| Alphapithovirus | |
|---|---|
 | |
| Alphapithovirus sibericum | |
Virus classification | |
| (unranked): | Virus |
| Realm: | Varidnaviria |
| Kingdom: | Bamfordvirae |
| Phylum: | Nucleocytoviricota |
| Class: | Megaviricetes |
| Order: | Pimascovirales |
| Family: | Pithoviridae |
| Subfamily: | Orthopithovirinae |
| Genus: | Alphapithovirus |
| Species[1] | |
Alphapithovirus, also known asPithovirus sibericum, is a genus ofgiant virus known from two species,Alphapithovirus sibericum, which infectsamoebae,[2][3] andAlphapithovirus massiliense.[4] It isDNA-based and is a member of thenucleocytoplasmic large DNA virusesclade. It was discovered in 2014, when a viable specimen was found in a 30,000-year-oldice core harvested frompermafrost inSiberia, Russia. It is the third-largest known giant virus, behind onlyMegaklothovirus horridgei andKlothovirus casanovai.
The genus nameAlphapithovirus, a reference to large storage containers of ancient Greece known aspithoi, was chosen to describe the new species. A specimen ofAlphapithovirus measures approximately 1.5 μm (1,500nm) in length and 0.5 μm (500 nm) in diameter, making it one of the largest viruses yet found, behind onlyMegaklothovirus andKlothovirus in size.[5] At the time of its discovery in 2014, thePithovirus was the largest known virus by diameter. It is 50% larger in size than thePandoraviridae, the previous largest-known viruses,[6] and is larger thanOstreococcus, the smallest eukaryotic cell, althoughPandoravirus has the largest viral genome, containing 1.9 to 2.5megabases ofDNA.[7]
Alphapithovirus has a thick, oval wall, with an opening at one end. Internally, its structure resembles ahoneycomb.[2]
Thegenome ofAlphapithovirus contains 467 distinctgenes, more than a typical virus, but far fewer than the 2556 putative protein-coding sequences found inPandoravirus.[6] Thus, its genome is far less densely packed than any other known virus. Two-thirds of itsproteins are unlike those of other viruses. Despite the physical similarity withPandoravirus, theAlphapithovirus genome sequence reveals that it is barely related to that virus, but more closely resembles members ofMarseilleviridae,Megaviridae, andIridoviridae.[8] These families all contain largeicosahedral viruses with DNA genomes. TheAlphapithovirus genome has 36%GC-content, similar to theMegaviridae, in contrast to greater than 61% for pandoraviruses.[9] The familyOrpheoviridae and genusAlphaorpheovirus, the familyPithoviridae and genusAlphapithovirus, and the familyCedratviridae and genus,Alphacedratvirus, has now been ratified by the ICTV.[10]
TheAlphapithovirusgenome is one circular, double-stranded DNA (dsDNA) chromosome of about 610,000base pairs (bp), encoding approximately 467open reading frames (ORFs), which translate into 467 different proteins.[11] The genome encodes all the proteins needed to producemRNA; these proteins are present in the purified virions.[8] Viral entry is initiated by attachment of virions to cells, leading to internalization, and uncoating to release genetic material for replication and propagation.[12]Alphapithovirus therefore undergoes its entire replication cycle in its host'scytoplasm, rather than the more typical method of taking over the host's nucleus.[2][8][13]
Alphapithovirus sibericum was discovered in a 30,000-year-old sample ofSiberianpermafrost by Chantal Abergel and Jean-Michel Claverie ofAix-Marseille University.[2][14] The virus was discovered buried 30 m (100 ft) below the surface of a latePleistocene sediment.[3][8] CalledPithovirus sibericum, it belongs to a class of giant viruses that were discovered 10 years ago.[15] It was found when riverbank samples collected in 2000 were exposed toamoebas.[16] 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 ofSilene stenophylla two years earlier.[2] TheAlphapithovirus findings were published in theProceedings of the National Academy of Sciences in March 2014.[6][9]
Although the virus is harmless to humans, its viability after being frozen for millennia has raised concerns that globalclimate change andtundra drilling operations could lead to previously undiscovered and potentially pathogenic viruses being unearthed.[6] 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 andorphan genes (ORFans) are well conserved between the two known species.[4]
Therate of mutation of the genome has been estimated to be 2.23 × 10−6 substitutions/site/year.[17] 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.[10]
