Pandoravirus

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Pandoravirus
41467 2018 4698 Fig1 HTML Pandoraviruses.jpg
Pandoravirus virion
Virus classification OOjs UI icon edit-ltr.svg
(unranked): Virus
Realm: Varidnaviria
Kingdom: Bamfordvirae
Phylum: Nucleocytoviricota
Class: Megaviricetes
Order: Algavirales (?)
Family: Pandoraviridae
Genus:Pandoravirus
Species

Pandoravirus is a proposed genus of giant virus, first discovered in 2013. [5] It is the third largest in physical size of any known viral genus, behind Pithovirus and Megaklothovirus. [6] Pandoraviruses have double stranded DNA genomes, with the largest genome size (2.5 million base pairs) of any known viral genus. [7]

Contents

Discovery

The discovery of Pandoraviruses by a team of French scientists, led by husband and wife Jean-Michel Claverie and Chantal Abergel, was announced in a report in the journal Science in July 2013. [5] Other scientists had previously observed the pandoravirus particles, but owing to their enormous size they were not expected to be viruses. [5] Patrick Scheid, a parasitologist from the Central Institute of the Bundeswehr Medical Service in Koblenz, Germany, found one in 2008, in an amoeba living in the contact lens of a woman with keratitis. Its development within the amoebal host was documented extensively. Unlike in other cases with such giant viruses, the large particles within Acanthamoeba were not mistaken for bacteria. The authors initially termed them "endocytobionts". [8]

Mimivirus , a nucleocytoplasmic large DNA virus with a genome size of about 1.1 megabases, was described in 1992 but not recognized as a virus until 2003. [9] Megavirus , discovered in seawater off the coast of Chile in 2011, has a genome size of approximately 1.2 megabases. [10]

The prior discovery of these viruses prompted a search for other types of large amoeba-infecting viruses, which led to the finding of two species; Pandoravirus salinus , found in seawater taken from the coast of Chile, with a genome size of ~2.5 megabases, and Pandoravirus dulcis , found in a shallow freshwater pond in La Trobe University, Melbourne, Australia, with a 1.9 megabase genome. [5] [11]

Description

Pandoraviruses are oval in shape and are about 1  micrometer  (1000 nanometers) in length. Other viruses range from 25 to 100 nanometers. In addition to being large physically, Pandoraviruses have a large genome made up of 2,500 genes, compared to only 10 genes on average in other viruses. For example, the Influenza A virus contains 7 genes and HIV contains only 9 genes. Gene content varies among species of Pandoravirus, with Pandoravirus salinus containing 2,500 genes and Pandoravirus dulcis containing about 1,500 genes. Pandoraviruses were originally mistaken for bacteria; however, they lack some of the characteristics of bacteria, such as the ability to make their own proteins. The dissimilarity of the remaining genes to any cellular genes led researchers to speculate that this virus represents a previously unknown branch of the tree of life. However, other experts have called this proposal premature because there is very little evidence supporting the idea. [12]

Replication

Pandoraviruses have double stranded DNA. Like most giant viruses, Pandoraviruses have a viral replication cycle. They lack the ability to make their own proteins, rely on the host cells for ATP (energy) and replication, and also do not contain ribosomes or produce energy to divide. Under the microscope, scientists observed the virus enter the amoeba through fusion with membrane vacuoles, and integrate their DNA into the host cells. The host cell replicates the viral particles and eventually splits open, releasing the viral particles. The process of replication lasts 10–15 hours. [13] Viral replication and assembly happens simultaneously. In other words, viral DNA is replicated within the cytoplasm of the host cell and assembled into new viral particles followed by lysis of the host cell. [14]

Prevalence in the environment

Pandoraviruses do not seem to be harmful to humans. They are mostly found in marine environments, infecting amoebae. One reason for their only relatively recent discovery is because they exist in environments that are not well studied. Pandoraviruses, like other marine viruses, infect plankton, which are organisms that live in the water column and form the basis of the food chain for other marine species. More study and research needs to be done in order to confirm the prevalence of Pandoraviruses in different environments. Currently, not much is known about their role in marine ecosystems. however, viruses are not mere pathogens for their host, but are also key players in aquatic ecosystems and the biosphere. Almost all genomes of cellular organisms contain viral sequences, elements of which are also essential in gene regulation. Viral infection and lysis can influence community structure, as well as the transfer of matter and energy in aquatic ecosystems. They can also dramatically alter host physiology through viral gene expression and drive evolutionary innovation through virus-mediated horizontal gene transfer. [15]

Phylogenetic affinities

Approximately 93% of Pandoravirus genes are not known from any other microbes, [16] suggesting that they belong to an as of yet undescribed "fourth domain" aside from Bacteria, Archaea, and Eukaryotes. [16] Viruses are not widely considered to belong within these three domains, although they have been proposed as one in the past by some biologists. [17]

Comparison with other giant viruses

Other giant viruses such as the Mimivirus, Pithovirus, and Megavirus have much smaller genomes. For example, Mimivirus, considered one of the largest giant viruses, has a genome size of 1.1 million base pairs compared to 2.5 million base pairs for Pandoraviruses. Another feature that is different in Pandoraviruses compared to other giant viruses is the replication cycle. Pandoraviruses infect amoebas, which are single celled eukaryotes. [18] Pandoravirus enters amoebas through phagocytic vacuoles, then fuses with the membrane vacuole of the amoeba. This leads to viral particles to be released into the cytoplasm of the amoeba. [19]

See also

Related Research Articles

Viral evolution is a subfield of evolutionary biology and virology that is specifically concerned with the evolution of viruses. Viruses have short generation times, and many—in particular RNA viruses—have relatively high mutation rates. Although most viral mutations confer no benefit and often even prove deleterious to viruses, the rapid rate of viral mutation combined with natural selection allows viruses to quickly adapt to changes in their host environment. In addition, because viruses typically produce many copies in an infected host, mutated genes can be passed on to many offspring quickly. Although the chance of mutations and evolution can change depending on the type of virus, viruses overall have high chances for mutations.

<i>Mimivirus</i> Genus of viruses

Mimivirus is a genus of giant viruses, in the family Mimiviridae. Amoeba serve as their natural hosts. This genus contains a single identified species named Acanthamoeba polyphaga mimivirus (APMV). It also refers to a group of phylogenetically related large viruses.

<span class="mw-page-title-main">Viroplasm</span>

A viroplasm, sometimes called "virus factory" or "virus inclusion", is an inclusion body in a cell where viral replication and assembly occurs. They may be thought of as viral factories in the cell. There are many viroplasms in one infected cell, where they appear dense to electron microscopy. Very little is understood about the mechanism of viroplasm formation.

<span class="mw-page-title-main">Mobilome</span>

The mobilome is the entire set of mobile genetic elements in a genome. Mobilomes are found in eukaryotes, prokaryotes, and viruses. The compositions of mobilomes differ among lineages of life, with transposable elements being the major mobile elements in eukaryotes, and plasmids and prophages being the major types in prokaryotes. Virophages contribute to the viral mobilome.

<span class="mw-page-title-main">Virophage</span> Viral parasites of giant viruses

Virophages are small, double-stranded DNA viral phages that require the co-infection of another virus. The co-infecting viruses are typically giant viruses. Virophages rely on the viral replication factory of the co-infecting giant virus for their own replication. One of the characteristics of virophages is that they have a parasitic relationship with the co-infecting virus. Their dependence upon the giant virus for replication often results in the deactivation of the giant viruses. The virophage may improve the recovery and survival of the host organism.

<span class="mw-page-title-main">Sputnik virophage</span> Subviral agent

Mimivirus-dependent virus Sputnik is a subviral agent that reproduces in amoeba cells that are already infected by a certain helper virus; Sputnik uses the helper virus's machinery for reproduction and inhibits replication of the helper virus. It is known as a virophage, in analogy to the term bacteriophage.

<i>Mimiviridae</i> Family of viruses

Mimiviridae is a family of viruses. Amoeba and other protists serve as natural hosts. The family is divided in up to 4 subfamilies. Viruses in this family belong to the nucleocytoplasmic large DNA virus clade (NCLDV), also referred to as giant viruses.

Mamavirus is a large and complex virus in the Group I family Mimiviridae. The virus is exceptionally large, and larger than many bacteria. Mamavirus and other mimiviridae belong to nucleocytoplasmic large DNA virus (NCLDVs) family. Mamavirus can be compared to the similar complex virus mimivirus; mamavirus was so named because it is similar to but larger than mimivirus.

<i>Cafeteria roenbergensis virus</i> Species of virus

Cafeteria roenbergensis virus (CroV) is a giant virus that infects the marine bicosoecid flagellate Cafeteria roenbergensis, a member of the microzooplankton community.

A giant virus, sometimes referred to as a girus, is a very large virus, some of which are larger than typical bacteria. All known giant viruses belong to the phylum Nucleocytoviricota.

<i>Megavirus</i> Genus of viruses

Megavirus is a viral genus, phylogenetically related to Acanthamoeba polyphaga mimivirus (APMV). In colloquial speech, Megavirus chilense is more commonly referred to as just "Megavirus". Until the discovery of pandoraviruses in 2013, it had the largest capsid diameter of all known viruses, as well as the largest and most complex genome among all known viruses.

<i>Pandoraviridae</i> Family of viruses

Pandoraviridae is a proposed family of double-stranded DNA viruses that infect amoebae. There is only one genus in this family: Pandoravirus. Several species in this genus have been described, including Pandoravirus dulcis, Pandoravirus salinus and Pandoravirus yedoma.

<i>Alphapithovirus</i> Genus of viruses

Alphapithovirus, is a genus of giant virus known from two species, Alphapithovirus sibericum, which infects amoebas, and Alphapithovirus massiliense. It is DNA-based and is a member of the nucleocytoplasmic large DNA viruses clade. It was discovered in 2014, when a viable specimen was found in a 30,000-year-old ice core harvested from permafrost in Siberia, Russia.

This glossary of virology is a list of definitions of terms and concepts used in virology, the study of viruses, particularly in the description of viruses and their actions. Related fields include microbiology, molecular biology, and genetics.

<span class="mw-page-title-main">Zamilon virophage</span> Virus type

Mimivirus-dependent virus Zamilon, or Zamilon, is a virophage, a group of small DNA viruses that infect protists and require a helper virus to replicate; they are a type of satellite virus. Discovered in 2013 in Tunisia, infecting Acanthamoeba polyphaga amoebae, Zamilon most closely resembles Sputnik, the first virophage to be discovered. The name is Arabic for "the neighbour". Its spherical particle is 50–60 nm in diameter, and contains a circular double-stranded DNA genome of around 17 kb, which is predicted to encode 20 polypeptides. A related strain, Zamilon 2, has been identified in North America.

<i>Faustovirus</i> Genus of viruses

Faustovirus is a genus of giant virus which infects amoebae associated with humans. The virus was first isolated in 2015 and shown to be around 0.2 micrometers in diameter with a double stranded DNA genome of 466 kilobases predicted to encode 451 proteins. Although classified as a nucleocytoplasmic large DNA virus (NCLDV), faustoviruses 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). 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), however, in faustovirus the MCP is encoded by 13 exons separated by 12 large introns. The exons have a mean length of 149 bp and the introns have a mean length of 1,273 bp. The presence of introns in faustovirus genes is highly unusual for viruses.

<i>Tupanvirus</i> Proposed genus of viruses

Tupanvirus is a genus of viruses first described in 2018. The genus is composed of two species of virus that are in the giant virus group. Researchers discovered the first isolate in 2012 from deep water sediment samples taken at 3,000 m depth off the coast of Brazil. The second isolate was collected from a soda lake in Southern Nhecolândia, Brazil in 2014. They are named after Tupã (Tupan), a Guaraní thunder god, and the places they were found. These are the first viruses reported to possess genes for amino-acyl tRNA synthetases for all 20 standard amino acids.

<i>Medusavirus</i> Type of virus

Medusavirus is a nucleocytoplasmic large DNA virus first isolated from a Japanese hot spring in 2019. It notably encodes all five types of histones — H1, H2A, H2B, H3, and H4 — which are involved in DNA packaging in eukaryotes, raising the possibility that they may have been involved in the origin of eukaryotes. The virus can harden amoebas of the species Acanthamoeba castellanii into stone-like cysts, but infection usually causes infected amoebas to burst open. The virus was named after Medusa, the monster in Greek mythology whose gaze turned people to stone.

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 -viricota 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.

Virosphere was coined to refer to all those places in which viruses are found or which are affected by viruses. However, more recently virosphere has also been used to refer to the pool of viruses that occurs in all hosts and all environments, as well as viruses associated with specific types of hosts, type of genome or ecological niche.

References

  1. ↑ "Pandoravirus dulcis". NCBI Taxonomy Browser. 1349409. Archived from the original on 31 August 2017. Retrieved 7 September 2017.
  2. ↑ "Pandoravirus salinus". NCBI Taxonomy Browser. 1349410. Archived from the original on 20 June 2017. Retrieved 7 September 2017.
  3. ↑ "Pandoravirus tropicalis". NCBI Taxonomy Browser. Archived from the original on 14 December 2022. Retrieved 14 December 2022.
  4. ↑ "'Zombie' virus revived after 50,000 years trapped in Siberian permafrost – National | Globalnews.ca". Global News. Archived from the original on 26 November 2022. Retrieved 26 November 2022.
  5. 1 2 3 4 Philippe N, Legendre M, Doutre G, Couté Y, Poirot O, Lescot M, Arslan D, Seltzer V, Bertaux L, Bruley C, Garin J, Claverie JM, Abergel C (July 2013). "Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes" (PDF). Science. 341 (6143): 281–286. Bibcode:2013Sci...341..281P. doi:10.1126/science.1239181. PMID   23869018. S2CID   16877147. Archived (PDF) from the original on 2 April 2020. Retrieved 5 March 2020.
  6. ↑ Sirucek S (3 March 2014). "Ancient "Giant Virus" Revived From Siberian Permafrost". National Geographic. Archived from the original on 4 March 2014.
  7. ↑ Yong E (3 March 2014). "Giant virus resurrected from 30,000-year-old ice : Nature News & Comment". Nature. doi:10.1038/nature.2014.14801. S2CID   87146458.
  8. ↑ Scheid P, Hauröder B, Michel R (2010). "Investigations of an extraordinary endocytobiont in Acanthamoeba sp.: development and replication". Parasitol Res. 106 (6): 1371–7. doi:10.1007/s00436-010-1811-4. PMID   20393749. S2CID   20548450.
  9. ↑ La Scola B, Audic S, Robert C, Jungang L, de Lamballerie X, Drancourt M, Birtles R, Claverie JM, Raoult D (2003). "A giant virus in amoebae". Science. 299 (5615): 2033. doi:10.1126/science.1081867. PMID   12663918. S2CID   39606235.
  10. ↑ Arslan D, Legendre M, Seltzer V, Abergel C, Claverie JM (2011). "Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae". Proceedings of the National Academy of Sciences. 108 (42): 17486–91. Bibcode:2011PNAS..10817486A. doi: 10.1073/pnas.1110889108 . PMC   3198346 . PMID   21987820.
  11. ↑ Smith B (26 July 2013). "Pandoravirus discovered in La Trobe uni pond". The Age. Archived from the original on 20 August 2013. Retrieved 18 August 2013.
  12. ↑ "Pandoraviruses Are Not Alive". www.virology.ws. 3 December 2020. Archived from the original on 12 September 2021. Retrieved 19 September 2021.
  13. ↑ "Pandoravirus, bigger and unlike anything seen before". www.virology.ws. August 2013. Archived from the original on 18 November 2017. Retrieved 25 November 2017.
  14. ↑ Pereira Andrade AC, Victor de Miranda Boratto P, Rodrigues RA, Bastos TM, Azevedo BL, Dornas FP, Oliveira DB, Drumond BP, Kroon EG, Abrahão JS (March 2019). Sandri-Goldin RM (ed.). "New Isolates of Pandoraviruses: Contribution to the Study of Replication Cycle Steps". Journal of Virology. 93 (5). doi:10.1128/JVI.01942-18. ISSN   0022-538X. PMC   6384056 . PMID   30541841.
  15. ↑ Zhang QY, Ke F, Gui L, Zhao Z (November 2022). "Recent insights into aquatic viruses: Emerging and reemerging pathogens, molecular features, biological effects, and novel investigative approaches". Water Biology and Security. 1 (4): 100062. Bibcode:2022WBSec...100062Z. doi: 10.1016/j.watbs.2022.100062 . ISSN   2772-7351.
  16. 1 2 Dell'Amore C (19 July 2013). "Biggest Virus Yet Found, May Be Fourth Domain of Life?". National Geographic. Archived from the original on 21 July 2013. Retrieved 20 March 2018.
  17. ↑ Berezow AB (16 November 2014). "Simmer Down: Viruses Not 'Fourth Domain' of Life | RealClearScience". realclearscience. Archived from the original on 20 March 2018. Retrieved 20 March 2018.
  18. ↑ "What Is an Amoeba?". Live Science. Archived from the original on 12 October 2017. Retrieved 10 November 2017.
  19. ↑ "Pandoravirus, bigger and unlike anything seen before". www.virology.ws. August 2013. Archived from the original on 18 November 2017. Retrieved 10 November 2017.
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