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56-554: Monodnaviria is a realm of viruses that includes all single-stranded DNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication 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
112-572: A reverse transcriptase (RT), assigned to the kingdom Pararnavirae . These enzymes are vital in the viral life cycle, as RdRp transcribes viral mRNA and replicates the genome, and RT likewise replicates the genome. Riboviria mostly contains eukaryotic viruses, and most eukaryotic viruses, including most human, animal, and plant viruses, belong to the realm. Most widely known viral diseases are caused by viruses in Riboviria , which includes influenza viruses , HIV , coronaviruses , ebolaviruses , and
168-530: A major capsid protein (MCP) that has the HK97 fold. Viruses in the realm also share a number of other characteristics involving the capsid and capsid assembly, including an icosahedral capsid shape and a terminase enzyme that packages viral DNA into the capsid during assembly. Two groups of viruses are included in the realm: tailed bacteriophages, which infect prokaryotes and are assigned to the order Caudovirales , and herpesviruses, which infect animals and are assigned to
224-506: A notable instance of convergent evolution , 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
280-404: A realm do not necessarily share a common ancestor based on common descent nor do the realms share a common ancestor . Instead, realms group viruses together based on specific traits that are highly conserved over time, which may have been obtained on a single occasion or multiple occasions. As such, each realm represents at least one instance of viruses coming into existence. While historically it
336-398: A realm: Anelloviridae , Finnlakeviridae , a proposed member of the realm Varidnaviria , and Spiraviridae . 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 , Riboviria , and Varidnaviria . Although Anelloviridae
392-404: 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
448-410: A result of a parvovirus genome becoming integrated into the genome of a polinton , a type of self-replicating genomic DNA molecule, which replaced the HUH endonuclease with a polinton's DNA polymerase. 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
504-677: A significant role in controlling algal blooms . 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 in humans. Papillomaviruses and polyomaviruses are known to cause different types of cancers and other diseases. A polyomavirus is responsible for Merkel-cell carcinoma , and papillomaviruses cause various genital and other cancers as well as warts . The Rep protein lacks homologues 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
560-574: A single jelly roll fold in their folded structure. Nearly all families of ssDNA viruses have a positive-sense genome, the sole exception being viruses in the family Anelloviridae , 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 , which creates the messenger RNA (mRNA) needed to produce viral proteins from ribosomal translation . CRESS-DNA viruses also have similar genome structures, genome lengths, and gene compositions. Lastly, ssDNA viruses have
616-452: 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 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 {description needed} from the recognition site, Rep binds to the DNA and nicks
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#1732844620173672-456: A vast undescribed diversity of viruses in this part of the virosphere. Ribozyviria is characterised by the presence of genomic and antigenomic ribozymes of the Deltavirus type. Additional common features include a rod-like structure and a RNA-binding "delta antigen" encoded in the genome. In general, virus realms have no genetic relation to each other based on common descent, in contrast to
728-477: A virus in Monodnaviria was made in a poem written in 752 by Japanese Empress Shotoku , describing a yellowing or vein clearing disease of Eupatorium plants that was likely caused by a geminivirus. Centuries later, a circovirus 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
784-444: 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 papillomaviruses and polyomaviruses , which are known to cause various cancers . 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. Monodnaviria
840-441: Is a portmanteau of mono , from Greek μόνος [mónos], 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 " c ircular R ep- e ncoding ssDNA " viruses. All prototypical viruses in Monodnaviria encode an endonuclease of
896-508: Is composed of asymmetric units containing two MCP molecules, a homodimer in the case of rudivirids and a heterodimer of paralogous MCPs in the case of lipothrixvirids and tristromavirids. The MCPs of ligamenviral particles have a unique α-helical fold first found in the MCP of rudivirid Sulfolobus islandicus rod-shaped virus 2 (SIRV2). All members of the Adnaviria share a characteristic feature in that
952-805: 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. The eukaryotic CRESS-DNA viruses are associated with a variety of diseases. Plant viruses in the families Geminiviridae and Nanoviridae infect economically important crops, causing significant damage to agricultural productivity. Animal viruses in Circoviridae are associated with many diseases, including respiratory illness, intestinal illness, and reproductive problems. Bacilladnaviruses , which primarily infect diatoms , are thought to have
1008-428: 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. 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 and Bidnaviridae , assigned to
1064-411: The positive-sense strand, creating a nick {description needed} site. In doing so, Rep binds to the 5'-end (five prime end) via a tyrosine residue that covalently bonds {source for covalent bonds needed} to the phosphate backbone of DNA, creating a phosphotyrosine molecule that connects Rep to the viral DNA. The 3'-end of the nicked strand remains as a free hydroxyl (OH) end that acts as a signal for
1120-413: The rabies virus , as well as the first virus to be discovered, Tobacco mosaic virus . Reverse transcribing viruses are a major source of horizontal gene transfer by means of becoming endogenized in their host's genome, and a significant portion of the human genome consists of this viral DNA. Varidnaviria contains DNA viruses that encode MCPs that have a jelly roll fold folded structure in which
1176-473: The HUH endonuclease. Eukaryotic viruses in the realm appear to have come into existence multiple times via genetic recombination events that merged deoxyribonucleic acid (DNA) from the aforementioned plasmids with capsid proteins of certain RNA viruses . 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
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#17328446201731232-418: 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
1288-457: The HUH superfamily. Endonucleases are enzymes that can cleave phosphodiester bonds within a polynucleotide chain. HUH, or HuH, endonucleases are endonucleases that contain a HUH motif made of two histidine residues separated by a bulky hydrophobic residue and a Y motif that contains one or two tyrosine residues. The HUH endonuclease of ssDNA viruses is often called the replication initiation protein, or simply Rep, because its cleavage of
1344-587: 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
1400-436: 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 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
1456-462: The atypical members of Monodnaviria . Eukaryotic monodnaviruses are associated with many diseases, and they include papillomaviruses and polyomaviruses , which cause many cancers, and geminiviruses , which infect many economically important crops. Riboviria contains all RNA viruses that encode an RNA-dependent RNA polymerase (RdRp), assigned to the kingdom Orthornavirae , and all reverse transcribing viruses, i.e. all viruses that encode
1512-569: The desire to establish higher-level taxonomy for viruses. In two votes in 2018 and 2019, the ICTV agreed to adopt a 15-rank classification system for viruses, ranging from realm to species. Riboviria was established in 2018 based on phylogenetic analysis of the RNA-dependent polymerases being monophyletic, Duplodnaviria was established in 2019 based on increasing evidence that tailed bacteriophages and herpesviruses shared many traits, Monodnaviria
1568-421: 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 {recognize the recognition site?} on the reformed double-stranded viral DNA and nick it, which starts the whole process again. Rep may nick
1624-401: 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
1680-470: The first part of Monodnaviria means "single DNA", referring to ssDNA viruses, the first part of Riboviria is taken from ribo nucleic acid (RNA), and the first part of Varidnaviria means "various DNA". For viroids , the suffix is designated as - viroidia , and for satellites , the suffix is - satellitia , but as of 2019 neither viroid nor satellite realms have been designated. Duplodnaviria contains double-stranded DNA (dsDNA) viruses that encode
1736-658: The formation of concatemers. In the case of human herpesvirus-6 , its entire genome is made over and over on a single strand. These long concatemers are subsequently cleaved between the pac-1 and pac-2 regions by ribozymes when the genome is packaged into individual virions. Bacteriophage T4 replicating DNA was labeled with tritiated thymidine and examined by autoradiography . The observed DNA replication intermediates included circular and branched circular concatemeric structures that likely arose by rolling circle replication . When assembling concatemers from synthetic oligonucleotides, increasing salt concentration to 200 mM
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1792-741: 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. Comparison of genomes and phylogenetic analyses of the HUH endonucleases, superfamily 3 helicases (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
1848-487: The genome). Concatemers are frequently the result of rolling circle replication , and may be seen in the late stage of infection of bacteria by phages . As an example, if the genes in the phage DNA are arranged ABC, then in a concatemer the genes would be ABCABCABCABC and so on (assuming synthesis was initiated between genes C and A). They are further broken by ribozymes . During active infection, some species of viruses have been shown to replicate their genetic material via
1904-454: 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. {refer to DNA 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
1960-447: 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 origins, the similar genome structure, genome length, and gene compositions of CRESS-DNA viruses provided
2016-407: The interaction between the MCP dimer and the linear dsDNA genome maintains the DNA in the A form. Consequently, the entire genome adopts the A form in virions. Like many structurally related viruses in the two other realms of dsDNA viruses ( Duplodnaviria and Varidnaviria ), there is no detectable sequence similarity among the capsid proteins of viruses from different tokiviricete families, suggesting
2072-705: The jelly roll (JR) fold is perpendicular to the surface of the viral capsid. Many members also share a variety of other characteristics, including a minor capsid protein that has a single JR fold, an ATPase that packages the genome during capsid assembly, and a common DNA polymerase . Two kingdoms are recognized: Helvetiavirae , whose members have MCPs with a single vertical JR fold, and Bamfordvirae , whose members have MCPs with two vertical JR folds. Marine viruses in Varidnaviria are ubiquitous worldwide and, like tailed bacteriophages, play an important role in marine ecology. Most identified eukaryotic DNA viruses belong to
2128-508: The justification to unite them under a realm. Realm (virology) In virology , realm is the highest taxonomic rank established for viruses by the International Committee on Taxonomy of Viruses (ICTV), which oversees virus taxonomy. Six virus realms are recognized and united by specific highly conserved traits: The rank of realm corresponds to the rank of domain used for cellular life, but differs in that viruses in
2184-417: 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
2240-496: The order Herpesvirales . The relation between caudoviruses and herpesviruses is not certain, as they may either share a common ancestor or herpesviruses may be a divergent clade from within Caudovirales . A common trait among duplodnaviruses is that they cause latent infections without replication while still being able to replicate in the future. Tailed bacteriophages are ubiquitous worldwide, important in marine ecology, and
2296-407: 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 or transpose 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
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2352-418: The phylum Cossaviricota of the kingdom Shotokuvirae . Parvoviruses use rolling hairpin replication , 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
2408-423: The phylum Cossaviricota . Instead of replicating via RCR, these viruses use theta bidirectional DNA replication . 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. Apart from
2464-446: 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 of the 5'-end, creating a free circular ssDNA genome that usually is either converted into dsDNA for transcription or further replication or
2520-519: The rank of family. This taxonomy is described further as follows: Monodnaviria includes the vast majority of identified ssDNA viruses, which are Group II: ssDNA viruses in the Baltimore classification 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
2576-612: The rank of subrealm. Prior to the 21st century, it was believed that deep evolutionary relations between viruses could not be discovered due to their high mutation rates and small number of genes making discovering these relations more difficult. Because of this, the highest taxonomic rank for viruses from 1991 to 2017 was order. In the 21st century, however, various methods have been developed that have enabled these deeper evolutionary relationships to be studied, including metagenomics, which has identified many previously unidentified viruses, and comparison of highly conserved traits, leading to
2632-416: The realm are called CRESS-DNA viruses and have circular ssDNA genomes. ssDNA viruses with linear genomes are descended from them, and in turn some dsDNA viruses with circular genomes are descended from linear ssDNA viruses. CRESS-DNA viruses include three kingdoms that infect prokaryotes: Loebvirae , Sangervirae , and Trapavirae . The kingdom Shotokuvirae contains eukaryotic CRESS-DNA viruses and
2688-897: The realm. Notable disease-causing viruses in Varidnaviria include adenoviruses , poxviruses , and the African swine fever virus . Poxviruses have been highly prominent in the history of modern medicine, especially Variola virus , which caused smallpox . Many varidnaviruses are able to become endogenized, and a peculiar example of this are virophages , which confer protection for their hosts against giant viruses during infection. Realm Adnaviria unifies archaeal filamentous viruses with linear A-form double-stranded DNA genomes and characteristic major capsid proteins unrelated to those encoded by other known viruses. The realm currently includes viruses from three families, Lipothrixviridae , Rudiviridae , and Tristromaviridae , all infecting hyperthermophilic archaea. The nucleoprotein helix of adnaviruses
2744-411: The realms generally have no genetic relation to each other, there are some exceptions: In virology, the second highest taxonomy rank established by the ICTV is subrealm, which is the rank below realm. Subrealms of viruses use the suffix - vira , viroid subrealms use the suffix - viroida , and satellites use the suffix - satellitida . The rank below subrealm is kingdom. As of 2019, no taxa are described at
2800-421: The subject of much research. Herpesviruses are known to cause a variety of epithelial diseases, including herpes simplex , chickenpox and shingles , and Kaposi's sarcoma . Monodnaviria contains single-stranded DNA (ssDNA) viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication and all other viruses descended from such viruses. The prototypical members of
2856-472: The three domains of cellular life— Archaea , Bacteria , and Eukarya —which share a common ancestor. Likewise, viruses within each realm are not necessarily descended from a common ancestor since realms group viruses together based on highly conserved traits, not common ancestry, which is used as the basis for the taxonomy of cellular life. As such, each virus realm is considered to represent at least one instance of viruses coming into existence. By realm: While
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#17328446201732912-608: 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 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. The earliest reference to
2968-498: Was difficult to determine deep evolutionary relations between viruses, in the 21st century methods such as metagenomics and cryogenic electron microscopy have enabled such research to occur, which led to the establishment of Riboviria in 2018, three realms in 2019, and two in 2020. The names of realms consist of a descriptive first part and the suffix - viria , which is the suffix used for virus realms. The first part of Duplodnaviria means "double DNA", referring to dsDNA viruses,
3024-525: Was established in 2019 after the relation and origin of CRESS-DNA viruses was resolved, and Varidnaviria was established 2019 based on the shared characteristics of member viruses. Concatemer A concatemer is a long continuous DNA molecule that contains multiple copies of the same DNA sequence linked in series. These polymeric molecules are usually copies of an entire genome linked end to end and separated by cos sites (a protein binding nucleotide sequence that occurs once in each copy of
3080-484: Was established in 2019 and contains four kingdoms: Loebvirae , Sangervirae , Trapavirae , and Shotokuvirae . Viruses in the first three kingdoms infect prokaryotes , and viruses in Shotokuvirae infect eukaryotes and include the atypical members of the realm. Viruses in Monodnaviria appear to have come into existence independently multiple times from circular bacterial and archaeal plasmids that encode
3136-560: Was the porcine circovirus 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
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