Realm (virology)

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In virology, realm is the highest taxonomic rank established for viruses by the International Committee on Taxonomy of Viruses (ICTV), which oversees virus taxonomy. Six virus realms are recognized and united by specific highly conserved traits: Adnaviria , which contains archaeal filamentous viruses with A-form double-stranded (ds) DNA genomes encoding a unique alpha-helical major capsid protein; Duplodnaviria , which contains all dsDNA viruses that encode the HK97-fold major capsid protein; Monodnaviria , which contains all single-stranded DNA (ssDNA) viruses that encode a HUH superfamily endonuclease and their descendents; Riboviria , which contains all RNA viruses that encode RNA-dependent RNA polymerase and all viruses that encode reverse transcriptase; Ribozyviria , which contains hepatitis delta-like viruses with circular, negative-sense ssRNA genomes; and Varidnaviria , which contains all dsDNA viruses that encode a vertical jelly roll major capsid protein.

Contents

The rank of realm corresponds to the rank of domain used for cellular life, but differs in that viruses in a realm do not necessarily share a common ancestor based on common descent nor do the realms share a common ancestor. Instead, realms group viruses together based on specific traits that are highly conserved over time, which may have been obtained on a single occasion or multiple occasions. As such, each realm represents at least one instance of viruses coming into existence. While historically it was difficult to determine deep evolutionary relations between viruses, in the 21st century methods such as metagenomics and cryogenic electron microscopy have enabled such research to occur, which led to the establishment of Riboviria in 2018, three realms in 2019, and two in 2020.

Naming

The names of realms consist of a descriptive first part and the suffix -viria, which is the suffix used for virus realms. [1] The first part of Duplodnaviria means "double DNA", referring to dsDNA viruses, [2] the first part of Monodnaviria means "single DNA", referring to ssDNA viruses, [3] the first part of Riboviria is taken from ribonucleic acid (RNA), [4] and the first part of Varidnaviria means "various DNA". [5] For viroids, the suffix is designated as -viroidia, and for satellites, the suffix is -satellitia, [1] but as of 2019 neither viroid nor satellite realms have been designated. [6]

Realms

Duplodnaviria

Illustrated sample of Duplodnaviria virions Duplodnaviria virion morphology.jpg
Illustrated sample of Duplodnaviria virions

Duplodnaviria contains double-stranded DNA (dsDNA) viruses that encode a major capsid protein (MCP) that has the HK97 fold. Viruses in the realm also share a number of other characteristics involving the capsid and capsid assembly, including an icosahedral capsid shape and a terminase enzyme that packages viral DNA into the capsid during assembly. Two groups of viruses are included in the realm: tailed bacteriophages, which infect prokaryotes and are assigned to the order Caudovirales , and herpesviruses, which infect animals and are assigned to the order Herpesvirales . [2]

The relation between caudoviruses and herpesviruses is not certain, as they may either share a common ancestor or herpesviruses may be a divergent clade from within Caudovirales. A common trait among duplodnaviruses is that they cause latent infections without replication while still being able to replicate in the future. [7] [8] Tailed bacteriophages are ubiquitous worldwide, [9] important in marine ecology, [10] and the subject of much research. [11] Herpesviruses are known to cause a variety of epithelial diseases, including herpes simplex, chickenpox and shingles, and Kaposi's sarcoma. [12] [13] [14]

Monodnaviria

Monodnaviria contains single-stranded DNA (ssDNA) viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication and all other viruses descended from such viruses. The prototypical members of the realm are called CRESS-DNA viruses and have circular ssDNA genomes. ssDNA viruses with linear genomes are descended from them, and in turn some dsDNA viruses with circular genomes are descended from linear ssDNA viruses. [3]

CRESS-DNA viruses include three kingdoms that infect prokaryotes: Loebvirae , Sangervirae , and Trapavirae . The kingdom Shotokuvirae contains eukaryotic CRESS-DNA viruses and the atypical members of Monodnaviria. [3] Eukaryotic monodnaviruses are associated with many diseases, and they include papillomaviruses and polyomaviruses, which cause many cancers, [15] [16] and geminiviruses, which infect many economically important crops. [17]

Riboviria

Riboviria contains all RNA viruses that encode an RNA-dependent RNA polymerase (RdRp), assigned to the kingdom Orthornavirae , and all reverse transcribing viruses, i.e. all viruses that encode a reverse transcriptase (RT), assigned to the kingdom Pararnavirae . These enzymes are vital in the viral life cycle, as RdRp transcribes viral mRNA and replicates the genome, and RT likewise replicates the genome. [4] Riboviria mostly contains eukaryotic viruses, and most eukaryotic viruses, including most human, animal, and plant viruses, belong to the realm. [18]

Most widely known viral diseases are caused by viruses in Riboviria, which includes influenza viruses, HIV, coronaviruses, ebolaviruses, and the rabies virus, [6] as well as the first virus to be discovered, Tobacco mosaic virus . [19] Reverse transcribing viruses are a major source of horizontal gene transfer by means of becoming endogenized in their host's genome, and a significant portion of the human genome consists of this viral DNA. [20]

Varidnaviria

A ribbon diagram of the MCP of Pseudoalteromonas virus PM2, with the two jelly roll folds colored in red and blue 2w0c monomer.png
A ribbon diagram of the MCP of Pseudoalteromonas virus PM2 , with the two jelly roll folds colored in red and blue

Varidnaviria contains DNA viruses that encode MCPs that have a jelly roll fold folded structure in which the jelly roll (JR) fold is perpendicular to the surface of the viral capsid. Many members also share a variety of other characteristics, including a minor capsid protein that has a single JR fold, an ATPase that packages the genome during capsid assembly, and a common DNA polymerase. Two kingdoms are recognized: Helvetiavirae , whose members have MCPs with a single vertical JR fold, and Bamfordvirae , whose members have MCPs with two vertical JR folds. [5]

Marine viruses in Varidnaviria are ubiquitous worldwide and, like tailed bacteriophages, play an important role in marine ecology. [21] Most identified eukaryotic DNA viruses belong to the realm. [22] Notable disease-causing viruses in Varidnaviria include adenoviruses, poxviruses, and the African swine fever virus. [6] Poxviruses have been highly prominent in the history of modern medicine, especially Variola virus, which caused smallpox. [23] Many varidnaviruses are able to become endogenized, and a peculiar example of this are virophages, which confer protection for their hosts against giant viruses during infection. [22]

Adnaviria

Realm Adnaviria unifies archaeal filamentous viruses with linear A-form double-stranded DNA genomes and characteristic major capsid proteins unrelated to those encoded by other known viruses. [24] The realm currently includes viruses from three families, Lipothrixviridae , Rudiviridae , and Tristromaviridae , all infecting hyperthermophilic archaea. The nucleoprotein helix of adnaviruses is composed of asymmetric units containing two MCP molecules, a homodimer in the case of rudivirids and a heterodimer of paralogous MCPs in the case of lipothrixvirids and tristromavirids. [25] [26] The MCPs of ligamenviral particles have a unique α-helical fold first found in the MCP of rudivirid Sulfolobus islandicus rod-shaped virus 2 (SIRV2). [27] All members of the Adnaviria share a characteristic feature in that the interaction between the MCP dimer and the linear dsDNA genome maintains the DNA in the A form. Consequently, the entire genome adopts the A form in virions. Like many structurally related viruses in the two other realms of dsDNA viruses (Duplodnaviria and Varidnaviria), there is no detectable sequence similarity among the capsid proteins of viruses from different tokiviricete families, suggesting a vast undescribed diversity of viruses in this part of the virosphere.

Ribozyviria

Ribozyviria is characterised by the presence of genomic and antigenomic ribozymes of the Deltavirus type. Additional common features include a rod-like structure and a RNA-binding "delta antigen" encoded in the genome. [28]

Origins

In general, virus realms have no genetic relation to each other based on common descent, in contrast to the three domains of cellular life—Archaea, Bacteria, and Eukarya—which share a common ancestor. Likewise, viruses within each realm are not necessarily descended from a common ancestor since realms group viruses together based on highly conserved traits, not common ancestry, which is used as the basis for the taxonomy of cellular life. As such, each virus realm is considered to represent at least one instance of viruses coming into existence. [29] By realm:

While the realms generally have no genetic relation to each other, there are some exceptions:

Subrealm

In virology, the second highest taxonomy rank established by the ICTV is subrealm, which is the rank below realm. Subrealms of viruses use the suffix -vira, viroid subrealms use the suffix -viroida, and satellites use the suffix -satellitida. The rank below subrealm is kingdom. As of 2019, no taxa are described at the rank of subrealm. [1] [6]

History

Prior to the 21st century, it was believed that deep evolutionary relations between viruses could not be discovered due to their high mutation rates and small number of genes making discovering these relations more difficult. Because of this, the highest taxonomic rank for viruses from 1991 to 2017 was order. In the 21st century, however, various methods have been developed that have enabled these deeper evolutionary relationships to be studied, including metagenomics, which has identified many previously unidentified viruses, and comparison of highly conserved traits, leading to the desire to establish higher-level taxonomy for viruses. [29]

In two votes in 2018 and 2019, the ICTV agreed to adopt a 15-rank classification system for viruses, ranging from realm to species. [29] Riboviria was established in 2018 based on phylogenetic analysis of the RNA-dependent polymerases being monophyletic, [4] [34] Duplodnaviria was established in 2019 based on increasing evidence that tailed bacteriophages and herpesviruses shared many traits, [2] [35] Monodnaviria was established in 2019 after the relation and origin of CRESS-DNA viruses was resolved, [3] [36] and Varidnaviria was established 2019 based on the shared characteristics of member viruses. [5] [37]

See also

Related Research Articles

DNA virus Virus that has DNA as its genetic material

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 dsDNA viruses. Additionally, many DNA viruses are unassigned to higher taxa. Viruses that have a DNA genome that is replicated through an RNA intermediate by a reverse transcriptase are separately considered reverse transcribing viruses and are assigned to the kingdom Pararnavirae in the realm Riboviria.

Virus classification is the process of naming viruses and placing them into a taxonomic system similar to the classification systems used for cellular organisms.

Baltimore classification Virus classification system made by David Baltimore

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 distinct group. Seven Baltimore groups are described that take into consideration whether the viral genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), whether the genome is single- or double-stranded, and whether the sense of a single-stranded RNA genome is positive or negative.

Double-stranded RNA viruses Type of virus according to Baltimore classification

Double-stranded RNA viruses are a polyphyletic group of viruses that have double-stranded genomes made of ribonucleic acid. The double-stranded genome is used to transcribe a positive-strand RNA by the viral RNA-dependent RNA polymerase (RdRp). The positive-strand RNA may be used as messenger RNA (mRNA) which can be translated into viral proteins by the host cell's ribosomes. The positive-strand RNA can also be replicated by the RdRp to create a new double-stranded viral genome.

<i>Lipothrixviridae</i> Family of viruses

Lipothrixviridae is a family of viruses in the order Ligamenvirales. Thermophilic archaea in the phylum Crenarchaeota serve as natural hosts. There are 11 species in this family, assigned to 4 genera.

Tristromaviridae is a family of viruses. Archaea of the genera Thermoproteus and Pyrobaculum serve as natural hosts. Tristromaviridae is the sole family in the order Primavirales. There are two genera and three species in the genus.

Polintons 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 known DNA transposons. Polintons encode up to 10 individual proteins and derive their name from two key proteins, a DNA polymerase and a retroviral-like integrase.

Negative-strand RNA virus Phylum of viruses

Negative-strand RNA viruses are a group of related viruses that have negative-sense, single-stranded genomes made of ribonucleic acid. They have genomes that act as complementary strands from which messenger RNA (mRNA) is synthesized by the viral enzyme RNA-dependent RNA polymerase (RdRp). During replication of the viral genome, RdRp synthesizes a positive-sense antigenome that it uses as a template to create genomic negative-sense RNA. Negative-strand RNA viruses also share a number of other characteristics: most contain a viral envelope that surrounds the capsid, which encases the viral genome, -ssRNA virus genomes are usually linear, and it is common for their genome to be segmented.

<i>Riboviria</i> Realm of viruses

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 that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase (RdRp), also called RNA replicase, produces RNA from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA (mRNA) for translation of viral proteins.

<i>Duplodnaviria</i> Realm of viruses

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 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 viral 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.

<i>Monodnaviria</i> Realm of viruses

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 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.

<i>Varidnaviria</i> realm of viruses

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

<i>Bamfordvirae</i> Kingdom of viruses

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 the evolutionary unity of all viruses encoding double jelly-roll major capsid proteins.

Duplornaviricota is a phylum of RNA viruses, which contains all double-stranded RNA viruses, except for those in phylum Pisuviricota. Characteristic of the group is a viral capsid composed of 60 homo- or heterodimers of capsid protein on a pseudo-T=2 lattice. Duplornaviruses infect both prokaryotes and eukaryotes. The name of the group derives from Italian duplo which means double, rna for the type of virus, and -viricota which is the suffix for a virus phylum.

Tolivirales is an order of RNA viruses which infect insects and plants. Member viruses have a positive-sense single-stranded RNA genome. The virions are non-enveloped, spherical, and have an icosahedral capsid. The name of the group is a syllabic abbreviation of "tombusvirus-like" with the suffix -virales indicating a virus order.

<i>Lenarviricota</i> Phylum of viruses

Lenarviricota is a phylum of RNA viruses, which includes all positive-strand RNA viruses, which infect prokaryotes. Some members also infect eukaryotes, most of these viruses do not have capsids, except for the genus Ourmiavirus. The name of the group is a syllabic abbreviation of the names of founding member families "Leviviridae and Narnaviridae" with the suffix -viricota denoting a virus phylum.

<i>Pisuviricota</i> Phylum of viruses

Pisuviricota is a phylum of RNA viruses, which includes all positive-strand and double-stranded RNA viruses, which infect eukaryotes and are not members of the phylum Kitrinoviricota,Lenarviricota, or Duplornaviricota. The name of the group is a syllabic abbreviation of “picornavirus supergroup” with the suffix -viricota indicating a virus phylum. Phylogenetic analyses suggest that Birnaviridae and Permutotetraviridae, both currently unassigned to a phylum in Orthornavirae, also belong to this phylum and that both are sister groups.

Archaeal virus

An archaeal virus is a virus that infects and replicates in archaea, a domain of unicellular, prokaryotic organisms. Archaeal viruses, like their hosts, are found worldwide, including in extreme environments inhospitable to most life such as acidic hot springs, highly saline bodies of water, and at the bottom of the ocean. They have even been found in the human body. The first known archaeal virus was described in 1974 and since then, a large diversity of archaeal viruses have been discovered, many possessing unique characteristics not found in other viruses. Little is known about their biological processes, such as how they replicate, but they are believed to have many independent origins, some of which likely predate the last archaeal common ancestor (LACA).

Portogloboviridae Family of viruses

Portogloboviridae is a family of DNA viruses that infect archaea. It is a proposed family of the realm Varidnaviria. Viruses in the family are related to Halopanivirales. The capsid proteins of these viruses and their characteristics are of evolutionary importance for the origin of the other Varidnaviria viruses since they seem to retain primordial characters.

<i>Adnaviria</i>

Adnaviria is a realm of viruses that includes archaeal viruses that have a filamentous virion and a linear, double-stranded DNA genome. The genome exists in A-form (A-DNA) and encodes a dimeric major capsid protein (MCP) that contains the SIRV2 fold, a type of alpha-helix bundle containing four helices. The virion consists of the genome encased in capsid proteins to form a helical nucleoprotein complex. For some viruses, this helix is surrounded by a lipid membrane called an envelope. Some contain an additional protein layer between the nucleoprotein helix and the envelope. Complete virions are long and thin and may be flexible or a stiff like a rod.

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Further reading