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52-409: Positive-strand RNA viruses Negative-strand RNA viruses Double-stranded RNA viruses Ambisense RNA viruses Orthornavirae is a kingdom of viruses that have genomes made of ribonucleic acid (RNA), including genes which encode an RNA-dependent RNA polymerase (RdRp). The RdRp is used to transcribe the viral RNA genome into messenger RNA (mRNA) and to replicate

104-401: A positive or negative sense strand , and dsRNA viruses have both. This structure of the genome is important in terms of transcription to synthesize viral mRNA as well as replication of the genome, both of which are carried out by the viral enzyme RNA-dependent RNA polymerase (RdRp), also called RNA replicase. Positive-strand RNA viruses have genomes that can function as mRNA, so transcription

156-458: A complete -ssRNA genome can be synthesized. -ssRNA viruses vary between those that initiate transcription by the RdRp creating a cap on the 5'-end (usually pronounced "five prime end") of the genome or by snatching a cap from host mRNA and attaching it to the viral RNA. For many -ssRNA viruses, at the end of transcription, RdRp stutters on a uracil in the genome, synthesizing hundreds of adenines in

208-426: 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 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

260-497: A need to some base pairing with the 3’ end of the viral genome. The nucleoprotein structure in Lassa virus ( Arenaviridae ) contains a second nuclease. Researchers propose that it is involved in attenuating interferon response, but it also contains a dTTP-binding site which may be used for cap-snatching. In this model, the L and N proteins cooperate in the cap-snatching process. The two-domain model has also been prosed for hantaviruses, but

312-482: A reduced number of progeny, so viral genomes typically contain sequences that are highly conserved over time with relatively few mutations. Many RdRp-encoding RNA viruses also experience a high rate of genetic recombination , though rates of recombination vary significantly, with lower rates in -ssRNA viruses and higher rates in dsRNA and +ssRNA viruses. There are two types of recombination: copy choice recombination and reassortment. Copy choice recombination occurs when

364-677: 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 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

416-428: A row as part of creating a polyadenylated tail for the mRNA. Some -ssRNA viruses are essentially ambisense, and have proteins encoded by both the positive and negative strand, so mRNA is synthesized directly from the genome and from a complementary strand. For dsRNA viruses, RdRp transcribes mRNA by using the negative strand as a template. Positive strands may also be used as templates to synthesize negative strands for

468-527: A single jelly roll fold , so named because the folded structure of the protein contains a structure that resembles a jelly roll . Many also possess an envelope , a type of lipid membrane that typically surrounds the capsid. In particular, the viral envelope is near-universal among negative-sense, single-stranded (-ssRNA) viruses. Viruses in Orthornavirae have three different types of genomes: dsRNA, +ssRNA, and -ssRNA. Single-stranded RNA viruses have either

520-543: A single virion, typically individual segments are swapped. Both forms of recombination can only occur if more than one virus is present in a cell, and the more alleles are present, the more likely recombination is to occur. A key difference between copy choice recombination and reassortment is that copy choice recombination can occur anywhere in a genome, whereas reassortment swaps fully-replicated segments. Therefore, copy choice recombination can produce non-functional viral proteins whereas reassortment cannot. The mutation rate of

572-553: 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

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624-593: A time period of major advancements in molecular biology, including the discovery of mRNA as the immediate carrier of genetic information for protein synthesis. Tobacco mosaic virus was discovered in 1898 and was the first virus to be discovered. Viruses in the kingdom that are transmitted by arthropods have been a key target in the development of vector control , which often aims to prevent viral infections. In modern history, numerous disease outbreaks have been caused by RdRp-encoding RNA viruses, including outbreaks caused by coronaviruses, ebola, and influenza. Orthornavirae

676-607: A unique fold, but it uses aromatic stacking to execute m G cap-binding similar to other cap-binding proteins. PA is a member of the PD(D/E)XK nuclease family, which uses divalent metal ions to cleave nucleic acid. However, it has a peculiar active site histidine residue which ligates the Mn2+ ion used for cleavage. In October 2018, the United States FDA approved baloxavir marboxil for treatment of acute uncomplicated influenza , marking

728-537: A virus is associated with the rate of genetic recombinations. Higher mutation rates increase both the number of advantageous and disadvantageous mutations, whereas higher rates of recombination allows for beneficial mutations to be separated from deleterious ones. Therefore, higher rates of mutations and recombinations, up to a certain point, improve viruses' ability to adapt. Notable examples of this include reassortments that enable cross-species transmission of influenza viruses, which have led to numerous pandemics, as well as

780-575: Is Duplopiviricetes , whose members are double-stranded RNA viruses that are descended from +ssRNA viruses. Cap snatching In the influenza virus , cap snatching occurs in the nucleus of the cell. The cap snatching endonuclease function is contained in the PA subunit of the RNA polymerase . In Arenaviridae and Bunyavirales , cap-snatching takes place in the cytoplasm. Cap-snatching occurs in three general steps: 1) The viral RdRp or N protein binds to

832-498: Is located at the N-terminus of the L protein. TN-terminal domain is conserved between various families, suggesting evolutionary similarity. However, the cap-binding domain is not confirmed for every virus family, but it is believed to be located in the L or nucleocapsid (N or NP) protein.[1] In the bunyavirales, endonuclease cleavage and nucleotide motif preferences vary between families, genera and species. This variation occurs because of

884-515: Is not necessary. However, +ssRNA will produce dsRNA forms as part of the process of replicating their genomes. From the dsRNA, additional positive strands are synthesized, which may be used as mRNA or for genomes for progeny. Because +ssRNA viruses create intermediate dsRNA forms, they have to avoid the host's immune system in order to replicate. +ssRNA viruses accomplish this by replicating in membrane-associated vesicles that are used as replication factories. For many +ssRNA viruses, subgenomic portions of

936-466: Is subdivided into five phyla that separate member viruses based on their genome type, host range, and genetic similarity. Viruses with three genome types are included: positive-strand RNA viruses , negative-strand RNA viruses , and double-stranded RNA viruses . Many of the most widely known viral diseases are caused by members of this kingdom, including coronaviruses , the Ebola virus , influenza viruses ,

988-407: Is the most important virus among stone fruit crops. Brome mosaic virus , while not causing significant economic losses, is found throughout much of the world and primarily infects grasses, including cereals. Diseases caused by RNA viruses in Orthornavirae have been known throughout much of history, but their cause was only discovered in modern times. As a whole, RNA viruses were discovered during

1040-412: 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 the kingdom Orthornavirae and realm Riboviria . They are monophyletic and descended from a common RNA virus ancestor. In

1092-776: The Flavivirus and Phlebovirus genera are numerous and often transmitted to humans. Coronaviruses and influenza viruses cause disease in various vertebrates, including bats, birds, and pigs. Plant viruses in the kingdom are numerous and infect many economically important crops. Tomato spotted wilt virus is estimated to cause more than US$ 1 billion in damages annually, affecting more than 800 plant species including chrysanthemum, lettuce, peanut, pepper, and tomato. Cucumber mosaic virus infects more than 1,200 plant species and likewise causes significant crop losses. Potato virus Y causes significant reductions in yield and quality for pepper, potato, tobacco, and tomato, and Plum pox virus

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1144-664: 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

1196-694: 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 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

1248-962: The Baltimore classification system, which groups viruses together based on their manner of mRNA synthesis, and which is often used alongside standard virus taxonomy, which is based on evolutionary history. Those three groups are Group III: dsRNA viruses, Group IV: +ssRNA viruses, and Group V: -ssRNA viruses. RNA viruses are associated with a wide range of disease, including many of the most widely known viral diseases. Notable disease-causing viruses in Orthornavirae include: Animal viruses in Orthornavirae include orbiviruses , which cause various diseases in ruminants and horses, including Bluetongue virus , African horse sickness virus , Equine encephalosis virus , and epizootic hemorrhagic disease virus . The vesicular stomatitis virus causes disease in cattle, horses, and pigs. Bats harbor many viruses including ebolaviruses and henipaviruses , which also can cause disease in humans. Similarly, arthropod viruses in

1300-453: The RNA world , suggesting that retroelements (retrotransposons and group II introns) originated from an ancestor related to the phylum Lenarviricota and that members of a newly discovered Taraviricota lineage (phylum) would be the ancestors of all RNA viruses. According to this study the genomes of both dsRNA, +ssRNA and -ssRNA evolved independently and were altered several times in evolution. RNA viruses that encode RdRp are assigned to

1352-418: The measles virus , and the rabies virus , as well as the first virus ever discovered, tobacco mosaic virus . In modern history, RdRp-encoding RNA viruses have caused numerous disease outbreaks, and they infect many economically important crops. Most eukaryotic viruses, including most human, animal, and plant viruses, are RdRp-encoding RNA viruses. In contrast, there are relatively few prokaryotic viruses in

1404-457: The 5’ end of the viral RNA (vRNA), activating PB2 and causing the 3’ end of the vRNA to form a double-stranded zone with the 5’ end. The PB2 proceeds to bind cellular mRNA at the N7-methyl guanosine (m G) capped 5’ end. The PA subunit subsequently cleaves the sequence 10-13 nucleotides from the cap structure via endonuclease activity at the N terminus. The exact cleavage location is dependent both on

1456-407: The N protein in the rift valley fever virus ( Phenuiviridae ) does not possess the same features. Cap snatching has also been investigated in depth for the family Hantaviridae ( Bunyavirales ). There is evidence that the N protein binds to the 5’ cap and protects them from degradation by cellular machinery. The N protein accumulates in cytoplasmic cellular processing bodies (P bodies), sequestering

1508-525: The RdRp switches templates during synthesis without releasing the prior, newly created RNA strand, which generates a genome of mixed ancestry. Reassortment , which is restricted to viruses with segmented genomes, has segments from different genomes packaged into a single virion, or virus particle, which also produces hybrid progeny. For reassortment, some segmented viruses package their genomes into multiple virions, which produces genomes that are random mixtures of parents, whereas for those that are packaged into

1560-402: The RdRp. The Hantaviridae RdRp can also engage in a “prime and realign” mechanism: The host oligonucleotide primes mRNA transcription and initiates transcription with a terminal G residue. After several nucleotides are added, the nascent RNA realigns by moving two nucleotides backwards on the repeated terminal sequence (AUCAUCAUC) so that the host G is once again the first nucleotide, creating

1612-478: 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

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1664-739: 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

1716-453: 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

1768-430: The conformation of the RdRp. Additionally, by reducing Pol II abundance, influenza can begin to shut off critical host transcription. Cap snatching is not used during replication. Instead, the RdRp performs a “prime and realign” step ensure that the genome is fully copied. In this mechanism, the RdRp sets down a primer internally, then the vRNA is realigned to continue replication. Influenza's PB2 cap-binding domain has

1820-723: The construction of genomic dsRNA. dsRNA is not a molecule produced by cells, so cellular life has evolved mechanisms to detect and inactivate viral dsRNA. To counter this, dsRNA viruses typically retain their genomes inside of viral capsid in order to evade the host's immune system. RNA viruses in Orthornavirae experience a high rate of genetic mutations because RdRp is prone to making errors in replication since it typically lacks proofreading mechanisms to repair errors. Mutations in RNA viruses are often influenced by host factors such as dsRNA-dependent adenosine deaminases , which edit viral genomes by changing adenosines to inosines . Mutations in genes that are essential for replication lead to

1872-494: The distance between the PB2 and the PA of the RdRp (around 50 angstroms or 10-13 nucleotides) and also the sequence of the mRNA. Then, the PB1 subunit, which contains the polymerase activity, initially adds on two new nucleotides. The cap snatched primer moves through the product exit tunnel in the PB1 domain to serve as the primer for transcription. The vRNA 3’-UCGUUUU nucleotides are not bound to

1924-523: The emergence of drug-resistance influenza strains via mutations that were reassorted. The exact origin of Orthornavirae is not well established, but the viral RdRp shows a relation to the reverse transcriptase (RT) enzymes of group II introns that encode RTs and retrotransposons , the latter of which are self-replicating DNA sequences that integrate themselves into other parts of the same DNA molecule. A larger study (2022) where new lieneages (phyla) were described, has suggested that RNA viruses descend from

1976-472: The first new influenza anti-viral drug class in over two decades. The drug utilizes knowledge about cap snatching by targeting and inhibiting the endonuclease function of the PA subunit, which will prevent the virus from initiating transcription. Baloxavir marboxil (Xofluza) is effective against both influenza A and B. The family Arenaviridae and order Bunyavirales are also segmented negative, single-stranded RNA viruses. A verified Mn dependent endonuclease

2028-415: The genome will be transcribed to translate specific proteins, whereas others will transcribe a polyprotein that is cleaved to produce separate proteins. Negative-strand RNA viruses have genomes that function as templates from which mRNA can be synthesized directly by RdRp. Replication is the same process but executed on the positive sense antigenome, during which RdRp ignores all transcription signals so that

2080-419: The genome. Viruses in this kingdom share a number of characteristics which promote rapid evolution , including high rates of genetic mutation , recombination , and reassortment . Viruses in Orthornavirae belong to the realm Riboviria . They are descended from a common ancestor that may have been a non-viral molecule that encoded a reverse transcriptase instead of an RdRp for replication. The kingdom

2132-480: The host mRNA 5’-methylated cap-1 or cap-2 structure. 2) Viral endonuclease cleaves mRNA several nucleotides downstream of the cap. 3) Capped RNA utilized as a primer to initiate viral mRNA synthesis carried out by the RdRp. Cap snatching is best described in influenza viruses, especially influenza A. In Orthomyxoviridae , the viral family of influenza, the RdRp is divided into three subunits: PA, PB1 and PB2.            PB1 first binds

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2184-423: 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

2236-410: The kingdom Orthornavirae , which contains six official phyla, six unofficial phyla and several taxa that are unassigned to a phylum due to lack of information. The five phyla are separated based on the genome types, host ranges, and genetic similarity of member viruses. The unassigned taxa are listed hereafter (- viridae denotes family and - virus denotes genus). The kingdom contains three groups in

2288-406: The kingdom. The first part of Orthornavirae comes from Greek ὀρθός [orthós], meaning straight, the middle part, rna , refers to RNA, and - virae is the suffix used for virus kingdoms. RNA viruses in Orthornavirae typically do not encode many proteins, but most positive-sense, single-stranded (+ssRNA) viruses and some double-stranded RNA (dsRNA) viruses encode a major capsid protein that has

2340-506: 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 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

2392-451: 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

2444-421: The polymerase but rather are free for complementary binding with the capped RNA primer to confer stability. Transcription then begins with G or C residue on the 3’ end of the capped primer. Finally, the PB1 subunit completes chain elongation in the canonical 5’ to 3’ direction, releasing the cap, but keeping the 5’ end bound. The viral 3’ poly-A tail is added at the end of transcription by polymerase stuttering from

2496-412: The positive-sense RNA genome proceeds through double-stranded RNA intermediates, and 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

2548-577: 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 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

2600-465: The protected 5’ caps as a pool of available primers for the RdRp to begin viral mRNA synthesis. There are four nucleotides on the vRNA that are adjacent the 5’ cap for binding. The virus preferentially cleaves mRNA cap at a G residue 14 nucleotides downstream from the cap. Additionally, it usually cleaves caps from nonsense mRNA instead of actively translated mRNA. The N protein can guard host mRNA caps without P-bodies, but they are not used as efficiently by

2652-429: The steric hindrance of the vRNA loop. The resulting viral mRNA looks is identical to host mRNA, allowing endogenous cellular machinery to carry out processing and nuclear export. The de-capped host mRNAs are targeted degradation, which lead to the downregulation of cellular mRNA. Influenza RdRp also interacts with the cell Polymerase II (Pol II) C terminal domain, which potentially promotes viral transcription by changing

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2704-541: Was established in 2019 as a kingdom within the realm Riboviria , intended to accommodate all RdRp-encoding RNA viruses. Prior to 2019, Riboviria was established in 2018 and included only RdRp-encoding RNA viruses. In 2019, Riboviria was expanded to also include reverse transcribing viruses, placed under the kingdom Pararnavirae , so Orthornavirae was established to separate RdRp-encoding RNA viruses from reversing transcribing viruses. Positive-strand RNA virus Positive-strand RNA viruses ( +ssRNA viruses ) are

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