''Riboviria'' 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 ...

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 viruses that use a homologous RNA-dependent polymerase for replication. It includes

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 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 ...

RNA-dependent RNA polymerase RNA-dependent RNA polymerase (RdRp) or RNA replicase is an enzyme that catalyzes the replication of RNA from an RNA template. Specifically, it catalyzes synthesis of the RNA strand complementary to a given RNA template. This is in contrast to t ...

, as well as reverse-transcribing viruses (with either RNA or DNA genomes) that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase (RdRp), also called RNA replicase, produces RNA (

ribonucleic acid Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

) from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA ( deoxyribonucleic acid) from RNA. These

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 are essential for replicating the viral genome and

transcribing Transcription in the linguistic sense is the systematic representation of spoken language in written form. The source can either be utterances (''speech'' or ''sign language'') or preexisting text in another writing system. Transcription shoul ...

viral genes into

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) for

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 ...

of viral

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

s. ''Riboviria'' was established in 2018 to accommodate all RdRp-encoding RNA viruses and was expanded a year later to also include RdDp-encoding retroviruses. These two groups of viruses are assigned to two separate kingdoms: ''Orthornavirae'' for RdRp-encoding RNA viruses, and ''Pararnavirae'' for RdDp-encoding viruses, i.e. all reverse-transcribing viruses. While the realm has few

prokaryotic A prokaryote () is a Unicellular organism, single-celled organism that lacks a cell nucleus, nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek language, Greek wikt:πρό#Ancient Greek, πρό (, 'before') a ...

viruses, it includes most

eukaryotic 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 ...

viruses, including most human, animal, and plant viruses, however, metagenomic studies are changing this perspective. Many of the most widely known viral diseases are caused by viruses in ''Riboviria'', which includes

coronavirus Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In humans and birds, they cause respiratory tract infections that can range from mild to lethal. Mild illnesses in humans include some cases of the com ...

es,

ebola virus ''Zaire ebolavirus'', more commonly known as Ebola virus (; EBOV), is one of six known species within the genus ''Ebolavirus''. Four of the six known ebolaviruses, including EBOV, cause a severe and often fatal hemorrhagic fever in humans and ot ...

HIV The human immunodeficiency viruses (HIV) are two species of ''Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immune ...

influenza virus ''Orthomyxoviridae'' (from Greek ὀρθός, ''orthós'' 'straight' + μύξα, ''mýxa'' 'mucus') is a family of negative-sense RNA viruses. It includes seven genera: ''Alphainfluenzavirus'', ''Betainfluenzavirus'', '' Gammainfluenzavirus'', ...

es, and the

rabies virus Rabies virus, scientific name ''Rabies lyssavirus'', is a neurotropic virus that causes rabies in humans and animals. Rabies transmission can occur through the saliva of animals and less commonly through contact with human saliva. ''Rabies lyss ...

. These viruses and others have been prominent throughout history, including ''

Tobacco mosaic virus ''Tobacco mosaic virus'' (TMV) is a positive-sense single-stranded RNA virus species in the genus ''Tobamovirus'' that infects a wide range of plants, especially tobacco and other members of the family Solanaceae. The infection causes characteri ...

'', which was the first virus to be discovered. Many reverse transcribing viruses notably become integrated into the genome of their host as part of their replication cycle. As a result of that, it is estimated that about 7–8% of the human genome originates from these viruses.

Etymology

''Riboviria'' is a

portmanteau A portmanteau word, or portmanteau (, ) is a blend of wordsentering a cell. As part of a virus's life cycle, the RNA-dependent polymerase also synthesizes copies of the viral genome as part of the process of creating new viruses. Viruses that replicate via RdRp belong to three groups in the Baltimore classification system, all of which are in the kingdom ''Orthornavirae'': single-stranded RNA (ssRNA) viruses, which are either positive (+) or negative (-)

sense A sense is a biological system used by an organism for sensation, the process of gathering information about the world through the detection of Stimulus (physiology), stimuli. (For example, in the human body, the brain which is part of the cen ...

, and double-stranded RNA viruses (dsRNA). +ssRNA viruses have genomes that can functionally act as mRNA, and a negative sense strand can also be created to form dsRNA from which mRNA is transcribed from the negative strand. The genomes of -ssRNA viruses and dsRNA viruses act as templates from which RdRp creates mRNA. Viruses that replicate via reverse transcription belong to two Baltimore groups, both of which are in the kingdom ''Pararnavirae'': single-stranded RNA (ssRNA-RT) viruses, all of which belong to the order ''

Ortervirales ''Ortervirales'' is an order that contains all accepted species of single-stranded RNA viruses that replicate through a DNA intermediate (Group VI) and all accepted species of double-stranded DNA viruses (except '' Hepadnaviridae'') that replic ...

'', and double-stranded DNA (dsDNA-RT) viruses, which belong to the family ''

Caulimoviridae ''Caulimoviridae'' is a family of viruses infecting plants. There are 94 species in this family, assigned to 11 genera. Viruses belonging to the family ''Caulimoviridae'' are termed double-stranded DNA (dsDNA) reverse-transcribing viruses (or pa ...

'', also in ''Ortervirales'', and the family ''

Hepadnaviridae ''Hepadnaviridae'' is a family of viruses. Humans, apes, and birds serve as natural hosts. There are currently 18 species in this family, divided among 5 genera. Its best-known member is hepatitis B virus. Diseases associated with this family i ...

'' of the order ''Blubervirales''. ssRNA-RT viruses have their positive-sense genome transcribed by RdDp to synthesize a negative sense complementary DNA (-cDNA) strand. The +RNA strand is degraded and later replaced by RdDp with a +DNA strand to synthesize a linear dsDNA copy of the viral genome. This genome is then integrated into the host cell's DNA. For dsDNA-RT viruses, a pregenomic +RNA strand is transcribed from the relaxed circular DNA (rcDNA), which is in turn used by RdDp to transcribe a -cDNA strand. The +RNA strand is degraded and replaced in a similar manner as +ssRNA-RT viruses to synthesize the rcDNA. The rcDNA genome is later repaired by the host cell's DNA repair mechanisms to synthesize a covalently closed circular DNA (cccDNA) genome. The integrated genome of +ssRNA-RT viruses and the cccDNA of dsDNA-RT viruses are then transcribed into mRNA by the host cell enzyme

RNA polymerase II RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryoti ...

. Viral mRNA is

translated Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...

by the host cell's

ribosome 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 ...

s to produce viral proteins. In order to produce more viruses, viral RNA-dependent polymerases use copies of the viral genome as templates to replicate the viral genome. For +ssRNA viruses, an intermediate dsRNA genome is created from which +ssRNA is synthesized from the negative strand. For -ssRNA viruses, genomes are synthesized from complementary positive sense strands. dsRNA viruses replicate their genomes from mRNA by synthesizing a complementary negative sense strand to form genomic dsRNA. For dsDNA-RT viruses, pregenomic RNA created from the cccDNA is retrotranscribed into new dsDNA genomes. For +ssRNA-RT viruses, the genome is replicated from the integrated genome. After replication and translation, the genome and the viral proteins are assembled into complete virions, which then leave the host cell.

Phylogenetics

Both kingdoms in ''Riboviria'' show a relation to the reverse transcriptases of

group II intron Group II introns are a large class of self-catalytic ribozymes and mobile genetic elements found within the genes of all three domains of life. Ribozyme activity (e.g., self- splicing) can occur under high-salt conditions ''in vitro''. However, ...

s that encode RTs and

retrotransposon Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through ...

s, which are self-replicating DNA sequences, the latter of which self-replicate via reverse transcription and integrate themselves into other parts of the same DNA molecule. Reverse transcribing viruses, assigned to ''Pararnavirae'', appear to have evolved from a retrotransposon on a single occasion. The origin of the RdRps of ''Orthornavirae'' is less clear due to a lack of information, that they originate from a reverse transcriptase from bacterial

before the emergence of eukaryotes or originated before the

last universal common ancestor The last universal common ancestor (LUCA) is the most recent population from which all organisms now living on Earth share common descent—the most recent common ancestor of all current life on Earth. This includes all cellular organisms; t ...

(LUCA) being descendants of the ancient

RNA world The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence ...

and that they preceded the retroelement reverse transcriptases. A larger study (2022) where new lieneages (phyla) were described, was in favor of the hypothesis that RNA viruses descend from the RNA world, suggesting that retroelements originated from an ancestor related to the phylum ''

Lenarviricota ''Lenarviricota'' is a phylum of RNA viruses that includes all positive-strand RNA viruses that infect prokaryotes. Some members also infect eukaryotes. Most of these viruses do not have capsids, except for the genus ''Ourmiavirus''. The name of ...

'' and that members of a newly discovered '' Taraviricota'' lineage (phylum) would be the ancestors of all RNA viruses.

Classification

''Riboviria'' contains two kingdoms: ''Orthornavirae'' and ''Pararnavirae''. ''Orthornavirae'' contains multiple phyla and unassigned taxa, whereas ''Pararnavirae'' is monotypic down to the rank of class. This taxonomy can be visualized hereafter. * Kingdom: '' Orthornavirae'', which contains all RdRp-encoding RNA viruses, i.e. all dsRNA, +ssRNA, and -ssRNA viruses, often collectively called RNA viruses * Kingdom: ''Pararnavirae'', which contains all RdDp-encoding viruses, i.e. all ssRNA-RT and dsDNA-RT viruses, collectively called reverse transcribing viruses ** Phylum: ''Arterviricota'' *** Class: '' Revtraviricetes'' Additionally, ''Riboviria'' contains two ''

incertae sedis ' () or ''problematica'' is a term used for a taxonomic group where its broader relationships are unknown or undefined. Alternatively, such groups are frequently referred to as "enigmatic taxa". In the system of open nomenclature, uncertainty ...

'' families and four ''incertae sedis'' genera. Additional information about them is needed to know their exact placement in higher taxa. They are listed hereafter (-''viridae'' indicates family and -''virus'' indicates genus). * '' Polymycoviridae'' * '' Sarthroviridae'' * ''

Albetovirus ''Albetovirus'' is a plant satellite virus genus. As a member of realm '' Riboviria'' without assigned family or order it contains just three species, ''Tobacco albetovirus 1'', ''2'', and ''3'' (alias Satellite tobacco necrosis virus 1, 2, resp ...

'' * ''

Aumaivirus Maize white line mosaic satellite virus (syn. Satellite maize white line mosaic virus, Satellite virus of maize white line mosaic virus, SMWLMV, SV-MWLMV) is a plant satellite virus. It is the only species in genus ''Aumaivirus'', which is a memb ...

'' * ''

Papanivirus Panicum mosaic satellite virus (SPMV) is a plant satellite virus in genus ''Papanivirus'', which is a member of realm ''Riboviria'' without assigned family or order. It only infects grasses which are infected by ''Panicum mosaic virus''. One stu ...

'' * ''

Virtovirus ''Tobacco virtovirus 1'', informally called Tobacco mosaic satellite virus, Satellite tobacco mosaic virus (STMV), or tobacco mosaic satellite virus, is a satellite virus first reported in ''Nicotiana glauca'' from southern California, U.S.. Its ...

'' Metagenomic studies have suggested the existence of five new phyla: '' Arctiviricota'', '' Taraviricota'', '' Pomiviricota'', '' Paraxenoviricota'' and '' Wamoviricota''. ''Riboviria'' partially merges

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 ...

with virus taxonomy, including the Baltimore groups for RNA viruses and reverse transcribing viruses in the realm. Baltimore classification is a classification system used for viruses based on their manner of mRNA production, often used alongside standard virus taxonomy, which is based on evolutionary history. All members of five Baltimore groups belong to ''Riboviria'': Group III: dsRNA viruses, Group IV: +ssRNA viruses, Group V: -ssRNA viruses, Group VI: ssRNA-RT viruses, and Group VII: dsDNA-RT viruses. Realms are the highest level of taxonomy used for viruses and ''Riboviria'' 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 ...

'', ''

Monodnaviria ''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 ...

'', 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 store ...

''. Most identified eukaryotic viruses are RNA viruses, and for that reason most eukaryotic viruses belong to ''Riboviria'', including most human, animal, and plant viruses. In contrast, only two groups of prokaryotic RNA viruses have been identified: +ssRNA ''

Leviviricetes ''Leviviricetes'' is a class of viruses, which infect prokaryotes. Most of these bacteriophages were discovered by metagenomics Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a ...

'', which appear to be some of the first RNA viruses to emerge and dsRNA ''

Cystoviridae ''Cystovirus'' is a genus of double-stranded RNA viruses which infects bacteria. It is the only genus in the family ''Cystoviridae.'' The name of the group c''ysto'' derives from Greek ''kystis'' which means bladder or sack. There are seven spec ...

'', which appears to be related to

reovirus ''Reoviridae'' is a family of double-stranded RNA viruses. Member viruses have a wide host range, including vertebrates, invertebrates, plants, protists and fungi. They lack lipid envelopes and package their segmented genome within multi-layered ...

es, which infect eukaryotes. Studies of megenomic samples have uncovered new prokaryotic RNA virus taxa including two new phyla that infect only prokaryotes, suggesting that their diversity is greater than previously thought and challenging the traditional view that RNA viruses only infect mostly eukaryotes. They also suggest that families '' Picobirnaviridae'' and ''

Partitiviridae ''Partitiviridae'' is a family of double-stranded RNA viruses. Plants, fungi, and protozoa serve as natural hosts. It has been suggested that they can also infect bacteria. The name comes from the Latin ''partitius,'' which means divided, and ...

'' previously associated with eukaryotes also infect prokaryotes. Other major branches of eukaryotic viruses include

herpesvirus ''Herpesviridae'' is a large family of DNA viruses that cause infections and certain diseases in animals, including humans. The members of this family are also known as herpesviruses. The family name is derived from the Greek word ''ἕρπειν ...

es in ''Duplodnaviria'', 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 ...

'' in ''Monodnaviria'', and many viruses in ''Varidnaviria''.

Interactions with hosts

Disease

Viruses in ''Riboviria'' are associated with a wide range of diseases, including many of the most widely known viral diseases. Notable disease-causing viruses in the realm include: *

es * '' Crimean-Congo hemorrhagic fever orthonairovirus'' * ''

Dengue virus ''Dengue virus'' (DENV) is the cause of dengue fever. It is a mosquito-borne, single positive-stranded RNA virus of the family ''Flaviviridae''; genus ''Flavivirus''. Four serotypes of the virus have been found, a reported fifth has yet to be co ...

'' * ''

Ebolavirus The genus ''Ebolavirus'' (- or ; - or ) is a virological taxon included in the family '' Filoviridae'' (filament-shaped viruses), order ''Mononegavirales''. The members of this genus are called ebolaviruses, and encode their genome in the for ...

'' *

hantavirus ''Orthohantavirus'' is a genus of single-stranded, enveloped, negative-sense RNA viruses in the family ''Hantaviridae'' within the order ''Bunyavirales''. Members of this genus may be called orthohantaviruses or simply hantaviruses. Orthohantav ...

es * ''

Hepatitis B virus ''Hepatitis B virus'' (HBV) is a partially double-stranded DNA virus, a species of the genus ''Orthohepadnavirus'' and a member of the ''Hepadnaviridae'' family of viruses. This virus causes the disease hepatitis B. Disease Despite there bein ...

'' * the

human immunodeficiency virus The human immunodeficiency viruses (HIV) are two species of ''Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause AIDS, acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the ...

es * ''

Human orthopneumovirus Respiratory syncytial virus (RSV), also called human respiratory syncytial virus (hRSV) and human orthopneumovirus, is a common, contagious virus that causes infections of the respiratory tract. It is a negative-sense, single-stranded RNA virus. ...

'' *

es * ''

Japanese encephalitis virus Japanese encephalitis (JE) is an infection of the brain caused by the Japanese encephalitis virus (JEV). While most infections result in little or no symptoms, occasional inflammation of the brain occurs. In these cases, symptoms may include he ...

'' * '' Lassa mammarenavirus'' * ''

Measles morbillivirus ''Measles morbillivirus'' (MeV), also called measles virus (MV), is a single-stranded, negative-sense, enveloped, non-segmented RNA virus of the genus ''Morbillivirus'' within the family ''Paramyxoviridae''. It is the cause of measles. Humans ...

'' * '' Mumps orthorubulavirus'' * ''

Norovirus Norovirus, sometimes referred to as the winter vomiting disease, is the most common cause of gastroenteritis. Infection is characterized by non-bloody diarrhea, vomiting, and stomach pain. Fever or headaches may also occur. Symptoms usually deve ...

'' *

Poliovirus A poliovirus, the causative agent of polio (also known as poliomyelitis), is a serotype of the species ''Enterovirus C'', in the family of ''Picornaviridae''. There are three poliovirus serotypes: types 1, 2, and 3. Poliovirus is composed of an ...

* ''

Rabies lyssavirus Rabies virus, scientific name ''Rabies lyssavirus'', is a neurotropic virus that causes rabies in humans and animals. Rabies transmission can occur through the saliva of animals and less commonly through contact with human saliva. ''Rabies lyss ...

'' *

Rhinovirus The rhinovirus (from the grc, ῥίς, rhis "nose", , romanized: "of the nose", and the la, vīrus) is the most common viral infectious agent in humans and is the predominant cause of the common cold. Rhinovirus infection proliferates in tem ...

es * '' Rift Valley fever phlebovirus'' * ''

Rotavirus ''Rotavirus'' is a genus of double-stranded RNA viruses in the family ''Reoviridae''. Rotaviruses are the most common cause of diarrhoeal disease among infants and young children. Nearly every child in the world is infected with a rotavirus a ...

'' * ''

Rubella virus Rubella virus (RuV) is the pathogenic agent of the disease rubella, transmitted only between humans via the respiratory route, and is the main cause of congenital rubella syndrome when infection occurs during the first weeks of pregnancy. Rube ...

'' * ''

Tick-borne encephalitis virus Tick-borne encephalitis virus (TBEV) is a positive-strand RNA virus associated with tick-borne encephalitis in the genus '' Flavivirus''. Classification Taxonomy TBEV is a member of the genus '' Flavivirus''. Other close relatives, members ...

'' * ''

West Nile virus West Nile virus (WNV) is a single-stranded RNA virus that causes West Nile fever. It is a member of the family ''Flaviviridae'', from the genus ''Flavivirus'', which also contains the Zika virus, dengue virus, and yellow fever virus. The virus ...

'' * ''

Yellow fever virus Yellow fever is a viral disease of typically short duration. In most cases, symptoms include fever, chills, loss of appetite, nausea, muscle pains – particularly in the back – and headaches. Symptoms typically improve within five days. In ...

'' * ''

Zika virus ''Zika virus'' (ZIKV; pronounced or ) is a member of the virus family ''Flaviviridae''. It is spread by daytime-active ''Aedes'' mosquitoes, such as '' A. aegypti'' and '' A. albopictus''. Its name comes from the Ziika Forest of Uganda, whe ...

'' Animal viruses in ''Riboviria'' include

orbivirus ''Orbivirus'' is a genus of double-stranded RNA viruses in the family ''Reoviridae'' and subfamily '' Sedoreovirinae''. Unlike other reoviruses, orbiviruses are arboviruses. They can infect and replicate within a wide range of arthropod and ver ...

es, which cause various diseases in ruminants and horses, including ''

Bluetongue virus Bluetongue disease is a noncontagious, insect-borne, viral disease of ruminants, mainly sheep and less frequently cattle, yaks, goats, buffalo, deer, dromedaries, and antelope. It is caused by ''Bluetongue virus'' (''BTV''). The virus is ...

'', ''

African horse sickness virus African horse sickness (AHS) is a highly infectious and deadly disease caused by ''African horse sickness virus''. It commonly affects horses, mules, and donkeys. It is caused by a virus of the genus ''Orbivirus'' belonging to the family ''Reovi ...

'', ''

Equine encephalosis virus ''Equine encephalosis virus'' (''EEV'') is a species of virus the ''Orbivirus'' genus, and a member of the ''Reoviridae'' family, related to '' African horse sickness virus'' (AHSV) and ''Bluetongue virus'' (BTV). First described in South Afric ...

'', and ''

epizootic hemorrhagic disease virus ''Epizootic hemorrhagic disease virus'', often abbreviated to EHDV, is a species of the genus ''Orbivirus'', a member of the family ''Reoviridae''. It is the causative agent of epizootic hemorrhagic disease, an acute, infectious, and often fatal ...

''. The

vesicular stomatitis virus ''Indiana vesiculovirus'', formerly ''Vesicular stomatitis Indiana virus'' (VSIV or VSV) is a virus in the family ''Rhabdoviridae''; the well-known ''Rabies lyssavirus'' belongs to the same family. VSIV can infect insects, cattle, horses and pigs ...

causes disease in cattle, horses, and pigs. Bats harbor many viruses including

ebolavirus The genus ''Ebolavirus'' (- or ; - or ) is a virological taxon included in the family '' Filoviridae'' (filament-shaped viruses), order ''Mononegavirales''. The members of this genus are called ebolaviruses, and encode their genome in the for ...

es and

henipavirus ''Henipavirus'' is a genus of negative-strand RNA viruses in the family ''Paramyxoviridae'', order ''Mononegavirales'' containing six established species, and numerous others still under study. Henipaviruses are naturally harboured by several sp ...

es, which also can cause disease in humans. Similarly, arthropod viruses in the ''

Flavivirus ''Flavivirus'' is a genus of positive-strand RNA viruses in the family ''Flaviviridae''. The genus includes the West Nile virus, dengue virus, tick-borne encephalitis virus, yellow fever virus, Zika virus and several other viruses which may cau ...

'' and ''

Phlebovirus ''Phlebovirus'' is one of twenty genera of the family ''Phenuiviridae'' in the order ''Bunyavirales''. The genus contains 66 species. It derives its name from Phlebotominae, the Vector (disease vector, vectors of member species ''Naples phlebovir ...

'' genera are numerous and often transmitted to humans. Coronaviruses and influenza viruses cause disease in various vertebrates, including bats, birds, and pigs. The family ''

Retroviridae A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptase e ...

'' contains many viruses that cause

leukemia Leukemia ( also spelled leukaemia and pronounced ) is a group of blood cancers that usually begin in the bone marrow and result in high numbers of abnormal blood cells. These blood cells are not fully developed and are called ''blasts'' or ' ...

immunodeficiency Immunodeficiency, also known as immunocompromisation, is a state in which the immune system's ability to fight infectious diseases and cancer is compromised or entirely absent. Most cases are acquired ("secondary") due to extrinsic factors that a ...

, and other cancers and immune system-related diseases in animals. Plant viruses in the realm are numerous and infect many economically important crops.

Tomato spotted wilt virus Transmission and lifespan TSWV, which is transmitted by thrips, causes serious losses in economically important crops and it is one of the most economically devastating plant viruses in the world. The circulative propagative transmission of T ...

is estimated to cause more than 1 billion USD in damages annually, affecting more than 800 plant species including chrysanthemum, lettuce, peanut, pepper, and tomato. ''

Cucumber mosaic virus ''Cucumber mosaic virus'' (CMV) is a plant pathogenic virus in the family ''Bromoviridae''. This virus has a worldwide distribution and a very wide host range, having the reputation of the widest host range of any known plant virus. It can be tra ...

'' infects more than 1,200 plant species and likewise causes significant crop losses. ''

Potato virus Y Potato virus Y (PVY) is a plant pathogenic virus of the family ''Potyviridae'', and one of the most important plant viruses affecting potato production. PVY infection of potato plants results in a variety of symptoms depending on the viral str ...

'' causes significant reductions in yield and quality for pepper, potato, tobacco, and tomato, and ''

Plum pox virus A plum is a fruit of some species in Prunus subg. Prunus, ''Prunus'' subg. ''Prunus'.'' Dried plums are called prunes. History Plums may have been one of the first fruits domesticated by humans. Three of the most abundantly cultivated spe ...

'' is the most important virus among stone fruit crops. ''

Brome mosaic virus ''Brome mosaic virus'' (BMV) is a small (28 nm, 86S), positive-stranded, icosahedral RNA plant virus belonging to the genus ''Bromovirus'', family ''Bromoviridae'', in the ''Alphavirus''-like superfamily. BMV was first isolated in 1942 from bro ...

'', while not causing significant economic losses, is found throughout much of the world and primarily infects grasses, including cereals.

Endogenization

Many reverse transcribing viruses, called retroviruses, in ''Riboviria'' are able to become integrated into the DNA of their host. These viruses become endogenized as part of their replication cycle. Namely, the viral genome is integrated into the host genome by the retroviral enzyme integrase, and viral mRNA is produced from that DNA. Endogenization is a form 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, and it is estimated that about 7–8% of the human genome consists of retroviral DNA. Endogenization can also be used to study the evolutionary history of viruses, showing an approximate time period when a virus first became endogenized into the host's genome as well as the rate of evolution for the viruses since endogenization first occurred.

History

Diseases caused by viruses in ''Riboviria'' have been known for much of recorded history, though their cause was only discovered in modern times. ''Tobacco mosaic virus'' was discovered in 1898 and was the first virus to be discovered. Viruses transmitted by arthropods have been central in the development of

vector control Vector control is any method to limit or eradicate the mammals, birds, insects or other arthropods (here collectively called " vectors") which transmit disease pathogens. The most frequent type of vector control is mosquito control using a varie ...

, which often aims to prevent viral infections. In modern history, numerous disease outbreaks have been caused by various members of the realm, including coronaviruses, ebola, and influenza. HIV especially has had dramatic effects on society as it causes a sharp decline in life expectancy and significant stigma for infected persons. For a long time, the relation between many viruses in ''Riboviria'' could not be established due to the high amount of genetic divergence among RNA viruses. With the development of viral

metagenomics Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microb ...

, many additional RNA viruses were identified, helping to fill in the gaps of their relations. This led to the establishment of ''Riboviria'' in 2018 to accommodate all RdRp-encoding RNA viruses based on phylogenetic analysis that they were related. A year later, all reverse transcribing viruses were added to the realm. The kingdoms were also established in 2019, separating the two RNA-dependent polymerase branches. When the realm was founded, it mistakenly included two

viroid Viroids are small single-stranded, circular RNAs that are infectious pathogens. Unlike viruses, they have no protein coating. All known viroids are inhabitants of angiosperms (flowering plants), and most cause diseases, whose respective economi ...

families, ''

Avsunviroidae The ''Avsunviroidae'' are a family of viroids. There are four species in three genera (''Avsunviroid'', ''Elaviroid'' and ''Pelamoviroid''). They consist of RNA genomes between 246 and 375 nucleotides in length. They are single-stranded covalent ...

'' and ''

Pospiviroidae The Pospiviroidae are a family of viroids, including the first viroid to be discovered, PSTVd. Their secondary structure is key to their biological activity. The classification of this family is based on differences in the conserved central re ...

'', and the genus ''

Deltavirus Hepatitis D is a type of viral hepatitis caused by the hepatitis delta virus (HDV). HDV is one of five known hepatitis viruses: A, B, C, D, and E. HDV is considered to be a satellite (a type of subviral agent) because it can propagate only in ...

'', which were promptly removed in 2019 because they use host cell enzymes for replication.

Etymology

Phylogenetics

Classification

Interactions with hosts

Disease

Endogenization

History

See also

References

Further reading