Megavirales (nucleocytoplasmic large DNA viruses): GREATEST HITS.

[KuriousKatKommittee]

One feature of this group is a large genome and the presence of many genes involved in DNA repair, DNA replication, transcription, and translation. There are 47 NCLDV core genes currently recognized. These include four key proteins involved in DNA replication and repair: the enzymes DNA polymerase family B, the topoisomerase II A, the FLAP endonuclease and the processing factor proliferating cell nuclear antigen. Other proteins include DNA dependent RNA polymerase II and transcription factor II B.

1. Pithovirus
Megavirales > Pithovirus
- It is 50% larger in size than the Pandoraviridae, the previous largest known viruses,^[3] is larger than Ostreococcus the smallest eukaryotic cell, although Pandoravirus has the largest viral genome, containing 1.9 to 2.5 megabases of DNA.^[4]

The genome of Pithovirus contains 467 distinct genes, more than a typical virus but far fewer than the 2556 putative protein-coding sequences found in Pandoravirus.^[3] Thus, its genome is far less densely packed than any other known virus. Two-thirds of its proteins are unlike those of other viruses. Despite the physical similarity with Pandoravirus, the Pithovirus genome sequence reveals that it is barely related to that virus, but more closely resembles members of Marseilleviridae, Megaviridae, and Iridoviridae.^[5]

Pithovirus' genome is one circular, double-stranded DNA (dsDNA) chromosome of about 610,000 base pairs (bp), encoding approximately 467 open reading frames (ORFs), which translate into 467 different proteins.^[7] The genome encodes all the proteins needed to produce mRNA; these proteins are present in the purified virions.^[5] Pithovirus therefore undergoes its entire replication cycle in its host's cytoplasm, rather than the more typical method of taking over the host's nucleus.^[1][5][8]

2. Tupanvirus
incertae sedis; translated "niggas going they own way"
- The genome contains roughly 1.5 million base pairs of double-stranded DNA,^[1] coding for 1276–1425 predicted proteins.

Unique to these viruses is they can incorporate (or translate) all 20 standard amino acids.^[1][2][3] As a giant virus, Tupanvirus present the largest translational apparatus within the known virosphere.

3. Faustovirus
Asfarviridae fam.
- a double stranded DNA genome of 466 kilobases predicted to encode 451 proteins

Similar to the mimivirus, in which a channel is created for particle proteins and DNA to travel though, the faustovirus particles empty their internal compartments into the amoeba’s cytoplasm. In both viruses, the fusion leads to an eclipse phase in which the contents of particles become invisible inside the cytoplasm of the host. However, the eclipse phase of the faustovirus is longer than the mimivirus, taking place from 4 to 6 hours post infection^[2]. Characterized by a loss of its spherical shape and a decrease in surface area, the amoeba host cell undergoes reorganization, such that at 8 to 10 hours post infection there are new particles in a region forming a donut shape. This region is the viral factory; it is distinct from the nucleus and is surrounded by mitochondria.

[F]austoviruses share less than a quarter of their genes with other NCLDVs; however, ~46% are homologous to bacterial genes and the remainder are orphan genes (ORFans)^[3]. Specifically, the gene encoding the major capsid protein (MCP) of faustovirus is different than that of its most closely related giant virus, asfivirus, as well as other NCLDVs. In asfivirus, the gene encoding MCP is a single genomic fragment of ~2000 base pairs (bp)^[1], however, in faustovirus the MCP is encoded by 13 exons separated by 12 large introns^[4]. The exons have a mean length of 149 bp and the introns have a mean length of 1,273 bp^[4]. The presence of introns in faustovirus genes is highly unusual for viruses ^[1].

4. Medusaviridae
incertae sedis

Medusavirus is a large DNA virus isolated from a Japanese hot spring, among other places worldwide, and is notable for having complete set of histone related genes.^[1] The virus can harden defenseless amoebas into stone-like cysts, but usually burst^[2]

5. Poxviridae
incertae sedis
- linear double-stranded DNA molecule that can have a length of up to 230 kilobases

The replication of poxvirus is unusual for a virus with double-stranded DNA genome because it occurs in the cytoplasm,^[7] although this is typical of other large DNA viruses.^[8] Poxvirus encodes its own machinery for genome transcription, a DNA dependent RNA polymerase,^[9] which makes replication in the cytoplasm possible. Most double-stranded DNA viruses require the host cell's DNA-dependent RNA polymerase to perform transcription. These host DNA are found in the nucleus, and therefore most double-stranded DNA viruses carry out a part of their infection cycle within the host cell's nucleus.

6. Herpesviridae
incertae sedis
- large, monopartite, double-stranded, linear DNA genome encoding 100-200 genes

Herpesviruses are known for their ability to establish lifelong infections. One way this is possible is through immune evasion. Herpesviruses have many different ways of evading the immune system. One such way is by encoding a protein mimicking human interleukin 10 (hIL-10) and another is by downregulation of the major histocompatibility complex II (MHC II) in infected cells.

[KuriousKatKommittee]

A certain type of latency could be ascribed to the endogenous retroviruses. These viruses have incorporated into the human genome in the distant past, and are now transmitted through reproduction. Generally these types of viruses have become highly evolved, and have lost the expression of many gene products.^[17] Some of the proteins expressed by these viruses have co-evolved with host cells to play important roles in normal processes.^[18]