Archaeal virus

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.

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).

Their complete bodies, called virions, come in many different forms, including being shaped like spindles or lemons, rods, bottles, droplets, and coils.

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[3] 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.

Many establish a persistent infection, during which progeny are continually produced at a low rate without killing the host archaeon.

Research areas in archaeal virology include gaining a better understanding of their diversity and learning about their means of replication.

[2] Putative archaeal viruses of Nitrososphaerota (formerly Thaumarchaeota) and "Euryarchaeota" in the water column and sediments have been identified but have not been cultured.

[17] Ampullaviruses are bottle-shaped; bicaudaviruses, fuselloviruses, thaspiviruses[18] and halspiviruses are spindle- or lemon-shaped, often pleomorphic;[19] spiraviruses are coil-shaped; guttaviruses are droplet-shaped.

[25] A shared characteristic of many groups of archaeal viruses is the folded structure of the major capsid protein (MCP).

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.

[28] Fuselloviruses and pleolipoviruses are frequently integrated into their hosts' genome, giving the false impression of encoding many cellular proteins.

Furthermore, archaea-specific virus groups lack shared hallmark genes involved in core replication and morphogenetic functions, such as a shared major capsid protein,[21] further indicating that archaea-specific virus groups lack common ancestry.

[17] Some MGEs may be descended from archaeal viruses, such as TKV4-like proviruses and pTN3-like integrative plasmids of Thermococcus, which encode proteins signature of Varidnaviria but do not appear to produce virions.

[5] Many unusual characteristics of archaeal viruses of hyperthermophiles likely represent adaptations required for replication in their hosts and for stability in extreme environmental conditions.

Similarly, the genome of clavavirus APBV1 is packaged in a tight, left-handed superhelix with its major capsid proteins, reflecting an adaptation allowing for DNA to survive at high temperatures.

Acidianus two-tailed virus (ATV), a bicaudavirus, undergoes a conformational change in virion structure after it leaves a cell.

Because of the aforementioned low cell density and rapid half-life, these viruses are more likely to replicate via a chronic or lysogenic lifecycle.

This type of recombination has been proposed for why haloarchaeal viruses within Halopanivirales and Pleolipoviridae can have the same core structural proteins but different genomic characteristics and replication methods.

In methanogenic archaea of the order Methanococcales, the cellular minichromosome maintenance (MCM) helicase has apparently undergone accelerated evolution due to acquisition by a virus, accelerated evolution as a viral gene, and re-integration into the host archaea, replacing the original MCM gene.

There is evidence of high viral-induced mortality, mainly of Nitrososphaerota, in deep-sea ecosystems, resulting in about 0.3–0.5 gigatons of carbon release globally each year.

The death of these archaea releases cellular content, thereby enhancing organic matter mineralization and respiration of uninfected heterotrophs.

In turn, this stimulates nitrogen regeneration processes, supplying 30–60% of the ammonia required to sustain archaeal chemoautotrophic carbon production in deep-sea sediments.

[9] Archaea dominate high-temperature, low-pH hot springs worldwide, such as those in Yellowstone National Park, to the point where eukaryotes are absent and bacteria constitute only a small percentage of cellular biomass present.

Culture-independent methods have also been used, including viral tagging, phage fluorescent in situ hybridization, single cell genomics, and bioinformatic analysis of previously published sequence data.

[9] Cryogenic electron microscopy (cryo-EM) has helped to analyze structural similarities between viruses, such as showing that lipothrixviruses, rudiviruses, and tristromaviruses encode the same MCP.

[9][28] The first description of an archaeal virus was made by Torsvik and Dundas in 1974 in a Nature paper titled "Bacteriophage of Halobacterium salinarum".

[9] In the 1980s, Wolfram Zillig and his colleagues began isolating viruses from thermophilic archaea of the orders Thermoproteales and Sulfolobales.

[9] In total, he and his colleagues would discover and characterize four archaeal virus families: Fuselloviridae, Rudiviridae, Lipothrixviridae, and Guttaviridae.

[26][37] The bicaudavirus ATV was described in 2005 and was noted for its ability to undergo a morphological change independent of its host cell.

[40] Portogloboviruses, along with halopaniviruses, would become important in understanding the evolutionary history of Varidnaviria, as they represent more basal lineages of the realm than previously described varidnaviruses such as turriviruses.