Alphapithovirus

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Alphapithovirus
Pithovirus sibericum sketch.jpg
Alphapithovirus sibericum
Virus classification OOjs UI icon edit-ltr.svg
(unranked): Virus
Realm: Varidnaviria
Kingdom: Bamfordvirae
Phylum: Nucleocytoviricota
Class: Megaviricetes
Order: Pimascovirales
Family: Pithoviridae
Genus:Alphapithovirus
Species [1]

Alphapithovirus, is a genus of giant virus known from two species, Alphapithovirus sibericum , which infects amoebas, [2] [3] and Alphapithovirus massiliense . [4] 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.

Contents

Description

Alphavirus is one of the two genera in the family Togaviridae, [5] Rubivirus (rubella virus), and the other togavirus genus. [5] Flavivirus is a single-stranded RNA virus transmitted especially by ticks and mosquitoes. [6] Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. [7]

The genus name Alphapithovirus, a reference to large storage containers of ancient Greece known as pithoi, was chosen to describe the new species. A specimen of Alphapithovirus measures approximately 1.5  μm (1500 nm) in length and 0.5 μm (500 nm) in diameter, making it the largest virus yet found. It is 50% larger in size than the Pandoraviridae , the previous largest-known viruses, [8] and is larger than Ostreococcus , the smallest eukaryotic cell, although Pandoravirus has the largest viral genome, containing 1.9 to 2.5 megabases of DNA. [9]

Alphapithovirus has a thick, oval wall with an opening at one end. Internally, its structure resembles a honeycomb. [2]

The genome of Alphapithovirus contains 467 distinct genes, more than a typical virus, but far fewer than the 2556 putative protein-coding sequences found in Pandoravirus . [8] 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 Alphapithovirus genome sequence reveals that it is barely related to that virus, but more closely resembles members of Marseilleviridae , Megaviridae , and Iridoviridae . [10] These families all contain large icosahedral viruses with DNA genomes. The Alphapithovirus genome has 36% GC-content, similar to the Megaviridae, in contrast to greater than 61% for pandoraviruses. [11] The family Orpheoviridae and genus Alphaorpheovirus, the family Pithoviridae and genus Alphapithovirus, and the family Cedratviridae and genus,Alphacedratvirus, has now been ratified by the ICTV. [12]

Replication

The Alphapithovirus 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. [13] The genome encodes all the proteins needed to produce mRNA; these proteins are present in the purified virions. [10] Viral entry is initiated by attachment of virions to cells, leading to internalization, and uncoating to release genetic material for replication and propagation. [7] Alphapithovirus therefore undergoes its entire replication cycle in its host's cytoplasm, rather than the more typical method of taking over the host's nucleus. [2] [10] [14]

Discovery

Alphapithovirus sibericum was discovered in a 30,000-year-old sample of Siberian permafrost by Chantal Abergel and Jean-Michel Claverie of Aix-Marseille University. [2] [15] The virus was discovered buried 30 m (100 ft) below the surface of a late Pleistocene sediment. [3] [10] Called Pithovirus sibericum, it belongs to a class of giant viruses that were discovered 10 years ago. [16] It was found when riverbank samples collected in 2000 were exposed to amoebas. [17] The amoebas started dying and, when examined, were found to contain giant virus specimens. The authors said they got the idea to probe permafrost samples for new viruses after reading about an experiment that revived a similar aged seed of Silene stenophylla two years earlier. [2] The Alphapithovirus findings were published in the Proceedings of the National Academy of Sciences in March 2014. [8] [11]

Although the virus is harmless to humans, its viability after being frozen for millennia has raised concerns that global climate change and tundra drilling operations could lead to previously undiscovered and potentially pathogenic viruses being unearthed. [8] However, other scientists dispute that this scenario poses a real threat. [2]

A modern species in the genus, Alphapithovirus massiliense, was isolated in 2016. The core features such as the order of ORFs and orphan genes (ORFans) are well conserved between the two known species. [4]

Evolution

The rate of mutation of the genome has been estimated to be 2.23 × 10−6 substitutions/site/year. [18] The authors have suggested that the two known Alphapithoviruses diverged around two hundred thousand years ago. The recently identified fish alphaviruses salmon pancreas disease virus and sleeping disease virus appear to be variants or subtypes of a new alphavirus species. [12]

See also

Related Research Articles

<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">Rubella virus</span> Species of virus

Rubella virus (RuV) is the pathogenic agent of the disease rubella, transmitted only between humans via the respiratory route, and is the main cause of congenital rubella syndrome when infection occurs during the first weeks of pregnancy.

<i>Alphavirus</i> Genus of viruses

Alphavirus is a genus of RNA viruses, the sole genus in the Togaviridae family. Alphaviruses belong to group IV of the Baltimore classification of viruses, with a positive-sense, single-stranded RNA genome. There are 32 alphavirus species, which infect various vertebrates such as humans, rodents, fish, birds, and larger mammals such as horses, as well as invertebrates. Alphaviruses that can infect both vertebrates and arthropods are referred dual-host alphaviruses, while insect-specific alphaviruses such as Eilat virus and Yada yada virus are restricted to their competent arthropod vector. Transmission between species and their vertebrate hosts occurs mainly via mosquitoes, making the alphaviruses a member of the collection of arboviruses – or arthropod-borne viruses. Alphavirus particles are enveloped, have a 70 nm diameter, tend to be spherical, and have a 40 nm isometric nucleocapsid.

<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.

<i>Corticovirus</i> Genus of viruses

Corticovirus is a genus of viruses in the family Corticoviridae. Corticoviruses are bacteriophages; that is, their natural hosts are bacteria. The genus contains two species. The name is derived from Latin cortex, corticis. However, prophages closely related to PM2 are abundant in the genomes of aquatic bacteria, suggesting that the ecological importance of corticoviruses might be underestimated. Bacteriophage PM2 was first described in 1968 after isolation from seawater sampled from the coast of Chile.

<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.

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>Marseilleviridae</i> Family of viruses

Marseilleviridae is a family of viruses first named in 2012. The genomes of these viruses are double-stranded DNA. Amoeba are often hosts, but there is evidence that they are found in humans as well. The family contains one genus and four species, two of which are unassigned to a genus. It is a member of the nucleocytoplasmic large DNA viruses clade.

<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>Pandoravirus</i> Genus of giant virus possessing a large double-stranded DNA genome

Pandoravirus is a proposed genus of giant virus, first discovered in 2013. It is the third largest in physical size of any known viral genus, behind Pithovirus and Megaklothovirus. Pandoraviruses have double stranded DNA genomes, with the largest genome size of any known viral genus.

<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.

Mollivirus sibericum is a giant virus discovered in 2015 by French researchers Chantal Abergel and Jean-Michel Claverie in a 30,000-year-old sample of Siberian permafrost, where the team had previously found the unrelated giant virus Alphapithovirus sibericum. Mollivirus sibericum is a spherical DNA virus with a diameter of 500–600 nanometers (0.5–0.6 μm).

<i>Eilat virus</i> Species of virus

Eilat virus (EILV) is a unique Alphavirus which is known mainly for its host range restriction generally to insects by means of RNA replication. The virus is found in the Negev desert. It is incapable of infecting vertebrate cells, differentiating it from other alphaviruses.

<i>Middelburg virus</i> Species of virus

Middelburg virus (MIDV) is an alphavirus of the Old World Group that has likely endemic and zoonotic potential. It is of the viral family Togaviridae. It was isolated from mosquitos in 1957 in South Africa, MDIV antigens have now been found in livestock, horses, and humans.

<span class="mw-page-title-main">Chrysochromulina ericina virus</span> Giant virus

Chrysochromulina ericina virus 01B, or simply Chrysochromulina ericina virus (CeV) is a giant virus in the family Mimiviridae infecting Haptolina ericina, a marine microalgae member of the Haptophyta. CeV is a dsDNA virus.

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.

<span class="mw-page-title-main">Pathogenic microorganisms in frozen environments</span> Pathogens which may re-emerge as ancient ice/permafrost is lost

On Earth, frozen environments such as permafrost and glaciers are known for their ability to preserve items, as they are too cold for ordinary decomposition to take place. This makes them a valuable source of archeological artefacts and prehistoric fossils, yet it also means that there are certain risks once ancient organic matter is finally subject to thaw. The best-studied risk is that of decomposition of such organic matter releasing a substantial quantity of carbon dioxide and methane, and thus acting as a notable climate change feedback. Yet, some scientists have also raised concerns about the possibility that some metabolically dormant bacteria and protists, as well as always metabolically inactive viruses, may both survive the thaw and either threaten humans directly, or affect some of the animal or plant species important for human wellbeing.

References

  1. ↑ "Virus Taxonomy: 2023 Release". International Committee on Taxonomy of Viruses. Retrieved 17 August 2024.
  2. 1 2 3 4 5 6 Yong, Ed (3 March 2014). "Giant virus resurrected from 69,000-year-old ice". Nature. doi:10.1038/nature.2014.14801. S2CID   87146458.
  3. 1 2 Morelle, Rebecca (3 March 2014). "30,000-year-old giant virus 'comes back to life'". BBC News.
  4. 1 2 Levasseur A, Andreani J, Delerce J, Bou Khalil J, Robert C, La Scola B, Raoult D (July 2016). "Comparison of a modern and fossil Pithovirus reveals its genetic conservation and evolution". Genome Biol Evol. 8 (8): 2333–9. doi:10.1093/gbe/evw153. PMC   5010891 . PMID   27389688.
  5. 1 2 Schmaljohn, Alan L.; McClain, David (1996). "Alphaviruses (Togaviridae) and Flaviviruses (Flaviviridae)". Medical Microbiology (4th ed.). University of Texas Medical Branch at Galveston. ISBN   978-0-9631172-1-2. PMID   21413253.
  6. ↑ De Matos, António Pedro Alves; Zé-Zé, Libia; Amaro, Fátima; Alves, Maria João (2021). "Location of virus antigens in murine tissues infected with Zika virus". Zika Virus Biology, Transmission, and Pathology. pp. 431–441. doi:10.1016/B978-0-12-820268-5.00040-7. ISBN   978-0-12-820268-5.
  7. 1 2 Rigou, Sofia; Schmitt, Alain; Alempic, Jean-Marie; Lartigue, Audrey; Vendloczki, Peter; Abergel, Chantal; Claverie, Jean-Michel; Legendre, Matthieu (3 November 2023). "Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses". Molecular Biology and Evolution. 40 (11). doi:10.1093/molbev/msad244.
  8. 1 2 3 4 Sirucek, Stefan (3 March 2014). "Ancient "Giant Virus" Revived From Siberian Permafrost". National Geographic. Archived from the original on 4 March 2014.
  9. ↑ Brumfiel, Geoff (18 July 2013). "World's Biggest Virus May Have Ancient Roots". National Public Radio.
  10. 1 2 3 4 Racaniello, Vincent (4 March 2014). "Pithovirus: Bigger than Pandoravirus with a smaller genome". Virology Blog.
  11. 1 2 Legendre, M.; Bartoli, J.; Shmakova, L.; Jeudy, S.; Labadie, K.; Adrait, A.; Lescot, M.; Poirot, O.; Bertaux, L.; Bruley, C.; Coute, Y.; Rivkina, E.; Abergel, C.; Claverie, J.-M. (March 2014). "Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology". Proc. Natl. Acad. Sci. U.S.A. 111 (11): 4274–9. Bibcode:2014PNAS..111.4274L. doi: 10.1073/pnas.1320670111 . PMC   3964051 . PMID   24591590.
  12. 1 2 Queiroz, Victória F.; Rodrigues, Rodrigo A. L.; Abrahão, Jônatas Santos (June 2024). "A taxonomic proposal for cedratviruses, orpheoviruses, and pithoviruses". Archives of Virology. 169 (6): 132. doi: 10.1007/s00705-024-06055-x . PMID   38822903.
  13. ↑ "Pithovirus sibericum". Swiss Institute of Bioinformatics (SIB). Retrieved 10 March 2014.
  14. ↑ Coghlan, Andy (3 March 2014). "Biggest-ever virus revived from Stone Age permafrost". NewScientist. Archived from the original on 5 March 2014.
  15. ↑ Pappas, Stephanie (16 September 2015). "Frozen Giant Virus Still Infectious After 30,000 Years". Yahoo News. Retrieved 20 September 2015.
  16. ↑ "30,000-year-old giant virus 'comes back to life'". BBC News. 4 March 2014. Retrieved 27 September 2024.
  17. ↑ Zimmer, Carl (3 March 2014). "Out of Siberian Ice, a Virus Revived". The New York Times.
  18. ↑ Duchêne, S; Holmes, EC (2018). "Estimating evolutionary rates in giant viruses using ancient genomes". Virus Evol. 4 (1): vey006. doi: 10.1093/ve/vey006 . PMC   5829572 . PMID   29511572.
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