Nucleocytoviricota is a phylum ofviruses.[2] Members of the phylum are also known as thenucleocytoplasmic large DNA viruses (NCLDV), which serves as the basis of the name of the phylum with the suffix -viricota for virus phylum. These viruses are referred to as nucleocytoplasmic because they are often able to replicate in both the host'scell nucleus andcytoplasm.[3]
The phylum is notable for containing thegiant viruses.[4][1] 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.[5] One feature of this group is a largegenome and the presence of manygenes involved inDNA repair,DNA replication,transcription, andtranslation. 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'snucleus andcytoplasm, thus the name nucleocytoplasmic.
Host organisms typically includeprotozoa,invertebrates and eukaryoticalgae. The classPokkesviricetes infects familiar vertebrates, including multiple farm animals and humans.
Phylogenetic tree of phylumNucleocytoviricota on base of Subramaniamet al. (2020).[7]
OrderPimascovirales. Members of the familyAscoviridae come in different shapes. Some can be rod-shaped, while others are oval. They measure up to 130 nm wide and 400 nm long. These 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.[8] 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.[9]
OrderAsfuvirales. A member of the familyAsfarviridae 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.[10]
OrderPimascovirales. TheIridoviridae 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.[11] TheAndrias davidianusranavirus (ADRV), a member of the familyIridoviridae, encodes a protein (Rad2 homolog) that has a key role in the repair of DNA byhomologous recombination, and indouble-strand break repair.[12]
OrderPimascovirales. TheMarseilleviridae viruses have double stranded DNA genomes that are about 368 kilobases long. Members of the family can have about 457open reading frames (ORFs) in its genome. The host organisms areamoebae. Once it infects, viral replication takes place in virus factories in the cytoplasm. It was found that the genome of the familyMarseilleviridae codes for about 28 different proteins.[13] 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.[14]
OrderImitervirales. TheMegaviridae contains some of the largest viruses ever discovered. They have linear double stranded DNA genomes with a length of 1,259,197 base pairs, which is larger than some small bacteria. Within this genome 1,100 proteins are coded. 74.76% of the base pairs are represented by thymine and adenine. TheMegaviridae 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.[15] Three enzymes employed in DNAbase excision repair were characterized from Mimivirus.[16] The pathway of DNA base excision repair (BER) was experimentally reconstituted using the purified recombinant proteinsAP endonuclease (mvAPE),uracil-DNA glycosylase (mvUDG), andDNA polymerase X protein (mvPolX).[16] When reconstituted in vitro, mvAPE, mvUDG and mvPolX were found to function cohesively to repair uracil-containing DNA mainly by long patch base excision repair.[16] Thus these processes likely participate in the BER pathway early in the Mimivirus life cycle.[16] Cafeteria roenbergensis, a giant virus of the Mimiviridae family, also encodes enzymes for DNA repair.[17]
Traditionally only these viruses have been grouped into a familyMimiviridae. Later it appeared that the viruses of theOrganic Lake Phycodna Group (OLPG) are more related to Mimiviruses than toPhycodnaviruses. For this reason it has been proposed adding them to legacyMimiviridae as new subfamilyMesomimivirinae in order to form the more comprehensive familyMegaviridae. For this reason, the termMimiviridae was usedsensu lato synonymous withMegaviridae.[18][19][20][21][22][23] However, since the ICTV has created a new orderImitervirales officially containing the (legacy)Mimiviridae, proposedMesomimivirinae are proposed to be upgraded as a new familyMesomimiviridae, i. e. as sister family of legacyMimiviridae (within this order).
Possibly orderAlgavirales.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.[24] The replication of this virus takes place in the cytoplasm. Like other giant viruses, it affects the host's nucleus and can take up to 15 hours to start infecting.[25] 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.[26]
OrderAlgavirales. ThePhycodnaviridae 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.[27]
OrderPimascovirales. ThePithoviridae 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.[28] 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.[29]
OrderChitovirales. ThePoxviridae 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 otherpox viruses belong to this family.[30]
This section'sfactual accuracy may be compromised due to out-of-date information. Please help update this article to reflect recent events or newly available information.(May 2020)
Cedratvirus — now underPithoviridae (Pimascovirales)
Choanovirus — part of extendedMimiviridae, a clade distinct fromMimiviridae proper;[31] (Imitervirales)
Yasminevirus — close toKlosneuvirus andBodo saltans virus; (together withGaeavirus,Homavirus,Barrevirus,Fadolivirus,Dasosvirus,Edafovirus,Terrestrivirus,Harvfovirus,Hyperionvirus from metagenomics) members ofMimiviridae (Imitervirales)
The general consensus is thatIridoviridae–Ascoviridae are closely related sister taxa in a clade.Pithovirus,Iridoviridae–Ascoviridae andMarseillevirus form a PIM or MAPI clade (Pimascovirales[2]) in trees built from conserved proteins.[7] The sister clade to PIM/MAPI is a clade made out ofAlgavirales[2] (Phycodnaviridae,Pandoraviridae), and possiblyImitervirales[2]/Mimiviridae ("P2" thereafter).[36]Poxviridae is consistently treated as a basal branch.Asfarviridae is either a sister group toPoxviridae (building togetherPokkesviricetes)[2] or a member of the P2 clade.[37] 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 theirRNA polymerase structures.[37]
^abcdLad SB, Upadhyay M, Thorat P, Nair D, Moseley GW, Srivastava S, Pradeepkumar PI, Kondabagil K (September 2023). "Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway".J Mol Biol.435 (17): 168188.doi:10.1016/j.jmb.2023.168188.PMID37380013.
^Fischer MG, Kelly I, Foster LJ, Suttle CA (October 2014). "The virion of Cafeteria roenbergensis virus (CroV) contains a complex suite of proteins for transcription and DNA repair".Virology.466–467:82–94.doi:10.1016/j.virol.2014.05.029.PMID24973308.
^Wilson, W. H.; Van Etten, J. L.; Allen, M. J. (2009). "The Phycodnaviridae: The Story of How Tiny Giants Rule the World".Lesser Known Large dsDNA Viruses. Current Topics in Microbiology and Immunology. Vol. 328. pp. 1–42.doi:10.1007/978-3-540-68618-7_1.ISBN978-3-540-68617-0.PMC2908299.PMID19216434.
^Needham, David M.; Yoshizawa, Susumu; Hosaka, Toshiaki; Poirier, Camille; Choi, Chang Jae; Hehenberger, Elisabeth; Irwin, Nicholas A. T.; Wilken, Susanne; Yung, Cheuk-Man; Bachy, Charles; Kurihara, Rika; Nakajima, Yu; Kojima, Keiichi; Kimura-Someya, Tomomi; Leonard, Guy; Malmstrom, Rex R.; Mende, Daniel R.; Olson, Daniel K.; Sudo, Yuki; Sudek, Sebastian; Richards, Thomas A.; DeLong, Edward F.; Keeling, Patrick J.; Santoro, Alyson E.; Shirouzu, Mikako; Iwasaki, Wataru; Worden, Alexandra Z. (8 October 2019)."A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators".Proceedings of the National Academy of Sciences.116 (41):20574–83.Bibcode:2019PNAS..11620574N.doi:10.1073/pnas.1907517116.PMC6789865.PMID31548428.
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Data related toNucleocytoviricota at Wikispecies
