| Orthornavirae | |
|---|---|
 | |
| Clockwise from top left:TEM ofavian coronavirus,polio virus,bacteriophage Qβ,ebolavirus,tobacco mosaic virus,influenzavirus A,rotavirus,vesicular stomatitis virus. Center: phylogenetic tree of shared replication proteinRdRp. | |
Virus classification | |
| (unranked): | Virus |
| Realm: | Riboviria |
| Kingdom: | Orthornavirae |
| Phyla and classes | |
Orthornavirae is a kingdom ofviruses that have genomes made ofribonucleic acid (RNA), including genes whichencode anRNA-dependent RNA polymerase (RdRp). The RdRp is used totranscribe the viral RNA genome intomessenger RNA (mRNA) and toreplicate the genome. Viruses in this kingdom share a number of characteristics which promote rapidevolution, including high rates ofgenetic mutation,recombination, andreassortment.
Viruses inOrthornavirae belong to the realmRiboviria. They are descended from acommon ancestor that may have been a non-viral molecule that encoded areverse transcriptase instead of an RdRp for replication. The kingdom is subdivided into seven 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, anddouble-stranded RNA viruses.
Many of the most widely known viral diseases are caused by members of this kingdom, includingcoronaviruses, theEbola virus,influenza viruses, themeasles virus, and therabies 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. Mosteukaryotic viruses, including most human, animal, and plant viruses, are RdRp-encoding RNA viruses. In contrast, there are relatively fewprokaryotic viruses in the kingdom.
The first part ofOrthornavirae comes fromGreek ὀρθός [orthós], meaning straight, the middle part,rna, refers to RNA, and -virae is the suffix used for virus kingdoms.[1]
RNA viruses inOrthornavirae 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 a singlejelly roll fold, so named because the folded structure of the protein contains a structure that resembles ajelly roll.[2] Many also possess anenvelope, a type oflipid membrane that typically surrounds the capsid. In particular, the viral envelope is near-universal among negative-sense, single-stranded (-ssRNA) viruses.[3][4]
Viruses inOrthornavirae have three different types of genomes: dsRNA, +ssRNA, and -ssRNA. Single-stranded RNA viruses have either apositive 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 enzymeRNA-dependent RNA polymerase (RdRp), also called RNA replicase.[1][2]
Positive-strand RNA viruses have genomes that can function as mRNA, so transcription 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.[5] For many +ssRNA viruses, subgenomic portions of the genome will be transcribed to translate specific proteins, whereas others will transcribe a polyprotein that is cleaved to produce separate proteins.[6][7]
Negative-strand RNA viruses have genomes that function as templates from which mRNA can be synthesized directly by RdRp.[8] Replication is the same process but executed on the positive sense antigenome, during which RdRp ignores all transcription signals so that a complete -ssRNA genome can be synthesized.[9] -ssRNA viruses vary between those that initiate transcription by the RdRp creating a cap on the 5'-end (pronounced "five prime end") of the genome or bysnatching a cap from host mRNA and attaching it to the viral RNA.[10] For many -ssRNA viruses, at the end of transcription, RdRpstutters on auracil in the genome, synthesizing hundreds ofadenines in a row as part of creating apolyadenylated tail for the mRNA.[11] 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.[12]
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 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.[13]
RNA viruses inOrthornavirae experience a high rate of geneticmutations because RdRp is prone to making errors in replication since it typically lacksproofreading mechanisms to repair errors.[note 1] Mutations in RNA viruses are often influenced by host factors such as dsRNA-dependentadenosine deaminases, which edit viral genomes by changingadenosines toinosines.[14][15] Mutations in genes that are essential for replication lead to a reduced number of progeny, so viral genomes typically contain sequences that arehighly conserved over time with relatively few mutations.[16]
Many RdRp-encoding RNA viruses also experience a high rate ofgenetic 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 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.[14][17]
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 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.[14][17][18][19]
The mutation rate of 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 allow 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.[14][20] Notable examples of this include reassortments that enable cross-species transmission of influenza viruses, which have led to numerous pandemics, as well as the emergence of drug-resistance influenza strains via mutations that were reassorted.[19]
The exact origin ofOrthornavirae is not well established, but the viral RdRp shows a relation to the reverse transcriptase (RT) enzymes ofgroup II introns that encode RTs andretrotransposons, the latter of which are self-replicating DNA sequences that integrate themselves into other parts of the same DNA molecule.[1][2] A larger study (2022) where new lieneages (phyla) were described, has suggested that RNA viruses descend from theRNA world, suggesting that retroelements (retrotransposons and group II introns) originated from an ancestor related to the phylumLenarviricota and that members of a newly discoveredTaraviricota 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.[21]
RNA viruses that encode RdRp are assigned to the kingdomOrthornavirae, which contains seven phyla and several taxa that are unassigned to a higher taxa due to lack of information. The phyla are separated based on the genome types, host ranges, and genetic similarity of member viruses.[1][22]
The following taxa inOrthornavirae are not assigned to any higher taxa:[1][22]
The kingdom contains three groups in theBaltimore 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.[1][2]
RNA viruses are associated with a wide range of disease, including many of the most widely known viral diseases. Notable disease-causing viruses inOrthornavirae include:[22]
Animal viruses inOrthornavirae includeorbiviruses, which cause various diseases in ruminants and horses, includingBluetongue virus,African horse sickness virus,Equine encephalosis virus, andepizootic hemorrhagic disease virus.[26] Thevesicular stomatitis virus causes disease in cattle, horses, and pigs.[27] Bats harbor many viruses includingebolaviruses andhenipaviruses, which also can cause disease in humans.[28] Similarly, arthropod viruses in theFlavivirus andPhlebovirus genera are numerous and often transmitted to humans.[29][30] Coronaviruses and influenza viruses cause disease in various vertebrates, including bats, birds, and pigs.[31][32]
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, andPlum pox virus 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.[22][33]
Diseases caused by RNA viruses inOrthornavirae have been known throughout much of history, but their cause was only discovered in modern times. As a whole, RNA viruses were discovered during a time period of major advancements in molecular biology, including the discovery of mRNA as the immediate carrier of genetic information for protein synthesis.[34] Tobacco mosaic virus was discovered in 1898 and was the first virus to be discovered.[35] Viruses in the kingdom that are transmitted by arthropods have been a key target in the development ofvector control, which often aims to prevent viral infections.[36] In modern history, numerous disease outbreaks have been caused by RdRp-encoding RNA viruses, including outbreaks caused by coronaviruses, ebola, and influenza.[37]
Orthornavirae was established in 2019 as a kingdom within the realmRiboviria, 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 kingdomPararnavirae, soOrthornavirae was established to separate RdRp-encoding RNA viruses from reversing transcribing viruses.[1][38]
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