Pithovirus

' Pithovirus sibericum'
Sketch of Pithovirus sibericum
Systematics
Classification : Viruses Area : Varidnaviria Empire : Bamfordvirae Phylum : Nucleocytoviricota Class : Megaviricetes Order : Pimascovirales Family : " Pithoviridae " Genre : "Pithovirus"
Taxonomic characteristics
Genome : dsDNA Baltimore : Group 1 Symmetry : amphora-shaped
Scientific name
'Pithovirus'
Left
NCBI  Taxonomy: 1450746 NCBI  Reference: NC_023423.1 ViralZone ( ExPASy , SIB): 4237

" Pithovirus " (from Greek  πίθος píthos : storage vessel, see also the - not entirely correct translation - Pandora 's box ) is a genus within its own (as of April 2020) not yet officially recognized by the International Committee on Taxonomy of Viruses (ICTV) proposed family " Pithoviridae " of giant viruses of the phylum Negarnaviricota (outdated Nucleocytoplasmic large DNA viruses , NCLDV). The naming of the order Pimascovirales (outdated: PMI group or MAPI super clade ) - the 'P' always stands for 'Pitho-' - has however indicated to the ICTV that, according to the general opinion, the pithoviruses are classified as this group (order) correspondingly looks.

discovery

The first species “ Pithovirus sibericum ” of the genus was isolated in 2014 from Siberian permafrost soil that is more than 30,000 years old . To date, it is the oldest DNA virus that infects eukaryotes that could be brought back to an infection. This suggests that further infectious viruses or microorganisms could be released from the thawing permafrost ground due to global warming . In order to look for viruses that were still infectious in the soil, a sterile sample was taken from late Pleistocene sediments of the Kolyma lowlands and incubated with a culture of Acanthamoeba castellanii as a possible host for viruses. After propagation in Acanthamoeba , the virus particles were purified and analyzed by means of transmission electron microscopy and genome sequencing .

In 2016 Levasseur and colleagues isolated another species in this genus, “ P. massiliensis ”.

properties

construction

" P. sibericum " can already be seen under the light microscope as egg-shaped particles. These have a length of about 1.5  µm and a width of about 500  nm . An approximately 60 nm thick virus envelope with parallel, upright stripes can be seen under an electron microscope . The opening at the tip of the virus envelope is closed by an approximately 160 nm wide and 80 nm thick structure made of 15 nm wide rods which, when viewed from above, has a hexagonal grid pattern and appears to be connected to a rolled membrane inside. Inside the virus envelope is a membrane-enclosed compartment that has no internal structures except for an electron-dense sphere with an occasional 50 nm diameter and a tubular structure along the longitudinal axis of the virus.

" P. sibericum ", distinguishing it from the outside like pandoravirus through the cork-like structure at the sheath tip and the much smaller, AT-rich genome with fewer genes.

Genome

The genome consists of double-stranded DNA , which could exist as a closed ring or as a linear molecule with redundant ends. The 610,033 base pairs have a GC content of 36% and code for 467 proteins .

Life cycle

The life cycle of " P. sibericum " is known from cultures with Acanthamoeba and begins with the phagocytosis of the virus particles by the host. After the loss of the cork-like structure, the viral membrane fuses with the vacuole membrane of the host, so that a channel-like connection between the viral compartment and the host's cytoplasm is formed. Four to six hours after infection, a clear zone becomes visible in the host cytoplasm in which numerous vesicles collect. The virus envelope and the inner compartment are formed together, whereby rectangular, closed particles, already with the characteristic cork-like structure, are formed, the outer wall of which later thickens and which then assume their egg-shaped shape. The striped, outermost layer is built up at the end and in individual pieces. In the end, the host cell is dissolved and hundreds of virus particles (virions) are released.

Systematics

Internal system

The following list only includes the suggestions for related virus species mentioned above. Neither the genus as such nor individual species have been officially recognized by the ICTV so far (as of April 2019):

• Family " Pithoviridae "

• Genus " Pithovirus "

• Species " P. massiliensis " (syn. Pithovirus massiliensis LC8 , Pithovirus sp. LC8 )
• Species " P. sibericum " ("PiVs")
• Species " P. lacustris " ("KC5 / 2")

External system

In the meantime, other viruses have been found that apparently belong to the genus " Pithovirus " (even if they were not officially recorded by the ICTV as of November 2018):

• Genus " Cedratvirus " (with species " Cedratvirus A11 ")
• Genus " Orpheovirus " (with species " Orpheovirus IHUMI-LCC2 ")
• Species " Solivirus " and
• Species " Solum Virus ". are proposed species from a metagenomic analysis of forest soil samples by F. Schulz and colleagues 2018.
• Species " Sissivirus S55 "
• Species " Misannotadedvirus "
• From Metagenomanalysen from black smokers Loki's Castle ( English Loki's castle (: LCVs) Other representatives come Loki's Castle Viruses, Pitho-like ), some of which are grouped into clades. There are the following four clades: Clade 1: LCPAC101, LCPAC102, LCPAC103; Clade 2: LCPAC104, LCPAC201, LCPAC102; Clade 3: LCPAC302, LCPAC304; Clade 4: LCPAC401, LCPAC403, LCPAC404, LCPAC406; as well as LCPAC001, LCDPAC01 and LCDPAC02 for themselves.

For the family of " Pithoviridae " extended by these finds , Schulz et al. the following system within the NCLDV:

" Pithovirus-like viruses " ( " Pithoviridae " sl )	-? " Orpheoviridae "  " Solum virus "     " Orpheovirus "  " Pithoviridae " ss  " Pithovirus "     " Cedratvirus "     " Solivirus "

This is in accordance with the system used by CNRS (2018) and Rolland et al. (2019) Fig. 2a. - Fig. 2b shows a slightly different picture there:

" Pithovirus-like viruses " ( " Pithoviridae " sl )	? " Orpheoviridae "  " Sissivirus S55 "     " Orpheovirus "  " Pithoviridae " ss  " Pithovirus "     " Cedratvirus "     " Solivirus "     " Misannotadedvirus "     " Solumnvirus "

It no longer says “ Solivirus ”, but “ Solumnvirus ” as a baseline , which shows that in 2019 no stable statement could be made.

Similar to Mimivirus , " Misannotadedvirus " was initially mistaken for a bacterium ( related to Rickettsiales ) because of its size , from which the current proposed name is derived.

Some authors also count orpheovirus and relatives to the Pithoviridae , i. H. interpret this family in a broader sense identically to the pithovirus-like viruses in the above cladogram.

For the phylogenetic position, see Disa Bäckström et al. (2019), Fig. 3.

literature

• Matthieu Legendre, Julia Bartoli, Lyubov Shmakova, Sandra Jeudy, Karine Labadie, Annie Adrait, Magali Lescot, Olivier Poirot, Lionel Bertaux, Christophe Bruley, Yohann Couté, Elizaveta Rivkina, Chantal Abergel, Jean-Michel Claveri: Thirty-thousand-year- old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology . In: PNAS . tape 111 , no. 11 , 2014, p. 4274-4279 , doi : 10.1073 / pnas.1320670111 (free full text).

Web links

• Julia Merlot: Siberia: 30,000 years of frozen virus brought to life ( Spiegel Online )

Individual evidence

1. ↑ ^{a b c d e} ICTV: ICTV Master Species List 2019.v1 , New MSL including all taxa updates since the 2018b release, March 2020 (MSL # 35)
2. ↑ Eugene V. Koonin, Natalya Yutin: Evolution of the Large Nucleocytoplasmatic DNA Viruses of Eukaryotes and Convergent Origins of Viral Gigantism , in: Advances in Virus Research, Volume 103, AP January 21, 2019, doi: 10.1016 / bs.aivir.2018.09 .002 , pp. 167-202.
3. ↑ ^{a b c} Julien Guglielmini, Anthony C. Woo, Mart Krupovic, Patrick Forterre, Morgan Gaia: Diversification of giant and large eukaryotic dsDNnA viruses predated the origin of modern eukaryotes , in: PNAS 116 (39), 10./24. September 2019, pp. 19585-19592, doi: 10.1073 / pnas.1912006116 , PMID 31506349 , Fig. 2
4. ^ ^{A b} Anthony Levasseur, Julien Andreani, Jeremy Delerce, Jacques Bou Khalil, Catherine Robert, Bernard La Scola, Didier Raoult: Comparison of a Modern and Fossil Pithovirus Reveals Its Genetic Conservation and Evolution . In: Genome Biology and Evolution . tape 8 , no. 8 , July 2016, ISSN  1759-6653 , p. 2333-2339 , doi : 10.1093 / gbe / evw153 , PMID 27389688 , PMC 5010891 (free full text).
5. ↑ David M. Needham, Alexandra Z. Worden et al .: A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators , in: PNAS, 23 September 2019, doi: 10.1073 / pnas.1907517116 , ISSN 0027-8424 , here: Supplement 1 (xlsx)
6. ↑ ^{a b c d e f} Julien Andreani, Jacques YB Khalil, Emeline Baptiste, Issam Hasni, Caroline Michelle, Didier Raoult, Anthony Levasseur, Bernard La Scola: Orpheovirus IHUMI-LCC2: A New Virus among the Giant Viruses . In: Frontiers in Microbiology . tape 8 , January 22, 2018, ISSN  1664-302X , doi : 10.3389 / fmicb.2017.02643 .
7. ↑ NCBI: Pithovirus sp. LC8 (species)
8. ↑ ^{a b c d} Julien Andreani, Jonathan Verneau, Didier Raoult, Anthony Levasseurn Bernard La Scola: Deciphering viral presences: two novel partial giant viruses detected in marine metagenome and in a mine drainage metagenome , in: Virology Journal, Volume 15, No. 66, April 10, 2018, doi: 10.1186 / s12985-018-0976-9
9. ↑ NCBI: Pithovirus sibericum (species)
10. ↑ NCBI: Pithovirus lacustris (species)
11. ↑ Julien Andreani, Sarah Aherfi, Jacques Yaacoub Bou Khalil, Fabrizio Di Pinto, Idir Bitam, Didier Raoult, Philippe Colson, Bernard La Scola: Cedratvirus, a Double-Cork Structured Giant Virus, is a Distant Relative of Pithoviruses . In: Viruses / Molecular Diversity Preservation International . tape 8 , no. November 11 , 2016, ISSN  1999-4915 , p. 300 , doi : 10.3390 / v8110300 , PMID 27827884 , PMC 5127014 (free full text).
12. ↑ NCBI: Solivirus (species)
13. ↑ ^{a b c d e} Clara Rolland, Julien Andreani, Amina Cherif Louazani, Sarah Aherfi, Rania Francis, Rodrigo Rodrigues, Ludmila Santos Silva, Dehia Sahmi, Said Mougari, Nisrine Chelkha, Meriem Bekliz, Lorena Silva, Felipe Assis, Fábio Dornas, Jacques Yaacoub Bou Khalil, Isabelle Pagnier, Christelle Desnues, Anthony Levasseur, Philippe Colson, Jônatas Abrahão, Bernard La Scola: Discovery and Further Studies on Giant Viruses at the IHU Mediterranee Infection That Modified the Perception of the Virosphere , in: Viruses 11 (4 ), March / April 2019, pii: E312, doi: 10.3390 / v11040312 , PMC 6520786 (free full text), PMID 30935049 , Fig. 2a and b.
14. ↑ NCBI: Solum virus (species)
15. ↑ ^{a b} Frederik Schulz, Lauren Alteio, Danielle Goudeau, Elizabeth M. Ryan, Feiqiao B. Yu, Rex R. Malmstrom, Jeffrey Blanchard, Tanja Woyke: Hidden diversity of soil giant viruses . In: Nature Communications . tape 9 , no. 1 , 2018, ISSN  2041-1723 , Article 4881, Note 38 , doi : 10.1038 / s41467-018-07335-2 ( nature.com ).
16. ↑ ^{a b} Disa Bäckström, Natalya Yutin, Steffen L. Jørgensen, Jennah Dharamshi, Felix Homa, Katarzyna Zaremba-Niedwiedzka, Anja Spang, Yuri I. Wolf, Eugene V. Koonin, Thijs J. G. Ettema; Richard P. Novick (Ed.): Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism , in: mBio Volume 10, No. 2, March 5, 2019, doi: 10.1128 / mBio.02497- 18 , PMID 30837339
17. ^ ^{A b} Eugene V. Koonin, Natalya Yutin: Multiple evolutionary origins of giant viruses , in: F1000 Research, November 22, 2018, doi: 10.12688 / f1000research.16248.1 , version 1
18. ↑ Center national de la recherche scientifique: List of the main “giant” viruses known as of today , Université Aix Marseille, April 18, 2018
19. ↑ NCBI: Pithoviridae (family)