Archaeal Viruses

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), but some may contain ribonucleic acid (RNA) genomes. 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'' 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, -''virales'' denotes order, and -''viridae'' denotes family):
* ''Adnaviria'' - among virus realms, this is the only one that exclusively contains archaeal viruses:
** ''Ligamenvirales''
*** ''Lipothrixviridae''
*** ''Rudiviridae''
** ''Primavirales''
*** ''Tristromaviridae''
* ''Duplodnaviria'':
** ''Caudovirales'' - the three families listed also contain bacterial viruses
*** ''Myoviridae''
*** ''Siphoviridae''
*** ''Podoviridae''
* ''Monodnaviria'':
** ''Pleolipoviridae''
* ''Varidnaviria''
** '' Halopanivirales''
*** '' Simuloviridae''
*** '' Sphaerolipoviridae''Prior 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''".
** ''Turriviridae''

Unassigned families:

* ''Ampullaviridae''
* ''Bicaudaviridae''
* ''Clavaviridae''
* ''Fuselloviridae''
* ''Globuloviridae''
* ''Guttaviridae''
* ''Halspiviridae''''Halspiviridae'' contains only one genus: ''Salterprovirus''. This genus is often named when referring to viruses of this family.
* '' Ovaliviridae''
* '' Portogloboviridae''Although ''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.

The genomes of archaeal viruses vary in size significantly, ranging from 5.3 kilobases (kb) in clavavirus ''Aeropyrum pernix bacilliform virus 1'' (APBV1) to 143.8 kb in the myovirus HGTV-1. Archaea-specific viruses tend to have smaller genomes than other archaeal viruses, especially viruses in ''Caudovirales''. APBV1 with a genome of about 5 kb, is one of the smallest known dsDNA viruses. Spiravirus ''Aeropyrum coil-shaped virus'' has the largest known genome of an ssDNA virus at about 35 kb. Some archaeal viruses, namely viruses of ''Adnaviria'', package their DNA in A-form as a result of an interaction between the MCP and B-form pre-genomic DNA.

Few proteins encoded by archaeal viruses, especially those that infect archaea of Thermoproteota, show a relation to other known proteins. For viruses in ''Ampullaviridae'', ''Globuloviridae'', ''Spiraviridae'', ''Portogloboviridae'', and ''Tristromaviridae'', less than 10% of encoded proteins are homologous to proteins found in cellular life or other viruses. In total, the functions of about 85% of crenarchaeal virus genes are unknown. Consequently, archaeal viruses constitute a large source of unknown genes to be researched. It is likely that many of these genes help overcome host defense responses, outcompete other viruses, and adapt to changes in the extreme geochemical environment of their hosts. Fuselloviruses and pleolipoviruses are frequently integrated into their hosts' genome, giving the false impression of encoding many cellular proteins. For most archaeal virus families, however, a significant minority of viral proteins are homologous to proteins found in archaea. Archaeal viruses also appear to share many genes with non-viral selfish replicons such as plasmids and transposons.

Life cycle

Many aspects of the life cycle of archaeal viruses are unknown and have mainly been inferred from recognizable genes encoded by them. Specific cellular receptors archaeal viruses bind to on the surface of cells have not been identified, but many are able to bind to extracellular structures such as pili, including Sulfolobus turreted icosahedral virus (STIV) and ''Acidianus filamentous virus 1'' (AFV1), which bind to pili via claw-like structures on the virion. Sulfolobus islandicus rod-shaped virus 2 (SIRV2) attaches to pili and then moves along the pili toward the cell. Caudoviruses attach to the surface of cells via their tail. Pleolipoviruses and halopaniviruses possess spike proteins that bind to the surface of cells. Little is known about how archaeal virus DNA enters the host cell. Caudoviruses inject their DNA through their tail. ''Haloarcula virus HCIV1'', a halopanivirus, has been observed to form tube-like structures between the virion and cell surface, which may be used to deliver the viral genome to the cell.

SIRV2 appears to replicate through a combination of strand-displacement, rolling circle, and strand-coupled replication. This process produces a highly branched, "brush-like" intermediate molecule containing many copies of the genome. Unit-length genomes are then processed from concatemers in the molecule. AFV1 has been suggested to start replication by forming a D-loop, then progressing through strand-displacement synthesis. Replication is then terminated by relying on recombination events through the formation of terminal loop-like structures. Pleolipoviruses with circular genomes replicate through rolling circle replication, and those with linear genomes via protein-primed replication. Overall, archaeal viruses follow the general trend observed in dsDNA viruses in which viruses with larger genomes approach self-sufficiency in replication. Caudoviruses in particular appear to have little reliance on host replication machinery.

The archaeal homolog of the endosomal sorting complex required for transport (ESCRT) is used by some archaeal viruses for assembly and exit. ''Sulfolobus turreted icosahedral virus 1

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