Realm (virology) in the context of Conserved sequence

A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase. They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and those that have one strand of DNA in their genome, called single-stranded DNA (ssDNA) viruses. dsDNA viruses primarily belong to two realms: Duplodnaviria and Varidnaviria, and ssDNA viruses are almost exclusively assigned to the realm Monodnaviria, which also includes some dsDNA viruses. Additionally, many DNA viruses are unassigned to higher taxa. Reverse transcribing viruses, which have a DNA genome that is replicated through an RNA intermediate by a reverse transcriptase, are classified into the kingdom Pararnavirae in the realm Riboviria.

DNA viruses are ubiquitous worldwide, especially in marine environments where they form an important part of marine ecosystems, and infect both prokaryotes and eukaryotes. They appear to have multiple origins, as viruses in Monodnaviria appear to have emerged from archaeal and bacterial plasmids on multiple occasions, though the origins of Duplodnaviria and Varidnaviria are less clear.

Positive-strand RNA viruses (+ssRNA viruses) are a group of related viruses that have positive-sense, single-stranded genomes made of ribonucleic acid. The positive-sense genome can act as messenger RNA (mRNA) and can be directly translated into viral proteins by the host cell's ribosomes. Positive-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) which is used during replication of the genome to synthesize a negative-sense antigenome that is then used as a template to create a new positive-sense viral genome.

Positive-strand RNA viruses are divided between the phyla Kitrinoviricota, Lenarviricota, and Pisuviricota (specifically classes Pisoniviricetes and Stelpavirictes) all of which are in the kingdom Orthornavirae and realm Riboviria. They are monophyletic and descended from a common RNA virus ancestor. In the Baltimore classification system, +ssRNA viruses belong to Group IV.

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 viral deoxyribonucleic acid (DNA). Viruses in the realm also share a number of other characteristics, such as an icosahedral capsid, an opening in the capsid called a portal, a protease enzyme that empties the inside of the capsid prior to DNA packaging, and a terminase enzyme that packages viral DNA into the capsid. There are three groups of viruses in the realm: caudoviruses, herpesviruses, and the putative group mirusviruses.

Caudoviruses are one of the most abundant group of viruses on Earth and are ubiquitous worldwide. They infect prokaryotes and are a major cause of death in them, which contributes to the recycling of organic material in a process called viral shunt. Caudoviruses have been used as model organisms to study biological processes and as a form of therapy to treat bacterial infections. Herpesviruses infect animals and are commonly associated with diseases such as herpes and chickenpox. Mirusviruses infect microscopic eukaryotes and are among the most common eukaryotic viruses in sunlit oceans. Many duplodnavirians are able to enter a latent state in which they persist in cells without forming virions. This is called the lysogenic cycle and contrasts with the lytic cycle, which produces virions.

Varidnaviria is a realm of viruses that includes all DNA viruses that encode major capsid proteins that contain two vertical jelly roll folds. The major capsid proteins (MCP) form into pseudohexameric subunits of the viral capsid, which stores the viral deoxyribonucleic acid (DNA). The jelly roll folds are vertical, or perpendicular, to the surface of the capsid. Apart from the double jelly roll fold MCP (DJR-MCP), most viruses in the realm share many other characteristics, such as minor capsid proteins (mCP) that has one vertical jelly roll fold, an ATPase that packages viral DNA into the capsid, a DNA polymerase that replicates the viral genome, and capsids that are icosahedral in shape.

Varidnaviria was established in 2019 based on the shared characteristics of the viruses in the realm. There are two kingdoms in the realm: Abadenavirae, which contains all prokaryotic DJR-MCP viruses except tectiviruses, and Bamfordvirae which contains tectiviruses and all eukaryotic DJR-MCP viruses. The DJR-MCP of Varidnaviria is believed to share common ancestry with the DUF2961 family of proteins, which are widespread in cellular life and which are mainly involved in carbohydrate metabolism and binding. Up to 2025, the realm included viruses that have a vertical single jelly roll (SJR) fold in the MCP, but these viruses were moved to a separate realm, Singelaviria, after it was shown that the vertical SJR and DJR folds have separate evolutionary origins.

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 (RCR) of the circular viral genome. Viruses descended from such viruses are also included in the realm, including certain linear single-stranded DNA (ssDNA) viruses and circular double-stranded DNA (dsDNA) viruses. These atypical members typically replicate through means other than rolling circle replication.

Monodnaviria was established in 2019 and contains four kingdoms: Loebvirae, Sangervirae, Trapavirae, and Shotokuvirae. Viruses in the first three kingdoms infect prokaryotes, and viruses in Shotokuvirae infect eukaryotes and include the atypical members of the realm. Viruses in Monodnaviria appear to have come into existence independently multiple times from circular bacterial and archaeal plasmids that encode the HUH endonuclease. Eukaryotic viruses in the realm appear to have come into existence multiple times via genetic recombination events that merged deoxyribonucleic acid (DNA) from the aforementioned plasmids with capsid proteins of certain RNA viruses. Most identified ssDNA viruses belong to Monodnaviria.

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 (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) from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA (deoxyribonucleic acid) from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA (mRNA) 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.