''Varidnaviria'' is a

realm A realm is a community or territory over which a sovereign rules. The term is commonly used to describe a monarchical or dynastic state. A realm may also be a subdivision within an empire, if it has its own monarch, e.g. the German Empire. Etym ...

virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky's 1 ...

es that includes all

DNA virus 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 ...

es that

encode The Encyclopedia of DNA Elements (ENCODE) is a public research project which aims to identify functional elements in the human genome. ENCODE also supports further biomedical research by "generating community resources of genomics data, software ...

major capsid proteins that contain a vertical

jelly roll fold The jelly roll or Swiss roll fold is a protein fold or supersecondary structure composed of eight beta strands arranged in two four-stranded sheets. The name of the structure was introduced by Jane S. Richardson in 1981, reflecting its resemblan ...

. The major capsid proteins (MCP) form into pseudohexameric subunits of the viral

capsid A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may ...

, which stores the viral deoxyribonucleic acid (DNA), and are perpendicular, or vertical, to the surface of the capsid. Apart from this,

es in the realm also share many other characteristics, such as minor capsid proteins (mCP) with the vertical jelly roll fold, an

ATPase ATPases (, Adenosine 5'-TriPhosphatase, adenylpyrophosphatase, ATP monophosphatase, triphosphatase, SV40 T-antigen, ATP hydrolase, complex V (mitochondrial electron transport), (Ca2+ + Mg2+)-ATPase, HCO3−-ATPase, adenosine triphosphatase) are ...

that packages viral DNA into the capsid, and a

DNA polymerase A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create ...

that replicates the viral genome. ''Varidnaviria'' was established in 2019 based on the shared characteristics of the viruses in the realm. There are two groups of viruses in ''Varidnaviria'': viruses that have a double vertical jelly roll (DJR) folds in the MCP, assigned to the kingdom ''Bamfordvirae'', and viruses that have a single vertical jelly roll (SJR) fold in the MCP, assigned to the kingdom ''Helvetiavirae''. The DJR-MCP lineage is thought to be descended from the SJR-MCP lineage via a gene fusion event, and the SJR-MCP shows a close relation to

nucleoplasmin Nucleoplasmin, the first identified molecular chaperone is a thermostable acidic protein with a pentameric structure. The protein was first isolated from Xenopus species Functions The pentameric protein participates in various significant cellula ...

s, pointing to a possible origin of the realm's jelly roll fold MCP. Most identified eukaryotic DNA viruses belong to ''Varidnaviria''.

Marine viruses Marine viruses are defined by their habitat as viruses that are found in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Viruses are small infectious agents that can only replicate i ...

in the realm are highly abundant worldwide and are important in marine ecology. Many animal viruses in the realm are associated with disease, including

adenovirus Adenoviruses (members of the family ''Adenoviridae'') are medium-sized (90–100 nm), nonenveloped (without an outer lipid bilayer) viruses with an icosahedral nucleocapsid containing a double-stranded DNA genome. Their name derives from the ...

es,

poxvirus ''Poxviridae'' is a family of double-stranded DNA viruses. Vertebrates and arthropods serve as natural hosts. There are currently 83 species in this family, divided among 22 genera, which are divided into two subfamilies. Diseases associated wit ...

es, and the ''

African swine fever virus ''African swine fever virus'' (ASFV) is a large, double-stranded DNA virus in the '' Asfarviridae'' family. It is the causative agent of African swine fever (ASF). The virus causes a hemorrhagic fever with high mortality rates in domestic pigs; ...

''. Poxviruses have been prominent in the history of medicine, especially

smallpox Smallpox was an infectious disease caused by variola virus (often called smallpox virus) which belongs to the genus Orthopoxvirus. The last naturally occurring case was diagnosed in October 1977, and the World Health Organization (WHO) c ...

, caused by ''Variola virus'', which was the target of the first vaccine and which later became the first disease eradicated. The realm also notably includes

giant virus A giant virus, sometimes referred to as a girus, is a very large virus, some of which are larger than typical bacteria. All known giant viruses belong to the phylum '' Nucleocytoviricota''. Description While the exact criteria as defined in the ...

es that are physically larger and contain a much larger number of genes than typical viruses.

Etymology

The name "''Varidnaviria''" is a

portmanteau A portmanteau word, or portmanteau (, ) is a blend of wordstailed dsDNA viruses of ''Duplodnaviria''.

Characteristics

MCP, mCP, and ATPase

Most viruses in ''Varidnaviria'' contain a capsid that is made of major capsid proteins that contain vertical single (SJR) or double jelly roll (DJR) 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 sheet The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a g ...

s in a layout resembling a jelly roll, also called a Swiss roll. Each beta strand is a specific sequence of

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...

s, and these strands bond to their antiparallel strands via

hydrogen bond In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a ...

s. The difference between SJR and DJR folds is that a DJR fold is simply two SJR 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, containing multiple copies of the MCP. Hexons then bond to form the relatively flat triangular sides of the icosahedral capsid. All viruses in ''Varidnaviria'' that encode a DJR-MCP that have been analyzed in high resolution also encode a minor capsid protein (mCP) that contains an SJR fold. These mCPs assemble into pentagonal structures called pentons that 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 is a family of proteins that contains a transmembrane protein with four membrane-spanning helices at the start of the protein's amino acid sequence and an ATPase with a P-loop fold at the end of the protein's amino acid sequence, and the HerA family is

homolog In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of prima ...

ous to FtsK. The exact function of the ATPase for some viruses in ''Varidnaviria'' is unclear since morphological features, such as the circular, supercoiled genome of '' Pseudoalteromonas virus 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(R) gene of ''Vaccinia virus''.

Other characteristics

Apart from the core morphogenetic triad of genes, the MCP, mCP, and ATPase, certain other characteristics are common or unique in various lineages within ''Varidnaviria'', listed hereafter. * 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

helicase Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separatin ...

s, or replication initiation proteins, in the case of the family '' Corticoviridae''. An exception is the order ''Halopanivirales'',Prior to 2020, ''Sphaerolipoviridae'' was the sole family in the order ''Halopanivirales'', but in that year it was split into three families in the same order, which are the only three families in the order. In accordance with this change, "''Halopanivirales''" is used throughout this article where sources refer to the previous ''Sphaerolipoviridae'' classification. whose members do not encode any recognizable replication enzymes. * Many eukaryotic DJR-MCP viruses encode a capsid maturation protease that is involved in assembling the capsid. * Some members of the realm encode

integrase Retroviral integrase (IN) is an enzyme produced by a retrovirus (such as HIV) that integrates—forms covalent links between—its genetic information into that of the host cell it infects. Retroviral INs are not to be confused with phage int ...

, an enzyme that integrates the viral genome into the genome of the host. * Most members of the realm have capsids in the shape of an icosahedron, containing 20 triangular faces and 12 vertices. * In various lineages, including ascoviruses and poxviruses, the ancestral icosahedral shape of the capsid has been lost and replaced with other shapes, such as ovoids and brick-like shapes. * Poxviruses encode a

scaffold protein In biology, scaffold proteins are crucial regulators of many key signalling pathways. Although scaffolds are not strictly defined in function, they are known to interact and/or bind with multiple members of a signalling pathway, tethering them in ...

, which guides the geometric construction of the viral capsid, that also folds into DJR pseudo-hexamers. * Some viruses have special vertices in their icosahedral capsids for transporting the genome out of the capsid and for making virus factories. * For certain viruses, the genome inside the capsid is surrounded by a

lipid membrane The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many vir ...

. * Nearly all recognized DJR-MCP viruses encode an ATPase of the FtsK-HerA superfamily. Adenoviruses are the exception, instead encoding their own distinct ATPase that has the same role as the FtsK-HerA ATPase. * The family '' Finnlakeviridae'' and a provisional group called the Odin group, both proposed members of ''Varidnaviria'', lack the signature FtsK-HerA superfamily ATPase. * All members of ''Varidnaviria'' except for ''Finnlakeviridae'', a proposed member family, have dsDNA genomes. Viruses in ''Finnlakeviridae'' instead have single-stranded DNA (ssDNA) genomes.

Phylogenetics

It has been suggested that ''Varidnaviria'' predates the

last universal common ancestor The last universal common ancestor (LUCA) is the most recent population from which all organisms now living on Earth share common descent—the most recent common ancestor of all current life on Earth. This includes all cellular organisms; t ...

(LUCA) of cellular life and that viruses in the realm were present in the LUCA. The vertical SJR-MCPs of ''Halopanivirales'', assigned to the kingdom ''Helvetiavirae'', unlike SJR folds found outside of ''Varidnaviria'', show a relation to a group of proteins that includes the

Cupin superfamily The cupin superfamily is a diverse superfamily of proteins named after its conserved barrel domain (''cupa'' being the Latin term for a small barrel). The superfamily includes a wide variety of enzymes as well as non-enzymatic seed storage p ...

and nucleoplasmins, pointing to a possible origin of the major capsid protein of ''Varidnaviria'' among this group. The DJR-MCP lineage, assigned to the kingdom ''Bamfordvirae'', thereafter appears to have come into existence by means of a gene fusion event that merged the two SJR-MCPs into one, indicated by the two SJR-MCPs forming a lattice in the capsid that structurally resembles the DJR-MCP capsid lattice. Archaeal dsDNA viruses in '' Portogloboviridae'' contain just one vertical SJR-MCP, which appears to have been duplicated to two for ''Halopanivirales'', so the MCP of ''Portogloboviridae'' likely represents an earlier stage in the evolutionary history of ''Varidnaviria'' MCPs. However, another scenario was later proposed in which the ''Bamfordvirae'' and ''Helvetiavirae'' kingdoms would originate independently from

mobile genetic elements Mobile genetic elements (MGEs) sometimes called selfish genetic elements are a type of genetic material that can move around within a genome, or that can be transferred from one species or replicon to another. MGEs are found in all organisms. In ...

such as

plasmids A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...

with the capture of two different cellular proteins when it was detected that the ''Bamfordvirae'' DJR-MCP protein is homologous to the bacterial DUF 2961 protein, leading to a revision of the realm ''Varidnaviria''. According to this scenario, the ''Bamfordvirae'' DJR-MCP fold evolved from the bacterial DUF 2961 protein, while the ''Helvetiavirae'' SJR-MCP evolved from the SJR-MCP related to the ''Portogloboviridae'' family, which in turn originated from the Cupin superfamily and the nucleoplasmins. Viruses in ''Bamfordvirae'' appear to have made crossed from prokaryotes to eukaryotes early in eukaryotic history, via infection by a

tectivirus ''Tectiviridae'' is a family of viruses with 10 species in five genera. Bacteria serve as natural hosts. Tectiviruses have no head-tail structure, but are capable of producing tail-like tubes of ~ 60×10 nm upon adsorption or after chlorofo ...

or tectivirus-like virus of a bacterium that became a bacterial

symbiont Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasit ...

in a proto-eukaryote. From there, based on phylogenetic analysis of the viral DNA polymerase and other characteristics, eukaryotic viruses in ''Bamfordvirae'' appear to have formed a complex relationship with various

selfish genetic element Selfish genetic elements (historically also referred to as selfish genes, ultra-selfish genes, selfish DNA, parasitic DNA and genomic outlaws) are genetic segments that can enhance their own transmission at the expense of other genes in the genome, ...

s, including

polinton Polintons (also called Mavericks) are large DNA transposons which contain genes with homology to viral proteins and which are often found in eukaryotic genomes. They were first discovered in the mid-2000s and are the largest and most complex kno ...

s,The exact nature of polintons is uncertain. While they encode many viral genes, including the MCP and mCP, and appear to both be partially descended from and the ancestors of certain viruses, their other ancestors being transposons, they have not been observed to form virions. It is therefore unclear if they are viruses or if they are a type of transposon. Reflecting this uncertainty is that polintons are sometimes called polintoviruses. a type of

transposon A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transpo ...

, portions of DNA that can self-replicate and integrate themselves into other parts of the same DNA molecule, and certain types of

plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; how ...

s, which are extra-chromosomal DNA molecules that self-replicate inside of the cell or organelle that they occupy. The initial bacterial symbiont is likely to have become mitochondria, with mitochondrial linear plasmids descended from tectiviruses remaining. Another divergent lineage reached the nucleus and recombined with transposons, becoming polintons, which may have been the first eukaryotic viruses in ''Bamfordvirae'' or related to the first ones. Polintons then gave rise to multiple lineages by various mechanisms. Among these lineages are full-fledged viruses, including adenoviruses and giant viruses,

cytoplasm In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The ...

ic linear plasmids,

virophage Virophages are small, double-stranded DNA viral phages that require the Coinfection, co-infection of another virus. The co-infecting viruses are typically giant viruses. Virophages rely on the viral replication factory of the co-infecting giant ...

s, which are satellite viruses of giant viruses, transpovirons, which are linear plasmid-like DNA molecules found in giant viruses, and bidnaviruses via genetic recombination with a

parvovirus Parvoviruses are a family of animal viruses that constitute the family ''Parvoviridae''. They have linear, single-stranded DNA (ssDNA) genomes that typically contain two genes encoding for a replication initiator protein, called NS1, and the p ...

, both of which are classified in the realm ''Monodnaviria''. While the jelly roll fold is found in other realms, including the family ''

Microviridae ''Microviridae'' is a family of bacteriophages with a single-stranded DNA genome. The name of this family is derived from the ancient Greek word (), meaning "small". This refers to the size of their genomes, which are among the smallest of the ...

'' in ''Monodnaviria'' and various single-stranded RNA viruses in ''Riboviria'', the jelly roll fold found in ''Varidnaviria'' is vertical, i.e. perpendicular to the capsid surface, contrary to the jelly roll folds in other realms, which are horizontal, i.e. parallel to the capsid surface. In general, the other virus realms have no apparent relation based on

common descent Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time. All living beings are in fact descendants of a unique ancestor commonly referred to as the last universal comm ...

to ''Varidnaviria''.

Classification

''Varidnaviria'' has two kingdoms: ''Bamfordvirae'' and ''Helvetiavirae'', the latter of which is monotypic down to the rank of family. This taxonomy can be visualized as follows: * Kingdom: ''

Bamfordvirae ''Bamfordvirae'' is a kingdom of viruses. This kingdom is recognized for its use of double jelly roll major capsid proteins. It was formerly known as the PRD1- adenovirus lineage. The kingdom is named after Dennis H. Bamford who first promoted ...

'', which encode a major capsid protein that contains a vertical double jelly roll fold * Kingdom: ''Helvetiavirae'', which encode a major capsid protein that contains a vertical single jelly roll fold ** Phylum: ''Dividoviricota'' *** Class: ''Laserviricetes'' **** Order: '' Halopanivirales'' All recognized members of ''Varidnaviria'' belong to Group I: dsDNA viruses of the

Baltimore classification Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a di ...

system, which groups viruses together based on how they produce messenger RNA. The family ''Finnlakeviridae'', a proposed family of ''Varidnaviria'', belongs to Group II: ssDNA viruses and would be the only ssDNA virus in the realm. Most identified DNA viruses that infect eukaryotes belong to ''Varidnaviria'', the other major lineages of eukaryotic DNA viruses being the order ''

Herpesvirales The ''Herpesvirales'' is an order of dsDNA viruses (Baltimore group I) with animal hosts, characterised by a common morphology consisting of an icosahedral capsid enclosed in a glycoprotein-containing lipid envelope. Common infections in humans ...

'', which infect animals, in ''Duplodnaviria'', and the class ''

Papovaviricetes ''Papovaviricetes'' is a class of viruses. The class shares the name of an abolished family, ''Papovaviridae'', which was split in 1999 into the two families ''Papillomaviridae'' and ''Polyomaviridae''. The class was established in 2019 and takes ...

'', which infect animals, in ''Monodnaviria''. Realms are the highest level of taxonomy used for viruses in and ''Varidnaviria'' is one of four, the other three being ''

Duplodnaviria ''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 v ...

'', ''

Monodnaviria ''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 of the circular viral genome. Viruses descended from such viruses ...

'', and ''

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 (with eithe ...

''. The unassigned family '' Portogloboviridae'' is a proposed family of the realm since its capsid proteins appear to be homologous to those of viruses in ''Varidnaviria''. Another proposed group is the '' Naldaviricetes'' class (including ''

Polydnaviridae A polydnavirus (PDV) is a member of the family ''Polydnaviridae'' of insect viruses. There are two genera in the family: '' Bracovirus'' and ''Ichnovirus''. Polydnaviruses form a symbiotic relationship with parasitoid wasps; (ichnoviruses (IV) ...

''). These viruses encompass several genes that are distantly related to core genes of the ''

Nucleocytoviricota ''Nucleocytoviricota'' is a phylum of viruses. Members of the phylum are also known as the nucleocytoplasmic large DNA viruses (NCLDV), which serves as the basis of the name of the phylum with the suffix - for virus phylum. These viruses are refe ...

'' and thus could be highly derived members of the DJR-MCP viruses, despite the absence of the DJR-MCP and formation of odd-shaped virions. Preliminary phylogenetic analysis of several essential genes that are shared by all these arthropod viruses and the ''Nucleocytoviricota'', such as PolB, RNAP subunits, helicase-primase and thiol oxidoreductase, has suggested that this group of viruses might be a highly derived offshoot of the ''Nucleocytoviricota''.

Interactions with hosts

Disease

Bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacteri ...

s in ''Varidnaviria'' are potentially a major cause of death among marine prokaryotes. This viewpoint is based on autolykiviruses having broad host ranges, infecting and killing many different strains of various bacteria species, in contrast to tailed bacteriophages, which have more limited host ranges, as well as on the apparently large number of marine non-tailed dsDNA viruses. Algal viruses of the family ''

Phycodnaviridae ''Phycodnaviridae'' is a family of large (100–560 kb) double-stranded DNA viruses that infect marine or freshwater eukaryotic algae. Viruses within this family have a similar morphology, with an icosahedral capsid (polyhedron with 20 fac ...

'' play an important role in controlling

algal bloom An algal bloom or algae bloom is a rapid increase or accumulation in the population of algae in freshwater or marine water systems. It is often recognized by the discoloration in the water from the algae's pigments. The term ''algae'' encompas ...

s as well as, with many

marine viruses Marine viruses are defined by their habitat as viruses that are found in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Viruses are small infectious agents that can only replicate i ...

in general, contributing to a process called

viral shunt The viral shunt is a mechanism that prevents marine microbial particulate organic matter (POM) from migrating up trophic levels by recycling them into dissolved organic matter (DOM), which can be readily taken up by microorganisms. The DOM rec ...

, whereby organic material from killed organisms are "shunted" by viruses away from higher

trophic level The trophic level of an organism is the position it occupies in a food web. A food chain is a succession of organisms that eat other organisms and may, in turn, be eaten themselves. The trophic level of an organism is the number of steps it i ...

s and recycled for consumption by those at lower trophic levels. The most notable disease-causing viruses in ''Varidnaviria'' are adenoviruses, poxviruses, and the ''African swine fever virus'' (ASFV). Adenoviruses typically cause mild respiratory, gastrointestinal, and conjunctival illnesses, but occasionally cause more severe illnesses, such as

hemorrhagic cystitis Hemorrhagic cystitis or haemorrhagic cystitis is an inflammation of the bladder defined by lower urinary tract symptoms that include dysuria, hematuria, and hemorrhage. The disease can occur as a complication of cyclophosphamide, ifosfamide and r ...

hepatitis Hepatitis is inflammation of the liver tissue. Some people or animals with hepatitis have no symptoms, whereas others develop yellow discoloration of the skin and whites of the eyes (jaundice), poor appetite, vomiting, tiredness, abdominal pa ...

, and

meningoencephalitis Meningoencephalitis (; from ; ; and the medical suffix ''-itis'', "inflammation"), also known as herpes meningoencephalitis, is a medical condition that simultaneously resembles both meningitis, which is an infection or inflammation of the menin ...

. Poxviruses infect many animals and typically cause non-specific symptoms paired with a characteristic rash that is called a pox. Notable poxviruses include ''

Variola virus Smallpox was an infectious disease caused by variola virus (often called smallpox virus) which belongs to the genus Orthopoxvirus. The last naturally occurring case was diagnosed in October 1977, and the World Health Organization (WHO) cer ...

'', which causes smallpox, and ''

Vaccinia virus ''Vaccinia virus'' (VACV or VV) is a large, complex, enveloped virus belonging to the poxvirus family. It has a linear, double-stranded DNA genome approximately 190 kbp in length, which encodes approximately 250 genes. The dimensions of the ...

'', which is used as the vaccine against smallpox. ASFV is usually asymptomatic in its

natural reservoir In infectious disease ecology and epidemiology, a natural reservoir, also known as a disease reservoir or a reservoir of infection, is the population of organisms or the specific environment in which an infectious pathogen naturally lives and r ...

s but causes a lethal hemorrhagic fever in domestic pigs that is a concern for agricultural production.

Endogenization

Many viruses in ''Varidnaviria'' encode the enzyme integrase, allowing them to integrate their genome into their host and behave like transposons. The closely related polintons are apparently always endogenized in their hosts. This integration of viral DNA into the host's genome is a form of

horizontal gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between Unicellular organism, unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offsprin ...

between unrelated organisms, although polintons are typically transmitted vertically from parent to child.

Adapative immunity

A peculiar example of endogenization in ''Varidnaviria'' are virophages, satellite viruses that are dependent on giant virus infection to replicate. Virophages replicate by hijacking the replication apparati of giant viruses, thereby suppressing the number of giant virus virions produced, increasing the likelihood of host survival. Some virophages are able to become endogenized, and this endogenization can be considered a form of

adaptive immunity The adaptive immune system, also known as the acquired immune system, is a subsystem of the immune system that is composed of specialized, systemic cells and processes that eliminate pathogens or prevent their growth. The acquired immune system ...

for the host against giant virus infection.

History

Diseases caused by poxviruses have been known for much of recorded history. Smallpox in particular has been highly prominent in modern medicine; the first vaccine to be invented targeted smallpox, and smallpox would later become the first disease to be eradicated. Human adenoviruses were the first DJR-MCP viruses in ''Varidnaviria'' to have their MCPs analyzed, standing out for having jelly roll folds that were perpendicular, rather than parallel, to the capsid surface. In 1999, the structure of the MCP of ''

Pseudomonas virus PRD1 ''Pseudomonas'' is a genus of Gram-negative, Gammaproteobacteria, belonging to the family Pseudomonadaceae and containing 191 described species. The members of the genus demonstrate a great deal of metabolic diversity and consequently are able to ...

'' was resolved, showing that the DJR-MCP lineage included prokaryotic viruses. ''

Haloarcula hispanica virus SH1 ''Haloarcula'' (common abbreviation ''Har.'') is a genus of extreme halophilic Archaeon, Archaea in the class of Halobactaria. Cell Structure ''Haloarcula'' species can be distinguished from other genera in the family Halobacteriaceae by the pre ...

'' would later, in 2003, become the first SJR-MCP virus discovered. Over time, the use of

metagenomics Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microb ...

has allowed for the identification of viruses in the environment even without identification of the host or laboratory specimens, leading to the discovery of many additional members of the realm. Morphological surveys of marine samples suggest that non-tailed dsDNA viruses may be more numerous than the tailed dsDNA viruses of ''Duplodnaviria'', which, as of 2019, are the largest and most diverse lineage of viruses documented. With the increased knowledge of the viruses of the realm, ''Varidnaviria'' was established in 2019 based on the shared traits of viruses in the realm. The establishment of ''Varidnaviria'' has allowed for newly discovered and related, yet divergent, viruses to be classified in higher taxa. This includes proposed families such as ''Finnlakeviridae'', which would be the only family in the realm with a single-stranded DNA genome, ''Autolykiviridae'', which have a broad host range and which may play a major role in the deaths of

marine bacteria Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular ...

, and the "Odin" group, which encode a protein that has no known relation to any other proteins in place of the FtsK-HerA superfamily ATPase. In 2020, autolykiviruses were officially classified for the first time.