Riboviria
Riboviria is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase, as well as reverse-transcribing viruses that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase, also called RNA replicase, produces RNA from RNA. RNA-dependent DNA polymerase, also called reverse transcriptase, produces DNA from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA for translation of viral proteins.
Riboviria was established in 2018 to accommodate all RdRp-encoding RNA viruses and was expanded a year later to also include RdDp-encoding viruses. 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. Most identified eukaryotic viruses belong to the realm, including most human, animal, and plant viruses. Historically, few prokaryotic RNA viruses had been discovered to be included in the realm, but in the 2020s metagenomic and metatranscriptomic studies have discovered many prokaryotic RNA viruses.
Many of the most widely known viral diseases are caused by viruses in Riboviria, which includes coronaviruses, ebola virus, HIV, influenza viruses, and the rabies virus. These viruses and others in the realm have been prominent throughout history, including Tobacco mosaic virus, which was the first virus to be discovered. Many reverse-transcribing viruses integrate their genome 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 of ribo, which refers to ribonucleic acid, and the suffix -viria, which is the suffix used for virus realms. Members of the realm are called ribovirians.Characteristics
All members of Riboviria contain a gene that encodes for an RNA-dependent polymerase, also called RNA-directed polymerase. There are two types of RNA-dependent polymerases: RNA-dependent RNA polymerase, also called RNA replicase, which synthesizes RNA from RNA, and RNA-dependent DNA polymerase, also called reverse transcriptase, which synthesizes DNA from RNA. For viruses in Riboviria, in a typical virus particle, called a virion, the RNA-dependent polymerase is bound to the viral genome in some manner and begins transcription of the viral genome after entering 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.Riboviria contains three types of viruses that replicate via RdRp: single-stranded RNA viruses, which are either positive or negative sense, and double-stranded RNA viruses, all of which belong to the kingdom Orthornavirae. +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 negative-sense strands of the genomes of -ssRNA viruses and dsRNA viruses act as templates from which RdRp creates mRNA.
There are two types of viruses in Riboviria that replicate via reverse transcription: single-stranded RNA viruses, all of which belong to the order Ortervirales, and double-stranded DNA viruses, which belong to the family Caulimoviridae, also in Ortervirales, and the family Hepadnaviridae of the order Blubervirales. Reverse-transcribing viruses all belong to the kingdom Pararnavirae. ssRNA-RT viruses have their positive-sense genome transcribed by RdDp to synthesize a negative-sense complementary DNA 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, 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 rcDNA. The rcDNA genome is later repaired by the host cell's DNA repair mechanisms to synthesize a covalently closed circular DNA 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.
Viral mRNA is translated by the host cell's ribosomes 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 viral proteins are assembled into complete virions, which then leave the host cell.
Viruses of Ambiviricota have ambisense, circular ssRNA genomes. Their genomes contain at least two open reading frames and ribozymes in opposite sense orientations of the genome—one positive-sense portion of the genome and one negative-sense portion of the genome. For that reason, they are not considered positive-sense or negative-sense but ambisense. Ambiviricots encode RdRp, but unlike other viruses of Orthornavirae, they replicate their genome via rolling circle replication, a form of replication used for circular genomes. Apart from ambiviricots, some other ssRNA viruses are ambisense because they contain ORFs on both sense strands, including influenza viruses and coronaviruses, but these viruses replicate in the manners typical of -ssRNA and +ssRNA viruses, respectively, so they are still considered -ssRNA and +ssRNA viruses.
Phylogenetics
Phylogenetic analysis of RNA polymerases is used to study the evolutionary history of Riboviria because it is the only gene preserved among all ribovirians. The reverse transcriptases of kingdom Pararnavirae show a relation to the RTs of group II introns that encode RTs and non-long terminal repeat retrotransposons, which are self-replicating DNA sequences. More specifically, the two orders of the kingdom, Blubervirales and Ortervirales, appear to have evolved from two different retrotransposon families on two separate occasions by acquiring host proteins and using them for virion formation. The origin of Orthornavirae is less clear and different hypotheses exist. In the first hypothesis, viruses of Orthornavirae also originate from retroelements such as group II introns and non-LTR retrotransposons. In the second hypothesis, both retroelements and the viral RdRp are descended from a capsidless RNA replicon that was present in the RNA world.The unclassified phylum Taraviricota may be such capsidless RNA ancestors as it appears to be the basal lineage from which all Orthornavirae phyla are descended from. The phylum Artimaviricota, so-called "hot spring riboviruses", encode an RdRp that is very distantly related to the RdRp of Orthornavirae and which, based on analysis of its structure, may be an intermediate between RdRps and RTs.
Ribovirians generally have no relation to viral agents outside the realm, with a few exceptions. Viruses of the kingdom Shotokuvirae in the realm Monodnaviria appear to have come into existence on multiple, independent occasions. These monodnavirians originate from multiple recombination events in which bacterial and archaeal plasmids merged with complementary DNA copies of positive-sense RNA viruses, which enabled these plasmids to obtain capsid proteins needed to form virions. Additionally, the ribovirian phylum Ambiviricota appears to have a chimeric origin in which a ribovirian and a ribozyme-containing viroid or ribozyvirian recombined to form a new lineage.
Classification
Riboviria contains two kingdoms: Orthornavirae and Pararnavirae, the latter of which 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, -ssRNA, and ambisense 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: Artverviricota
- ** Class: Revtraviricetes
Riboviria partially merges Baltimore classification with virus taxonomy as it includes the Baltimore groups for RNA viruses and reverse-transcribing viruses in the realm. Baltimore classification is a system used to classify viruses based on their manner of mRNA production. It is 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 seven. The others are Adnaviria, Duplodnaviria, Monodnaviria, Ribozyviria, Singelaviria, and Varidnaviria.