...
es, which are known to cause various
cancer Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. These contrast with benign tumors, which do not spread. Possible signs and symptoms include a lump, abnormal b ...
s. Members of ''Monodnaviria'' are also known to frequently become integrated into the DNA of their hosts as well as experience a relatively high rate of genetic mutations and recombinations.


Etymology

''Monodnaviria'' is a
portmanteau A portmanteau word, or portmanteau (, ) is a blend of wordsGreek Greek may refer to: Greece Anything of, from, or related to Greece, a country in Southern Europe: *Greeks, an ethnic group. *Greek language, a branch of the Indo-European language family. **Proto-Greek language, the assumed last common ancestor ...
μόνος ónos meaning single, ''DNA'' from deoxyribonucleic acid (DNA), referencing single-stranded DNA, and the suffix -''viria'', which is the suffix used for virus realms. The prototypic members of ''Monodnaviria'' are often called CRESS-DNA, or CRESS DNA, viruses, which stands for "circular Rep-encoding ssDNA" viruses.


Characteristics


Endonuclease-initiated replication

All prototypical viruses in ''Monodnaviria'' encode an endonuclease of the HUH superfamily.The only exception to this is that certain inoviruses do not encode the HUH endonuclease.
Endonuclease Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonucleases ...
s are
enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...
s that can cleave
phosphodiester bond In chemistry, a phosphodiester bond occurs when exactly two of the hydroxyl groups () in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds. The "bond" involves this linkage . Discussion of phosphodiesters is ...
s within a
polynucleotide A polynucleotide molecule is a biopolymer composed of 13 or more nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (D ...
chain. HUH, or HuH, endonucleases are endonucleases that contain a HUH motif made of two
histidine Histidine (symbol His or H) is an essential amino acid that is used in the biosynthesis of proteins. It contains an α-amino group (which is in the protonated –NH3+ form under biological conditions), a carboxylic acid group (which is in the de ...
residues separated by a bulky hydrophobic residue and a Y motif that contains one or two
tyrosine -Tyrosine or tyrosine (symbol Tyr or Y) or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins. It is a non-essential amino acid with a polar side group. The word "tyrosine" is from the Gr ...
residues. The HUH endonuclease of ssDNA viruses is often called the replication initiation protein, or simply Rep, because its cleavage of a specific site in the viral genome initiates replication. Once the viral ssDNA is inside of the host cell, it is replicated by the host cell's
DNA polymerase A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create ...
to produce a double-stranded form of the viral genome. Rep then recognizes a short sequence on the 3'-end ("three prime end") at the origin of replication. Upstream from the recognition site, Rep binds to the DNA and nicks the
positive-sense In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, ...
strand, creating a nick site. In doing so, Rep binds to the 5'-end (five prime end) via a tyrosine residue that covalently bonds to the phosphate backbone of DNA, creating a
phosphotyrosine -Tyrosine or tyrosine (symbol Tyr or Y) or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins. It is a non-essential amino acid with a polar side group. The word "tyrosine" is from the Gr ...
molecule that connects Rep to the viral DNA. The 3'-end of the nicked strand remains as a free
hydroxyl In chemistry, a hydroxy or hydroxyl group is a functional group with the chemical formula and composed of one oxygen atom covalently bonded to one hydrogen atom. In organic chemistry, alcohols and carboxylic acids contain one or more hydroxy ...
(OH) end that acts as a signal for the host DNA polymerase to replicate the genome. Replication commences at the 3'-OH end and is performed by extending the 3'-end of the positive strand using the negative strand as a template for replication. Synthesis of the new positive strand uses the negative strand as a template, and so synthesizes a newly connected strand of DNA which displaces the nicked positive strand to reform double-stranded DNA. The 3'-OH end of the displaced positive strand disrupts the original phosphotyrosine bond which releases and circularizes the displaced positive strand as its own circular copy of viral DNA. After one cycle of replicating the genome, Rep is able to recognize the newly replicated recognition site on the reformed double-stranded viral DNA and nick it, which starts the whole process again. Rep may nick the positive strand a second time, doing so with a second tyrosine residue, or a new Rep may nick the DNA. Multiple copies of the genome may be produced in a single strand. After the positive strand is completely detached from the negative strand and nicked, the 3'-OH end bonds to the
phosphotyrosine -Tyrosine or tyrosine (symbol Tyr or Y) or 4-hydroxyphenylalanine is one of the 20 standard amino acids that are used by cells to synthesize proteins. It is a non-essential amino acid with a polar side group. The word "tyrosine" is from the Gr ...
of the 5'-end, creating a free circular ssDNA genome that usually is either converted into dsDNA for transcription or further replication or is packaged into newly constructed viral capsids. The replication process can be repeated numerous times on the same circular genome to produce many copies of the original viral genome.


Atypical members

While the prototypical viruses in ''Monodnaviria'' have circular ssDNA genomes and replicate via RCR, some have linear ssDNA genomes with different replication methods, including the families ''
Parvoviridae Parvoviruses are a family of animal viruses that constitute the family ''Parvoviridae''. They have linear, single-stranded DNA (ssDNA) genomes that typically contain two genes encoding for a replication initiator protein, called NS1, and the pr ...
'' and '' Bidnaviridae'', assigned to the phylum ''
Cossaviricota ''Cossaviricota'' is a phylum of viruses. Classes The following classes are recognized: * '' Mouviricetes'' * ''Papovaviricetes ''Papovaviricetes'' is a class of viruses. The class shares the name of an abolished family, ''Papovaviridae'', ...
'' of the kingdom ''Shotokuvirae''. Parvoviruses use
rolling hairpin replication Rolling hairpin replication (RHR) is a unidirectional, strand displacement form of DNA replication used by parvoviruses, a group of viruses that constitute the family ''Parvoviridae''. Parvoviruses have linear, single-stranded DNA (ssDNA) genomes in ...
, in which the ends of the genome have hairpin loops that repeatedly unfold and refold during replication to change the direction of DNA synthesis to move back and forth along the genome, producing numerous copies of the genome in a continuous process. Individual genomes are then excised from this molecule by the HUH endonuclease. In place of the HUH endonuclease, bidnaviruses encode their own protein-primed DNA polymerase that replicates the genome, which is bipartite and packaged into two separate virions, instead of using the host cell's DNA polymerase for replication. Additionally, some viruses in the realm are dsDNA viruses with circular genomes, including ''Polyomaviridae'' and ''Papillomaviridae'', also assigned to the phylum ''Cossaviricota''. Instead of replicating via RCR, these viruses use
theta Theta (, ; uppercase: Θ or ; lowercase: θ or ; grc, ''thē̂ta'' ; Modern: ''thī́ta'' ) is the eighth letter of the Greek alphabet, derived from the Phoenician letter Teth . In the system of Greek numerals, it has a value of 9. Gr ...
bidirectional
DNA replication In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
. This begins by unwinding the dsDNA at a site called the origin to separate the two DNA strands from each other. Two replication forks are established that move in opposite directions around the circular genome until they meet at the side opposite of the origin and replication is terminated.


Other characteristics

Apart from the aforementioned replication methods, ssDNA viruses in ''Monodnaviria'' share a number of other common characteristics. The capsids of ssDNA viruses, which store the viral DNA, are usually
icosahedral In geometry, an icosahedron ( or ) is a polyhedron with 20 faces. The name comes and . The plural can be either "icosahedra" () or "icosahedrons". There are infinitely many non- similar shapes of icosahedra, some of them being more symmetrica ...
in shape and composed of either one type of protein or, in the case of parvoviruses, multiple types of proteins. All ssDNA viruses that have had the structure of their capsid proteins analyzed in high resolution have shown to contain a single
jelly roll fold The jelly roll or Swiss roll fold is a protein fold or supersecondary structure composed of eight beta strands arranged in two four-stranded sheets. The name of the structure was introduced by Jane S. Richardson in 1981, reflecting its resemblance ...
in their folded structure. Nearly all families of ssDNA viruses have a positive-sense genome, the sole exception being viruses in the family ''
Anelloviridae ''Anelloviridae'' is a family Family (from la, familia) is a Social group, group of people related either by consanguinity (by recognized birth) or Affinity (law), affinity (by marriage or other relationship). The purpose of the family is t ...
'', unassigned to a realm, which have a negative-sense genome. In any case, ssDNA viruses have their genomes converted to a dsDNA form prior to
transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...
, which creates the
messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the p ...
(mRNA) needed to produce viral proteins from
ribosomal Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to fo ...
translation Translation is the communication of the Meaning (linguistic), meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The ...
. CRESS-DNA viruses also have similar genome structures, genome lengths, and gene compositions. Lastly, ssDNA viruses have a relatively high rate of genetic recombinations and substitution mutations. Genetic recombination, or mixture, of ssDNA genomes can occur between closely related viruses when a gene is replicated and transcribed at the same time, which may cause the host cell's DNA polymerases to switch DNA templates (negative strands) during the process, causing recombination. These recombinations usually occur in the negative strand and either outside of or at the peripheries of genes rather than toward the middle of genes. The high substitution rate seen in ssDNA viruses is unusual since replication is performed primarily by the host cell's DNA polymerase, which contains proofreading mechanisms to prevent mutations. Substitutions in ssDNA viral genomes may occur because the viral DNA may become oxidatively damaged while the genome is inside the capsid. The prevalence of recombinations and substitutions among ssDNA viruses means that eukaryotic ssDNA viruses can emerge as threatening pathogens.


Phylogenetics

Comparison of genomes and phylogenetic analyses of the HUH endonucleases, superfamily 3
helicase Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separatin ...
s (S3H), and capsid proteins of viruses in ''Monodnaviria'' have shown that they have multiple, chimeric origins. HUH endonucleases of CRESS-DNA viruses are most similar to those found in small, RCR bacterial and archael plasmids, extra-chromosomal DNA molecules inside bacteria and archaea, and appear to have evolved from them at least three times. HUH endonucleases of prokaryotic CRESS-DNA viruses seem to have originated from plasmid endonucleases that lacked the S3H domain, whereas eukaryotic CRESS-DNA viruses evolved from ones that had S3H domains. The capsid proteins of eukaryotic CRESS-DNA viruses are most closely related those of various animal and plant positive-sense RNA viruses, which belong to the realm ''Riboviria''. Because of this, eukaryotic CRESS-DNA viruses appear to have emerged multiple times from recombination events that merged DNA from bacterial and archaeal plasmids with complementary DNA (cDNA) copies of positive-sense RNA viruses. CRESS-DNA viruses therefore represent a notable instance of
convergent evolution Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last com ...
, whereby organisms that are not directly related evolve the same or similar traits. Linear ssDNA viruses, specifically parvoviruses, in ''Monodnaviria'' are likely to have evolved from CRESS-DNA viruses via loss of the joining activity used by CRSS-DNA viruses to create circular genomes. In turn, the circular dsDNA viruses in ''Monodnaviria'' appear to have evolved from parvoviruses through inactivation of the endonuclease's HUH domain. The HUH domain then became a DNA-binding domain, changing these viruses' manner of replication to theta bidirectional replication. The capsid proteins of these circular dsDNA viruses are highly divergent, so it is unclear if they evolved from parvovirus capsid proteins or through other means. Bidnaviruses, which are linear ssDNA viruses, appear to have been created as a result of a parvovirus genome becoming integrated into the genome of a
polinton Polintons (also called Mavericks) are large DNA transposons which contain genes with homology to viral proteins and which are often found in eukaryotic genomes. They were first discovered in the mid-2000s and are the largest and most complex known ...
, a type of self-replicating genomic DNA molecule, which replaced the HUH endonuclease with a polinton's DNA polymerase.


Classification

''Monodnaviria'' has four kingdoms: ''Loebvirae'', ''Sangervirae'', ''Shotokuvirae'', and ''Trapavirae''. ''Loebvirae'' is monotypic down to the rank of order, and ''Sangervirae'' and ''Trapavirae'' are monotypic down to the rank of family. This taxonomy is described further as follows: *Kingdom: ''Loebvirae'', which only infect bacteria, have filamentous or rod-shaped virions formed from an alpha-helical capsid protein, and encode a morphogenesis protein that is an ATPase of the FtsK-HerA superfamily **Phylum: ''Hofneiviricota'' ***Class: ''Faserviricetes'' ****Order: ''
Tubulavirales ''Tubulavirales'' is an order of viruses. Taxonomy The following families are recognized: * ''Inoviridae Filamentous bacteriophage is a family of viruses (''Inoviridae'') that infect bacteria. The phages are named for their filamentous sha ...
'' *Kingdom: ''Sangervirae'', which only infect bacteria, have a capsid protein that contains a single jelly roll fold, and have a pilot protein required for transferring DNA across the
cell envelope The cell envelope comprises the inner cell membrane and the cell wall of a bacterium. In gram-negative bacteria an outer membrane is also included. This envelope is not present in the Mollicutes where the cell wall is absent. Bacterial cell env ...
. The endonuclease of ''Sangervirae'' may also be a unifying trait since it appears to be monophyletic. **Phylum: ''Phixviricota'' ***Class: ''Malgrandaviricetes'' ****Order: ''Petitvirales'' *****Family: ''
Microviridae ''Microviridae'' is a family of bacteriophages with a single-stranded DNA genome. The name of this family is derived from the ancient Greek word (), meaning "small". This refers to the size of their genomes, which are among the smallest of the ...
'' *Kingdom: ''
Shotokuvirae ''Shotokuvirae'' is a kingdom of virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bac ...
'', which encode an endonuclease containing an endonuclease domain, or a derivative of one, at the start of the protein's amino acid sequence and a superfamily 3 helicase domain at the end of the protein's amino acid sequence. ''Shotokuvirae'' notably includes linear ssDNA and circular dsDNA viruses, assigned to its phylum ''Cossaviricota'', that are descended from CRESS-DNA viruses, assigned to the kingdom's other phylum ''
Cressdnaviricota ''Cressdnaviricota'' is a phylum of virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including ...
''. *Kingdom: ''Trapavirae'', which only infect archaea and which have a
viral envelope A viral envelope is the outermost layer of many types of viruses. It protects the genetic material in their life cycle when traveling between host cells. Not all viruses have envelopes. Numerous human pathogenic viruses in circulation are encase ...
that contains a membrane fusion protein **Phylum: ''Saleviricota'' ***Class: ''Huolimaviricetes'' ****Order: ''Haloruvirales'' *****Family: ''
Pleolipoviridae ''Pleolipoviridae'' is a family of DNA virus A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, ...
'' ''Monodnaviria'' includes the vast majority of identified ssDNA viruses, which are Group II: ssDNA viruses in the
Baltimore classification Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a di ...
system, which groups viruses together based on how they produce mRNA, often used alongside standard virus taxonomy, which is based on evolutionary history.. Of the 16 ssDNA virus families, three are not assigned to ''Monodnaviria'', all three being unassigned to a realm: ''Anelloviridae'', '' Finnlakeviridae'', a proposed member of the realm ''Varidnaviria'', and ''
Spiraviridae ''Spiraviridae'' is a family of viruses that replicate in hyperthermophilic archaea of the genus ''Aeropyrum'', specifically ''Aeropyrum pernix''. The family contains one genus, ''Alphaspiravirus'', which contains one species, ''Aeropyrum coil-sh ...
''. The dsDNA viruses in ''Monodnaviria'' are assigned to Baltimore Group I: dsDNA viruses. Realms are the highest level of taxonomy used for viruses and ''Monodnaviria'' is one of four, the other three being ''
Duplodnaviria ''Duplodnaviria'' is a realm of viruses that includes all double-stranded DNA viruses that encode the HK97 fold major capsid protein. The HK97 fold major capsid protein (HK97 MCP) is the primary component of the viral capsid, which stores the v ...
'', ''
Riboviria ''Riboviria'' is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase, as well as reverse-transcribing viruses (with eithe ...
'', and ''
Varidnaviria ''Varidnaviria'' is a realm of viruses that includes all DNA viruses that encode major capsid proteins that contain a vertical jelly roll fold. The major capsid proteins (MCP) form into pseudohexameric subunits of the viral capsid, which stores t ...
''. Although ''Anelloviridae'' is currently unassigned to a realm, it is a potential member of ''Monodnaviria'' since it appears to be morphologically similar to circoviruses. It has been suggested that anelloviruses are essentially CRESS-DNA viruses with negative sense genomes, unlike the typical positive sense genomes.


Interactions with hosts


Disease

The eukaryotic CRESS-DNA viruses are associated with a variety of diseases. Plant viruses in the families ''
Geminiviridae ''Geminiviridae'' is a family of plant viruses that encode their genetic information on a circular genome of single-stranded (ss) DNA. There are 520 species in this family, assigned to 14 genera. Diseases associated with this family include: bri ...
'' and ''
Nanoviridae ''Nanoviridae'' is a family of viruses. Plants serve as natural hosts. There are currently 12 species in this family, divided among 2 genera and one unassigned species. Diseases associated with this family include: stunting. Their name is derive ...
'' infect economically important crops, causing significant damage to agricultural productivity. Animal viruses in ''
Circoviridae ''Circoviridae'' is a family of DNA viruses. Birds and mammals serve as natural hosts. There are 101 species in this family, assigned to 2 genera. Diseases associated with this family include: PCV-2: postweaning multisystemic wasting syndrome; ...
'' are associated with many diseases, including respiratory illness, intestinal illness, and reproductive problems. Bacilladnaviruses, which primarily infect
diatom A diatom (Neo-Latin ''diatoma''), "a cutting through, a severance", from el, διάτομος, diátomos, "cut in half, divided equally" from el, διατέμνω, diatémno, "to cut in twain". is any member of a large group comprising sev ...
s, are thought to have a significant role in controlling
algal bloom An algal bloom or algae bloom is a rapid increase or accumulation in the population of algae in freshwater or marine water systems. It is often recognized by the discoloration in the water from the algae's pigments. The term ''algae'' encompas ...
s. The atypical members of the realm are also associated with many widely known diseases. Parvoviruses are most widely known for causing a lethal infection in canids as well as causing
fifth disease Erythema infectiosum, fifth disease, or slapped cheek syndrome is one of several possible manifestations of infection by parvovirus B19. Fifth disease typically presents as a rash and is more common in children. While parvovirus B19 can affect hu ...
in humans. Papillomaviruses and polyomaviruses are known to cause different types of cancers and other diseases. A polyomavirus is responsible for
Merkel-cell carcinoma Merkel cell carcinoma (MCC) is a rare and aggressive skin cancer occurring in about 3 people per 1,000,000 members of the population. It is also known as cutaneous APUDoma, primary neuroendocrine carcinoma of the skin, primary small cell carcino ...
, and papillomaviruses cause various genital and other cancers as well as
wart Warts are typically small, rough, hard growths that are similar in color to the rest of the skin. They typically do not result in other symptoms, except when on the bottom of the feet, where they may be painful. While they usually occur on the ...
s.


Endogenization

The Rep protein lacks
homolog In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of prima ...
ues in cellular organisms, so it can be searched for within an organism's genome to identify if viral DNA has become endogenized as part of the organism's genome. Among eukaryotes, endogenization is most often observed in plants, but it is also observed in animals, fungi, and various protozoans. Endogenization can occur through several means such as the
integrase Retroviral integrase (IN) is an enzyme produced by a retrovirus (such as HIV) that integrates—forms covalent links between—its genetic information into that of the host cell it infects. Retroviral INs are not to be confused with phage int ...
or
transpose In linear algebra, the transpose of a matrix is an operator which flips a matrix over its diagonal; that is, it switches the row and column indices of the matrix by producing another matrix, often denoted by (among other notations). The tr ...
enzymes or by exploiting the host cell's recombination machinery. Most endogenized ssDNA viruses are in non-coding regions of the organism's genome, but sometimes the viral genes are expressed, and the Rep protein may be used by the organism. Because viral DNA can become a part of an organism's genome, this represents an example of
horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...
between unrelated organisms that can be used to study evolutionary history. By comparing related organisms, it is possible to estimate the approximate age of ssDNA viruses. For example, comparison of animal genomes has shown that circoviruses and parvoviruses first integrated into their hosts' genomes at least 40-50 million years ago.


History

The earliest reference to a virus in ''Monodnaviria'' was made in a poem written in 752 by Japanese
Empress Shotoku An emperor (from la, imperator, via fro, empereor) is a monarch, and usually the sovereign ruler of an empire or another type of imperial realm. Empress, the female equivalent, may indicate an emperor's wife ( empress consort), mother ( e ...
, describing a yellowing or vein clearing disease of ''
Eupatorium ''Eupatorium'' is a genus of flowering plants in the family Asteraceae, containing from 36 to 60 species depending on the classification system. Most are herbaceous perennials growing to tall. A few are shrubs. The genus is native to temperate ...
'' plants that was likely caused by a geminivirus. Centuries later, a
circovirus ''Circovirus'' is a genus of viruses, in the family ''Circoviridae''. Birds (such as pigeons and ducks) and pigs serve as natural hosts, though dogs have been shown to be infected as well. It is a single stranded DNA virus (ssDNA). There are 49 ...
infection that caused balding in birds was observed in Australia in 1888, marking the first reference to ssDNA viruses in modern times. The first animal CRESS-DNA virus to be characterized was the
porcine circovirus Porcine circovirus (PCV) is a group of four single-stranded DNA viruses that are non-enveloped with an unsegmented circular genome. They are members of the genus '' Circovirus'' that can infect pigs. The viral capsid is icosahedral and approxim ...
in 1974, and in 1977, the first genome of an ssDNA virus, the '' Bean golden mosaic virus'', was detailed. Beginning in the 1970s, the families of related members in ''Monodnaviria'' began to be organized, ''Parvoviridae'' becoming the first ssDNA family recognized with additional families being continually discovered. In recent years, analyses of viral DNA in various contexts such as fecal matter and marine sediments have shown that ssDNA viruses are widespread throughout nature, and the increased knowledge of their diversity has helped to greater understand their evolutionary history. The relation between CRESS-DNA viruses was resolved from 2015 to 2017, leading to the establishment of ''Monodnaviria'' in 2019 based on their shared relation, including viruses descended from them. Despite appearing to have
polyphyletic A polyphyletic group is an assemblage of organisms or other evolving elements that is of mixed evolutionary origin. The term is often applied to groups that share similar features known as homoplasies, which are explained as a result of converg ...
origins, the similar genome structure, genome length, and gene compositions of CRESS-DNA viruses provided the justification to unite them under a realm.


See also

*
List of higher virus taxa :''This is a list of biological virus upper-level taxa. See also Comparison of computer viruses'' This is an alphabetical list of biological virus higher taxa. It includes those taxa above Family (biology), family, ranging from Realm (virology), r ...


Notes


References


Further reading

* {{Taxonbar, from=Q91894429 Virus realms