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 been also 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).
Much of the diversity observed in archaeal viruses is their morphology. Their complete bodies, called virions, come in many different forms, including being shaped like spindles or lemons, rods, bottles, droplets, and coils. Some contain a viral envelope, a lipid membrane that surrounds the viral capsid, which stores the viral genome. In some cases, the envelope surrounds the genome inside the capsid. All known archaeal viruses have genomes made of deoxyribonucleic acid (DNA). Almost all that have been identified contain double-stranded DNA genomes, a small minority having single-stranded DNA genomes. A large portion of the genes encoded by archaeal viruses have no known function or homology to any other genes.
Compared to bacterial and eukaryotic viruses, few archaeal viruses have been described in detail. Despite this, those that have been studied are highly diverse and classified to more than 20 families, many of which show no relation to any other known viruses. In general, all archaeal viruses can be placed into two broad groups: those that are related to bacterial and eukaryotic viruses and those that are not. The former includes viruses found in the realms Duplodnaviria, Singelaviria, and Varidnaviria, which likely have ancient origins preceding the LACA, and the latter includes the realm Adnaviria and all archaeal virus families unassigned to higher taxa, which are thought to have more recent origins from non-viral mobile genetic elements such as plasmids.
How archaeal viruses interact with their hosts and the environment is largely unknown. Many establish a persistent infection, during which progeny are continually produced at a low rate without killing the host archaeon. Some have evolved alongside their hosts, adapting to the environments in which archaea live. For example, bicaudaviruses grow two tails on opposite ends of their bodies after they leave their host cell, which may help them find a new host in sparsely populated environments. In oceans, archaeal viruses are believed to play a major role in recycling nutrients, especially at the bottom of the ocean where they are a major cause of death. For some archaeal viruses in hypersaline environments, the level of salinity can affect infectivity and virus behavior.
Research areas in archaeal virology include gaining a better understanding of their diversity and learning about their means of replication. Some environments, such as acidic hot springs, are almost exclusively populated by archaea, so these environments are highly useful for studying how archaeal viruses interact with their hosts. Because a large portion of their genes have no known function, there is a large reserve of genetic material to be explored. In the early decades of archaeal virus research, Wolfram Zillig and his colleagues discovered numerous archaeal virus families. Since 2000, methods such as metagenomics have identified many novel archaeal viruses, and methods such as cryogenic electron microscopy and gene synteny have helped to better understand their evolutionary history.
Terminology Archaeal viruses were originally referred to as "bacteriophages" or simply "phages", terms shared with bacterial viruses. This reflected the classification at the time of archaea with bacteria in a system that separated prokaryotes from eukaryotes. The first official name given to archaea was "archaebacteria", leading to terms such as "archaebacterial phages" being used. At around the same time as the adoption of archaebacteria as a name, though, archaeal viruses began to be referred to as viruses, not phages. The trend from "phage" to "virus" when describing archaeal viruses progressed throughout the 1980s. In 1990, Archaea was established as a domain with the adoption of a three domain classification system that separated archaea, bacteria, and eukaryotes from each other. Within a few years, the term "archaebacterial virus" began to be replaced by "archaeal virus".
Since 1990, "archaeal virus" has been the dominant term when describing viruses that infect archaea. Many synonyms of "archaeal virus" have been used, including archaeovirus, archaeavirus, archaevirus, archeovirus, archael virus, archeal virus, archae virus, archaeon virus, and archaeon virus. It is common for "archaeal virus" to be prefixed by the type of archaea infected. For example, "crenarchaeal virus" denotes viruses of the Archaea phylum Thermoproteota (formerly Crenarchaeota). The terms "thermophilic", "mesophilic", "psychrophilic", and "halophilic" are also commonly used when discussing archaeal viruses, denoting viruses of archaea in high-temperature, moderate-temperature, low-temperature, and saline environments respectively. In the latter case, "halovirus" and "haloarchaeal virus" are also used.
Classification
The number of classified archaeal viruses is relatively small, but due to their high level of diversity they are assigned to many different families, most of which were established specifically so the viruses could be classified. Many of these archaeal virus families are unassigned to higher taxa. The highest rank in virus taxonomy is realm, and archaeal viruses that are assigned to a realm fall into one of four realms. Their classification is shown hereafter (-viria denotes realm, -viricetes denotes class, -virales denotes order, and -viridae denotes family): Adnaviria - among virus realms, this is the only one that exclusively contains archaeal viruses: Tokiviricetes Ligamenvirales Lipothrixviridae Rudiviridae Primavirales Tristromaviridae Duplodnaviria: Caudoviricetes Monodnaviria: Huolimaviricetes Haloruvirales Pleolipoviridae Singelaviria Laserviricetes Halopanivirales Simuloviridae SphaerolipoviridaePrior to 2020, Sphaerolipoviridae was the sole family in the order Halopanivirales, but it was split and its two previous genera that contained archaeal viruses now correspond to the families Simuloviridae and Sphaerolipoviridae. Where sources prior to 2020 refer to Sphaerolipoviridae, this article uses "Halopanivirales". Varidnaviria Belvinaviricetes Belfryvirales Turriviridae
Unassigned families:
Ampullaviridae Bicaudaviridae Clavaviridae Fuselloviridae Globuloviridae Guttaviridae HalspiviridaeHalspiviridae contains only one genus: Salterprovirus. This genus is often named when referring to viruses of this family. Ovaliviridae PortogloboviridaeAlthough Portogloboviridae is unassigned to any higher taxa, the family is related to viruses in the realm Varidnaviria. Spiraviridae Thaspiviridae
A distinction is often made between archaeal viruses that have no morphological or genetic relation to non-archaeal viruses and those that do. The latter include: halophilic archaeal caudoviruses, which are related to bacterial caudoviruses and eukaryotic herpesviruses; Simuloviridae and Sphaerolipoviridae, which infect halophilic archaea and which are related to bacterial viruses in Matshushitaviridae; and Turriviridae, which is related to bacterial virus families Tectiviridae and Corticoviridae and many eukaryotic virus families such as Adenoviridae.
An additional group of unclassified archaeal viruses named Magroviruses show a relation to other caudoviruses. Many mesophilic archaeal caudoviruses have been identified through metagenomics but have yet to be isolated. Putative archaeal viruses of Nitrososphaerota (formerly Thaumarchaeota) and "Euryarchaeota" in the water column and sediments have been identified but have not been cultured.
Archaea-specific virus groups include the realm Adnaviria, pleolipoviruses, which are classified in Monodnaviria, and all archaeal virus families unassigned to higher taxa. Two archaeal viruses first described in 2017 are Metallosphaera turreted icosahedral virus and Methanosarcina spherical virus. These two viruses are both unique and show no relation to any other known viruses, so they are likely to be classified into novel families in the future. Additionally, there are viruses that are morphologically similar to bicaudaviruses called monocaudaviruses, but these viruses have yet to be classified.
Morphology
Although few archaeal viruses have been described, they are very diverse morphologically and have some structural characteristics not found in other types of viruses. Ampullaviruses are bottle-shaped; bicaudaviruses, fuselloviruses, thaspiviruses and halspiviruses are spindle- or lemon-shaped, often pleomorphic; spiraviruses are coil-shaped; guttaviruses are droplet-shaped. Clavaviruses, rudiviruses, lipothrixviruses, and tristromaviruses have filamentous – flexible or rigid – virions, the latter two of which contain envelopes surrounding the capsid, in contrast to all other known filamentous viruses, which lack a lipid membrane.
Globuloviruses are spherical or pleomorphic, pleolipoviruses have a pleomorphous membrane vesicle-like shape, and ovaliviruses have a spool-like capsid enclosed in an ellipsoidal or ovoid envelope. Caudoviruses have a head-tail structure in which an icosahedral capsid is the "head" of the virion and is connected to a "tail". The tail may be long and contractile, long and non-contractile, or short. Portogloboviruses, halopaniviruses, and turriviruses are tailless with icosahedral capsids. Among these, halopaniviruses contain a lipid membrane within the capsid around the genome.
A shared characteristic of many groups of archaeal viruses is the folded structure of the major capsid protein (MCP). Portogloboviruses MCPs contain two antiparallel beta sheets, called a single jelly roll (SJR) fold, halopaniviruses have two paralogous SJR fold MCPs, and turriviruses have a single MCP with two jelly roll folds. This jelly roll fold is a uniting feature of viruses in Varidnaviria. The MCPs of archaeal viruses in Caudovirales, along with other viruses in Duplodnaviria, are marked by the HK97-like fold. Those of Adnaviria possess the SIRV2 fold, a type of alpha-helix bundle, and the MCPs of bicaudaviruses possess the ATV-like fold, another type of alpha-helix bundle. The architectural classes of the MCPs of other archaeal virus groups are unknown, although a four-helix bundle domain is common in the MCPs of spindle-shaped viruses.
Genetics All isolated archaeal viruses have genomes made of deoxyribonucleic acid (DNA). Metagenomic research has detected putative archaeal viruses that have genomes made of ribonucleic acid (RNA), but the actual hosts of these viruses have not been identified, and they have not been isolated yet. The vast majority of archaeal viruses have double-stranded DNA (dsDNA) genomes. Pleolipoviridae and Spiraviridae are the only known archaeal virus families to have single-stranded DNA (ssDNA) genomes. Among pleolipoviruses, closely related alphapleolipoviruses can have either dsDNA or ssDNA genomes, indicating there is flexibility in which structure can be incorporated into mature virus particles. Genetic relation can, however, still be shown between these viruses based on gene homology and synteny.