Varidnaviria
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 form into pseudohexameric subunits of the viral capsid, which stores the viral deoxyribonucleic acid. The jelly roll folds are vertical, or perpendicular, to the surface of the capsid. Apart from the double jelly roll fold MCP, most viruses in the realm share many other characteristics, such as minor capsid proteins 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 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.
Marine viruses in the realm are highly abundant worldwide in the upper ocean and are important in marine ecology. Many animal viruses in Varidnaviria are associated with disease, including adenoviruses, poxviruses, and the African swine fever virus. Poxviruses have been prominent in the history of medicine, especially smallpox, caused by Variola virus. The first vaccine to be invented prevented smallpox, which later became the first disease eradicated. The realm includes a number of highly unusual viruses, including giant viruses that are much larger in size and contain a significantly greater number of genes than typical viruses, and virophages, which are viruses that are parasites of giant viruses.
Etymology
The name "Varidnaviria" is a portmanteau of various DNA viruses and the suffix -viria, which is the suffix used for virus realms. Double-stranded DNA viruses in the realm are often called non-tailed or tailless dsDNA viruses to distinguish them from the tailed dsDNA viruses of Duplodnaviria. Members of the realm are called varidnavirians.Characteristics
MCP, mCP, and ATPase
Most viruses in Varidnaviria contain a capsid that is made of major capsid proteins that contain vertical double jelly roll folds. The major capsid proteins are named so because they are the primary proteins that the capsid is made of. A jelly roll fold is a type of folded structure in a protein in which eight antiparallel beta strands are organized into four antiparallel beta sheets in a layout resembling a jelly roll, also called a Swiss roll. Each beta strand is a specific sequence of amino acids, and these strands bond to their antiparallel strands via hydrogen bonds. A double jelly roll fold MCP is one that has two jelly roll folds in a single protein. Vertical folds are those that are perpendicular to the capsid surface, in contrast to horizontal folds that are parallel to the capsid surface.During the process of assembling the viral capsid, MCPs self-assemble into hexagonal structures, called hexons, that contain three copies of the MCP. Hexons then bond to form the relatively flat triangular sides of the capsid, which is icosahedral in shape with 20 triangular faces and 12 vertices. All varidnavirians that encode a DJR-MCP that have been analyzed in high resolution also encode a minor capsid protein that contains a single jelly roll fold. These mCPs assemble into pentagonal structures called pentons that contain five copies of the mCP and form the pentagonal vertices of the icosahedral capsid.
Most members of the realm also encode genome packaging ATPases of the FtsK-HerA superfamily. The ATPases in Varidnaviria are enzymes that package the viral DNA into the capsid during the process of assembling virions. FtsK-HerA is a family of proteins that contains a transmembrane domain with four membrane-spanning helices at the start of the protein's amino acid sequence, a central coiled-coil region, and an ATPase with a P-loop fold at the end of the protein's amino acid sequence. FtsK proteins are found in nearly all bacteria and HerA proteins in all archaea and some bacteria. The exact function of the ATPase for some viruses in Varidnaviria is unclear since morphological features, such as the circular, supercoiled genome of bacteriophage PM2, seemingly prohibit translocation by the ATPase of DNA from outside the capsid to the inside. The subset of the FtsK-HerA superfamily found in Varidnaviria is often called the A32 clade, named after the ATPase-encoding A32 gene of Vaccinia virus. The family Finnlakeviridae and the provisional Odin group lack the signature FtsK-HerA ATPase, as do adenoviruses, which instead encode their own ATPase that has the same role.
Other characteristics
Apart from the core morphogenetic triad of traits, certain other characteristics are common or unique in various lineages within Varidnaviria, listed hereafter.- All members of Varidnaviria, except for the family Finnlakeviridae, have dsDNA genomes. Viruses in Finnlakeviridae instead have single-stranded DNA genomes.
- Many members of the realm encode a type B DNA polymerase, which copies the viral DNA, and often additional components of the DNA polymerase, such as superfamily 3 helicases, or replication initiation proteins in the case of the family Corticoviridae.
- Many eukaryotic DJR-MCP viruses encode a capsid maturation protease that is involved in assembling the capsid.
- Some members of the realm encode integrase, an enzyme that integrates the viral genome into the genome of the host.
- In some unrelated lineages, the ancestral icosahedral shape of the capsid has been lost and replaced with other shapes. For example, ascoviruses have ovoid virions, and pandoraviruses have amphora-shaped virions. Poxviruses retain the DJR-MCP and use it to form intermediate virions, but mature virions are brick- or ovoid-shaped.
- Some varidnavirians have special vertices in their icosahedral capsids for transporting the genome out of the capsid and for making virus factories.
Phylogenetics
In general, viruses in Varidnaviria do not share common descent with viruses in other realms. The main exception is the unclassified phylum Mirusviricota in the realm Duplodnaviria. Mirusviricots share some core replication and transcription-related genes with the varidnavirian phylum Nucleocytoviricota, including DNA polymerase B, RNA polymerase A, RNA polymerase B, and transcription factor TFIIS. Herpesviruses, also in Duplodnaviria, encode DNA polymerase B as well. It is proposed that this group of genes first emerged either in the ancestors of nucleocytoviricots or in the ancestors of mirusviricots and horizontally transferred to the other lineage. In both scenarios, herpesviruses lost most of them through reductive evolution. Despite the relation, mirusviricots and nucleocytoviricots belong to different realms because they have different MCPs, which are the defining characteristics of Duplodnaviria and Varidnaviria. The family Microviridae in Monodnaviria and various RNA viruses in Riboviria also encode MCPs that have jelly roll folds, but they are horizontal to the capsid surface, in contrast to the jelly roll folds of Varidnaviria, which are vertical to the capsid surface.
Classification
Varidnaviria has two kingdoms: Abadenavirae and Bamfordvirae. Abadenavirae is monotypic down to the rank of phylum. This taxonomy can be visualized as follows:- Kingdom: Abadenavirae, which contains all prokaryotic DJR-MCP viruses except tectiviruses
- * Phylum: Produgelaviricota
- Kingdom: Bamfordvirae, which contains tectiviruses and all eukaryotic DJR-MCP viruses