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40-535: See text Potyviridae is a family of positive-strand RNA viruses that encompasses more than 30% of known plant viruses , many of which are of great agricultural significance. The family has 12 genera and 235 species, three of which are unassigned to a genus. Potyvirid virions are nonenveloped, flexuous filamentous, rod-shaped particles. The diameter is around 11–20 nm, with a length of 650–950 nm. Genomes are linear and usually nonsegmented, around 8–12kb in length, consisting of positive-sense RNA, which

80-438: A genome and as messenger RNA ; it can be directly translated into protein in the host cell by host ribosomes . The first proteins to be expressed after infection serve genome replication functions; they recruit the positive-strand viral genome to viral replication complexes formed in association with intracellular membranes. These complexes contain proteins of both viral and host cell origin, and may be associated with

120-572: 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

160-650: 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 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

200-403: 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, 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 ,

240-472: A single occasion or multiple occasions. As such, each realm represents at least one instance of viruses coming into existence. While historically it 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

280-553: A sister clade in relation to Lenarviricota . The third phylum that contains +ssRNA viruses is Pisuviricota , which has been informally called the "picornavirus supergroup". The phylum contains a large assemblage of eukaryotic viruses known to infect animals, plants, fungi, and protists. The phylum contains three classes, two of which contain only +ssRNA viruses: Pisoniviricetes , which contains nidoviruses , picornaviruses , and sobeliviruses , and Stelpaviricetes , which contains potyviruses and astroviruses . The third class

320-405: 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 the order Herpesvirales . The relation between caudoviruses and herpesviruses is not certain, as they may either share

360-456: 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

400-504: Is Duplopiviricetes , whose members are double-stranded RNA viruses that are descended from +ssRNA viruses. Realm (virology) The rank of realm corresponds to the rank of domain used for cellular life, but differs in that viruses in 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

440-508: 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

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480-473: Is further disrupted by viral proteases degrading components required to initiate translation of cellular mRNA. All positive-strand RNA virus genomes encode RNA-dependent RNA polymerase , a viral protein that synthesizes RNA from an RNA template. Host cell proteins recruited by +ssRNA viruses during replication include RNA-binding proteins , chaperone proteins , and membrane remodeling and lipid synthesis proteins, which collectively participate in exploiting

520-463: Is surrounded by a protein coat made up of a single viral encoded protein called a capsid . All induce the formation of virus inclusion bodies called cylindrical inclusions (‘pinwheels’) in their hosts. These consist of a single protein (about 70 kDa ) made in their hosts from a single viral genome product. Member viruses encode large polypeptides that are cleaved into mature proteins . In 5'–3' order these proteins are There may be some variation in

560-428: Is the largest genus in the family, with 183 known species. These viruses are 720–850 nm in length and are transmitted by aphids . They can also be easily transmitted by mechanical means. These viruses shared a common ancestry 6,600 years ago and are transmitted by over 200 species of aphids. The species in the genus Macluravirus are 650–675 nm in length and are also transmitted by aphids. The plant viruses in

600-664: The Retroviridae (e.g. HIV ), genome damage appears to be avoided during reverse transcription by strand switching, a form of recombination. Recombination occurs in the Coronaviridae (e.g. SARS ). Recombination in RNA viruses appears to be an adaptation for coping with genome damage. Recombination can also occur infrequently between +ssRNA viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans, as in

640-480: The host cell's ribosomes . Positive-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) which is used during replication of the genome to synthesize a negative-sense antigenome that is then used as a template to create a new positive-sense viral genome. Positive-strand RNA viruses are divided between the phyla Kitrinoviricota , Lenarviricota , and Pisuviricota (specifically classes Pisoniviricetes and Stelpavirictes ) all of which are in

680-450: The chytrid fungus , Polymyxa graminis . The following genera are recognized: The following species are unassigned to a genus: Positive-strand RNA virus Positive-strand RNA viruses ( +ssRNA viruses ) are a group of related viruses that have positive-sense , single-stranded genomes made of ribonucleic acid . The positive-sense genome can act as messenger RNA (mRNA) and can be directly translated into viral proteins by

720-413: 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

760-605: The HUH superfamily that initiates rolling circle replication and all other viruses descended from such viruses. The prototypical members of 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

800-478: The apparent descendants of leviviruses, which infect eukaryotes . The phylum is divided into four classes: Leviviricetes , which contains leviviruses and their relatives, Amabiliviricetes , which contains narnaviruses and their relatives, Howeltoviricetes , which contains mitoviruses and their relatives, and Miaviricetes , which contains botourmiaviruses and their relatives. Based on phylogenetic analysis of RdRp, all other RNA viruses are considered to comprise

840-462: 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

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880-739: The case of SARS and MERS. Positive-strand RNA viruses are common in plants. In tombusviruses and carmoviruses , RNA recombination occurs frequently during replication. The ability of the RNA-dependent RNA polymerase of these viruses to switch RNA templates suggests a copy choice model of RNA recombination that may be an adaptive mechanism for coping with damage in the viral genome. Other +ssRNA viruses of plants have also been reported to be capable of recombination, such as Brom mosaic bromovirus and Sindbis virus . Positive-strand RNA viruses are found in three phyla: Kitrinoviricota , Lenarviricota , and Pisuviricota , each of which are assigned to

920-453: The cell's secretory pathway for viral replication. Numerous positive-strand RNA viruses can undergo genetic recombination when at least two viral genomes are present in the same host cell. The capability for recombination among +ssRNA virus pathogens of humans is common. RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution among Picornaviridae (e.g. poliovirus). In

960-519: The coronaviruses and rhinoviruses that cause the common cold . Positive-strand RNA virus genomes usually contain relatively few genes, usually between three and ten, including an RNA-dependent RNA polymerase. Coronaviruses have the largest known RNA genomes, between 27 and 32 kilobases in length, and likely possess replication proofreading mechanisms in the form of an exoribonuclease within nonstructural protein nsp14. Positive-strand RNA viruses have genetic material that can function both as

1000-569: 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

1040-482: The genus Ipomovirus are transmitted by whiteflies and they are 750–950 nm long. Tritimovirus and the Rymovirus viruses are 680–750 nm long and are transmitted by eriophydid mites . (The rymoviruses are closely related to the potyviruses and may eventually be merged with the potyviruses.) The Bymovirus genome consists of two particles instead of one (275 and 550 nm) and these viruses are transmitted by

1080-463: The host cell is achieved by penetration. Replication follows the positive-stranded RNA virus replication model. Positive-stranded RNA virus transcription is the method of transcription. Translation takes place by −1 ribosomal frameshifting. The virus exits the host cell by tubule-guided viral movement. Plants serve as the natural host. The virus is transmitted via a vector (often an insect or mite). Transmission routes are vector and mechanical. Potyvirus

1120-453: 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

1160-705: 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

1200-590: The kingdom Orthornavirae and realm Riboviria . They are monophyletic and descended from a common RNA virus ancestor. In the Baltimore classification system, +ssRNA viruses belong to Group IV. Positive-sense RNA viruses include pathogens such as the Hepatitis C virus , West Nile virus , dengue virus , and the MERS , SARS , and SARS-CoV-2 coronaviruses , as well as less clinically serious pathogens such as

1240-423: The kingdom Orthornavirae in the realm Riboviria . In the Baltimore classification system, which groups viruses together based on their manner of mRNA synthesis, +ssRNA viruses are group IV. The first +ssRNA phylum is Kitrinoviricota . The phylum contains what have been referred to as the " alphavirus supergroup" and " flavivirus supergroup" along with various other short-genome viruses. Four classes in

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1280-451: The membranes of a variety of organelles —often the rough endoplasmic reticulum , but also including membranes derived from mitochondria , vacuoles , the Golgi apparatus , chloroplasts , peroxisomes , plasma membranes , autophagosomal membranes , and novel cytoplasmic compartments. The replication of the positive-sense RNA genome proceeds through double-stranded RNA intermediates, and

1320-410: The number of the proteins depending on the genera and species. For instance some genera lack P1, some virus of the genus Ipomovirus lack HC and have a P1 tandem. Pretty interesting sweet potato potyviral ORF (PISPO), alkylation B (AlkB), and inosine triphosphate pyrophosphatase (known as ITPase or HAM1) are protein domains identified in atypical members. Viral replication is cytoplasmic. Entry into

1360-451: The phylum are recognized: Alsuviricetes , the alphavirus supergroup, which contains a large number of plant viruses and arthropod viruses; Flasuviricetes , which contains flaviviruses, Magsaviricetes , which contains nodaviruses and sinhaliviruses ; and Tolucaviricetes , which primarily contains plant viruses. Lenarviricota is the second +ssRNA phylum. It contains the class Leviviricetes , which infect prokaryotes , and

1400-528: The purpose of replication in these membranous invaginations may be the avoidance of cellular response to the presence of dsRNA. In many cases subgenomic RNAs are also created during replication. After infection, the entirety of the host cell's translation machinery may be diverted to the production of viral proteins as a result of the very high affinity for ribosomes by the viral genome's internal ribosome entry site (IRES) elements; in some viruses, such as poliovirus and rhinoviruses , normal protein synthesis

1440-612: 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

1480-897: 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

1520-411: 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

1560-493: 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 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

1600-472: 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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