Realm (virology)

Did You Know?

• The rank of subrealm uses the suffix -vira for viruses, -viroida for viroids, and -satellitida for satellites; as of 2019, no taxa are described at this rank.
• Duplodnaviria includes tailed bacteriophages, which are ubiquitous worldwide and important in marine ecology.

Naming

The names of virus realms consist of a descriptive first part and the suffix -viria. For example, Duplodnaviria means "double DNA", referring to dsDNA viruses; Monodnaviria means "single DNA"; Riboviria is taken from ribonucleic acid; and Varidnaviria means "various DNA". For viroids, the suffix is -viroidia, and for satellites, the suffix is -satellitia, but as of 2019 neither viroid nor satellite realms have been designated.

Realms

Duplodnaviria contains dsDNA viruses that encode a major capsid protein with the HK97 fold, share an icosahedral capsid shape, and use a terminase enzyme for DNA packaging. It includes tailed bacteriophages (order Caudovirales) and herpesviruses (order Herpesvirales). Their relation is uncertain; they may share a common ancestor or herpesviruses may be a divergent clade from within Caudovirales. Duplodnaviruses cause latent infections. Monodnaviria contains ssDNA viruses encoding an HUH superfamily endonuclease that initiates rolling circle replication, plus their descendants. Prototypical members are CRESS-DNA viruses with circular ssDNA genomes. Eukaryotic monodnaviruses include papillomaviruses, polyomaviruses, and geminiviruses. Riboviria contains all RNA viruses encoding an RNA-dependent RNA polymerase (kingdom Orthornavirae) and all reverse transcribing viruses encoding a reverse transcriptase (kingdom Pararnavirae). Most eukaryotic viruses belong to this realm.

Origins

Virus realms generally have no genetic relation to each other based on common descent, unlike the three domains of cellular life. Each realm represents at least one instance of viruses coming into existence. Adnaviria is of unknown origin but may have infected the last archaeal common ancestor. Duplodnaviria is either monophyletic or polyphyletic and may predate the last universal common ancestor; its HK97-fold MCP is also found in encapsulins. Monodnaviria is polyphyletic and appears to have emerged multiple times from bacterial and archaeal circular plasmids. Riboviria is monophyletic or polyphyletic; its reverse transcriptase likely evolved from a retrotransposon, while its RdRp may originate from a bacterial group II intron or predate the LUCA. A 2022 study favored the hypothesis that RNA viruses descend from the RNA world. Ribozyviria is of unknown origin, possibly derived from retrozymes or a viroid-like element with capsid protein capture.

History

Before the 21st century, deep evolutionary relations between viruses were thought undiscoverable due to high mutation rates and small gene numbers, so the highest taxonomic rank from 1991 to 2017 was order. In the 21st century, metagenomics and comparison of highly conserved traits enabled deeper study, leading the ICTV to adopt a 15-rank classification system in votes in 2018 and 2019. Riboviria was established in 2018, and Duplodnaviria, Monodnaviria, and Varidnaviria were established in 2019.