Nucleocytoplasmic Large DNA Viruses

''Nucleocytoviricota'' is a phylum of viruses. Members of the phylum are also known as the nucleocytoplasmic large DNA viruses (NCLDV), which serves as the basis of the name of the phylum with the suffix - for virus phylum. These viruses are referred to as nucleocytoplasmic because they are often able to replicate in both the host's cell nucleus and cytoplasm.

The phylum is notable for containing the giant viruses. There are nine families of NCLDVs that all share certain genomic and structural characteristics; however, it is uncertain whether the similarities of the different families of this group have a common viral ancestor. One feature of this group is a large genome and the presence of many genes involved in DNA repair, DNA replication, transcription, and translation. Typically, viruses with smaller genomes do not contain genes for these processes. Most of the viruses in this family also replicate in both the host's nucleus and cytoplasm, thus the name nucleocytoplasmic.

There are 47 NCLDV core genes currently recognised. 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.

Taxonomy

The following classes are recognized, under which are orders that contain families mentioned in this article:
* ''Megaviricetes''
** ''Pimascovirales''
*** ''Ascoviridae''
*** ''Iridoviridae''
*** ''Marseilleviridae''
*** (''Pithoviridae?'') – by etymology of ''Pimascovirales''
*** ('' Mininucleoviridae?'') – by phylogeny
** ''Imitervirales''
*** ''Mimiviridae''
** ''Algavirales''
*** ''Phycodnaviridae''
*** (''Pandoraviridae?'') – by phylogeny
* ''Pokkesviricetes''
** '' Asfuvirales''
*** '' Asfarviridae''
** ''Chitovirales''
*** ''Poxviridae''

The unrecognized families are parenthesized and placed in the most likely location.

Hosts

Host organisms typically include protozoa, invertebrates and eukaryotic algae. The class Pokkesviricetes infects familiar vertebrates, including multiple farm animals and humans.

Examples

''Ascoviridae''

Order ''Pimascovirales''. Members of the family ''Ascoviridae'' come in different shapes. Some can be rod-shaped, while others are oval. They measure up to 130 nm wide and 400 nm long. Theses viruses have circular double stranded DNA that have a length of about 100–200 kilobase pairs. They infect lepidopteran insect larvae and can infect through parasitoid wasps. Once they infect they replicate and cause death in insect pest. This allows them to control insect populations. Ascoviridae can have up to 180 genes in its genome. The replication of this virus takes place in the nucleus of the host cell. When it replicates, it causes the nucleus to increase in size and eventually burst. After, the virion starts to form and spread.

''Asfarviridae''

Order ''Asfuvirales''. A member of the family '' Asfarviridae'' is known as an asfarvirus. This virus is the cause of African swine fever. Some of the symptoms for this flu include fever, high pulse, fast breathing, and it can cause death. These symptoms can be similar to those from hog cholera, the difference is that the African swine flu can not be cured. There is no vaccine developed to fight this virus.

''Iridoviridae''

Order ''Pimascovirales''. The ''Iridoviridae'' have linear double stranded DNA genomes up to 220 kilobases long and can code for about 211 proteins. The capsid of this virion is icosahedral shaped and can be up to 350 nm wide. The replication cycle of this virus begins in the nucleus of the host and end in the cytoplasm. Some viruses of this family are often found infecting fish and amphibians while other are found in insect and crustaceans.

''Marseilleviridae''

Order ''Pimascovirales''. The ''Marseilleviridae'' viruses have double stranded DNA genomes that are about 368 kilobases long. Members of the family can have about 457 open reading frames (ORFs) in its genome. The host organisms are amoebae. Once it infects, viral replication takes place in virus factories in the cytoplasm. It was found that the genome of the family ''Marseilleviridae'' codes for about 28 different proteins. The capsid of the marseillevirus is about 250 nm wide with a geometry shape of an icosahedral. The replication of this virus usually occurs near the nucleus once it infects the amoeba. Once the virus infects it can cause a shape change in the host's nucleus.

''Mimiviridae''

Order ''Imitervirales''. The ''Megaviridae'' contains some of the largest viruses ever discovered. They have linear double stranded DNA genomes with the length of 1,259,197 base pairs, which is larger than some small bacteria. Within in this genome 1,100 proteins are coded. 74.76% of the base pairs are represented by thymine and adenine. The ''Megaviridae'' virus can be found infecting acanthamoeba or other protozoan clades.  Once the virus infects the host, the replication cycle takes place in the cytoplasm. Within the genome, DNA repair enzymes can be found. These are used when the DNA is harmed such as when it is exposed to ionizing radiation or UV light.

Traditionally only these viruses have been grouped into a family ''Mimiviridae''. Later it appeared that the viruses of the ''Organic Lake Phycodna Group'' (OLPG) are more related to Mimiviruses than to Phycodnaviruses. For this reason it has been proposed adding them to legacy ''Mimiviridae'' as new subfamily ''Mesomimivirinae'' in order to form the more comprehensive family ''Megaviridae''. For this reason, the term ''Mimiviridae'' was used ''sensu lato'' synonymous with ''Megaviridae''., UCPMS ID: 1889607
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/ref> Figure 6 However, since the ICTV has created a new order ''Imitervirales'' officially containing the (legacy) ''Mimiviridae'', proposed ''Mesomimivirinae'' are proposed to be upgraded as a new family ''Mesomimiviridae'', i. e. as sister family of legacy ''Mimiviridae'' (within this order).

''Pandoraviridae''

Possibly order ''Algavirales''. ''Pandoraviridae'' Discovered in 2013 from a coastal water sample in Chile. It is mostly found infecting amoebae. It has a length of 1 micrometer long and .5 micrometer wide. Its genome can be up to 2.5 million base pairs long. The replication of this virus take place in the cytoplasm. Like other giant viruses, it affect the host's nucleus and can take up to 15 hours to start infecting. Although it is found in water, it does not affect humans, it may actually help us by increasing the production of oxygen in aquatic environments. 

''Phycodnaviridae''

Order ''Algavirales''. The ''Phycodnaviridae'' are icosahedral in shape with a double-stranded DNA molecule. Some members of this family can have a linear double-stranded DNA while others have a circular double stranded DNA. The genome has been found to be up to 560 kilobases in length. Up to 50% of the DNA can be represented by guanine or cytosine. This virus is known to infect algae, which means it is found in the ocean.

''Pithoviridae''

Possibly order ''Pimascovirales''. The ''Pithoviridae'' have only two known representatives. These viruses infects amoebas and can survive in low temperatures. For years this virus was believed to be frozen, but due to climate change it has begun to show up again. This is a double stranded DNA virus with its size being 610 kilobases long. The genome is estimated to code for 476 open reading frames. The viron is rod shaped with a length of 1,100 nm long and 500 nm in diameter.

''Poxviridae''

Order ''Chitovirales''. The ''Poxviridae'' have a linear double-stranded DNA molecule that can have a length of up to 230 kilobases. The replication of these viruses takes place in the cytoplasm. Smallpox, cowpox, and other pox viruses belong to this family. 

''Mininucleoviridae''

Possibly order ''Pimascovirales''. A new family has been proposed - '' Mininucleoviridae'' - for a family of large viruses that replicate in crustacea. Members of this proposed family include '' Carcinus maenas virus 1'' (CmV1),CmV1 infects ''Carcinus maenas'' ''Dikerogammarus haemobaphes virus 1'' (DhV1),DhV1 infects ''Dikerogammarus haemobaphes'' and '' Panulirus argus virus 1'' (PaV1).PaV1 infects ''Panulirus argus''

Unclassified taxa

* '' Cedratvirus'' – now under ''Pithoviridae'' (''Pimascovirales'')
* '' Choanovirus'' – part of extended ''Mimiviridae'', a clade distinct from ''Mimiviridae'' proper; (''Imitervirales'')
* ''Dinodnavirus'' – possibly under ''Asfarviridae'' (''Asfuvirales'')
* '' Faustovirus'' – now under ''Asfarviridae'' (''Asfuvirales'')
* '' Kaumoebavirus'' – clusters under ''Asfarviridae'' (''Asfuvirales'')
* '' Klothovirus'' – no sequences available
* '' Megaklothovirus'' – no sequences available
* ''Medusavirus'' – proposed to be its own family ''Medusaviridae'', possibly close to ''Mollivirus'' or basal in ''Nucleocytoviricota''
* '' Meelsvirus''  – no sequences available
* '' Mollivirus'' – close to ''Pandoravirus'' (''Algavirales'')
* ''Namao virus'' – (together with ''Faunusvirus sp.'' from metagenomics) close to ''Cafeteriavirus''; possibly together with other Sturgeon-NCLDVs; (''Imitervirales'')
* '' Orpheovirus'' – likely under ''Pithoviridae''; sister group to ''Cedratvirus'' (''Pimascovirales'')
* '' Pacmanvirus'' – likely under ''Asfarviridae'' (''Asfuvirales'')
* '' Platanovirus'' – similar to ''Megavirus'' or ''Tupanvirus'' (''Imitervirales'')
* '' Sissivirus'' and ''Misannotatedvirus'' – (together with ''Solumnvirus'', ''Solivirus'' from metagenomics) possibly under ''Pithoviridae''
* ''Tupanvirus'' – possibly under ''Mimiviridae'' (''Imitervirales'')
* '' Urceolovirus'' – possibly under ''Nucleocytoviricota''
* '' Usurpativirus'' and '' Clandestinovirus'' – a clade possibly under ''Phycodnaviridae'' nearby ''Chlorovirus'' (''Algavirales'')
* '' Yasminevirus'' – close to ''Klosneuvirus'' and ''Bodo saltans virus''; (together with ''Gaeavirus'', ''Homavirus'', ''Barrevirus'', ''Fadolivirus'', ''Dasosvirus'', ''Edafovirus'', ''Terrestrivirus'', ''Harvfovirus'', ''Hyperionvirus'' from metagenomics) members of ''Mimiviridae'' (''Imitervirales'')

Phylogenetics

The general consensus is that ''Iridoviridae''–''Ascoviridae'' are closely related sister taxa in a clade. ''Pithovirus'', ''Iridoviridae''–''Ascoviridae'' and '' Marseillevirus'' form a PIM or MAPI clade (''Pimascovirales'') in trees built from conserved proteins. The sister clade to PIM/MAPI is a clade made out of ''Algavirales'' (''Phycodnaviridae'', ''Pandoraviridae''), and possibly ''Imitervirales''/''Mimiviridae'' ("P2" thereafter).PDF
/ref> ''Poxviridae'' is consistently treated as a basal branch. ''Asfarviridae'' is either a sister group to ''Poxviridae'' (building together ''Pokkesviricetes'') or a member of the P2 clade. The ICTV classification, as of 2019, matches the general shape of the tree.

The origin of the NCLDVs may predate that of their eukaryotic hosts, judging from their RNA polymerase structures.

See also

* Viral eukaryogenesis

Notes

References

External links

*

{{Taxonbar, from=Q92194946

Nucleocytoplasmic large DNA viruses
Viruses