Riboviria

Riboviria is a portmanteau of ribo, referencing ribonucleic acid, and the suffix -viria, which is the suffix used for virus realms.[1]

A general scenario of RNA virus evolution

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 (RdRp), also called RNA replicase, which synthesizes RNA from RNA, and RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), which synthesizes DNA from RNA.[2] 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.

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, 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.[3] The genomes of -ssRNA viruses and dsRNA viruses act as templates from which RdRp creates mRNA.[4][5]

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, and double-stranded DNA (dsDNA-RT) viruses, which belong to the family Caulimoviridae, also in Ortervirales, and the family Hepadnaviridae 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.[6]

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.[7] 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.[6][7]

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.[3] For -ssRNA viruses, genomes are synthesized from complementary positive sense strands.[5] dsRNA viruses replicate their genomes from mRNA by synthesizing a complementary negative sense strand to form genomic dsRNA.[4] For dsDNA-RT viruses, pregenomic RNA created from the cccDNA is retrotranscribed into new dsDNA genomes.[7] For +ssRNA-RT viruses, the genome is replicated from the integrated genome.[6] After replication and translation, the genome and the viral proteins are assembled into complete virions, which then leave the host cell.

Phylogeny of Orthornavirae RNA-dependent polymerase. The five colored branches are the five phyla of Orthornavirae.

Both kingdoms in Riboviria show a relation to the reverse transcriptases of group II introns that encode RTs and retrotransposons, 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, but two scenarios have been suggested. The most likely scenario is that the RdRps of viruses in Orthornavirae originated from the reverse transcriptase of a bacterial group II intron shortly before the emergence of eukaryotes.[2][8][9] The other possibility is that the RdRps of Orthornavirae originated before the last universal common ancestor (LUCA) and that they preceded the retroelement reverse transcriptases.[10][11]

With regard to the second possibility, it has been noted that the capsid proteins of leviviruses, which infect bacteria, have no homologues with cellular organisms and other viruses. Furthermore, it has been claimed that the RdRps of other RNA viruses are more similar to reverse transcriptases than they are to the RdRps of leviviruses and their relatives in the phylum Lenarviricota. From that, it has been proposed that numerous lineages of prokaryotic RNA viruses may have gone extinct when they lost competition with prokaryotic DNA viruses, after which RNA viruses reemerged once they began to infect eukaryotes.[10][11]

It is also probable that there are RNA viruses that infect archaea based on metagenomic samples. Phylogenetic analysis of extracted sequences suggests that they are the most divergent RNA viruses and that they may be ancestors of eukaryotic RNA viruses, especially those of Pisuviricota, Kitrinoviricota, Duplornaviricota, and Negarnaviricota, which do not have an apparent prokaryotic ancestor.[12] The discovery of these viruses could change the ideas about the origin of RNA viruses.[10][11]

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.[13]

• 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 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).[2][13]

• Polymycoviridae
• Sarthroviridae
• Albetovirus
• Aumaivirus
• Papanivirus
• Virtovirus

Riboviria partially merges Baltimore classification 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, Monodnaviria, and Varidnaviria.[8][9][13]

Most identified eukaryotic viruses are RNA viruses, and for that reason most eukaryotic viruses belong to Riboviria, including most human, animal, and plant viruses. Prokaryotic RNA viruses are seemingly rare as only two such families have been identified: +ssRNA Leviviridae, whose origin is unclear, and dsRNA Cystoviridae, who appear to be related to reoviruses, which infect eukaryotes.[8] Other major branches of eukaryotic viruses include herpesviruses in Duplodnaviria,[14] the kingdom Shotokuvirae in Monodnaviria,[15] and various viruses in Varidnaviria.[16]

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.[28] Viruses transmitted by arthropods have been central in the development of vector control, which often aims to prevent viral infections.[29] In modern history, numerous disease outbreaks have been caused by various members of the realm, including coronaviruses, ebola, and influenza.[30] HIV especially has had dramatic effects on society as it causes a sharp decline in life expectancy and significant stigma for infected persons.[31][32]

For a long time, the relation between many viruses in Riboviria couldn't be established due to the high amount of genetic divergence among RNA viruses. With the development of viral metagenomics, many additional RNA viruses were identified, helping to fill in the gaps of their relations.[8] This led to the establishment of Riboviria in 2018 to accommodate all RdRp-encoding RNA viruses based on phylogenetic analysis that they were related.[1]

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.[2] When the realm was founded, it mistakenly included two viroid families, Avsunviroidae and Pospiviroidae, and the genus Deltavirus, which were promptly removed in 2019 because they use host cell enzymes for replication.[33]

• List of higher virus taxa

• Ward, C. W. (1993). "Progress towards a higher taxonomy of viruses". Research in Virology. 144 (6): 419–53. doi:10.1016/S0923-2516(06)80059-2. PMC 7135741. PMID 8140287.