''Alphapithovirus'', is a genus of

giant virus 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''. Description While the exact criteria as defined in the sc ...

known from two species, '' Alphapithovirus sibericum'', which infects amoebas, and '' Alphapithovirus massiliense''. It is

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

-based and is a member of the

nucleocytoplasmic large DNA viruses ''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 - for virus phylum. These viruses are refe ...

clade In biology, a clade (), also known as a Monophyly, monophyletic group or natural group, is a group of organisms that is composed of a common ancestor and all of its descendants. Clades are the fundamental unit of cladistics, a modern approach t ...

. It was discovered in 2014, when a viable specimen was found in a 30,000-year-old

ice core An ice core is a core sample that is typically removed from an ice sheet or a high mountain glacier A glacier (; or ) is a persistent body of dense ice, a form of rock, that is constantly moving downhill under its own weight. A glacier ...

harvested from

permafrost Permafrost () is soil or underwater sediment which continuously remains below for two years or more; the oldest permafrost has been continuously frozen for around 700,000 years. Whilst the shallowest permafrost has a vertical extent of below ...

Siberia Siberia ( ; , ) is an extensive geographical region comprising all of North Asia, from the Ural Mountains in the west to the Pacific Ocean in the east. It has formed a part of the sovereign territory of Russia and its predecessor states ...

, Russia.

Description

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 one of the largest viruses yet found, second to Megaklothovirus. It is 50% larger in size than the '' Pandoraviridae'', the previous largest-known viruses, and is larger than '' Ostreococcus'', the smallest eukaryotic cell, although ''Pandoravirus'' has the largest viral genome, containing 1.9 to 2.5 megabases of

. ''Alphapithovirus'' has a thick, oval wall with an opening at one end. Internally, its structure resembles a

honeycomb A honeycomb is a mass of Triangular prismatic honeycomb#Hexagonal prismatic honeycomb, hexagonal prismatic cells built from beeswax by honey bees in their beehive, nests to contain their brood (eggs, larvae, and pupae) and stores of honey and pol ...

. The

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

of ''Alphapithovirus'' contains 467 distinct

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

s, more than a typical virus, but far fewer than the 2556 putative protein-coding sequences found in '' Pandoravirus''. Thus, its genome is far less densely packed than any other known virus. Two-thirds of its

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

s 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 ''Iridoviridae'' is a family of viruses with double-stranded DNA genomes. Amphibians, fish, and invertebrates such as arthropods serve as natural hosts. There are currently 22 species in this family, divided among two subfamilies and seven genera ...

''. These families all contain large icosahedral viruses with DNA genomes. The ''Alphapithovirus'' genome has 36%

GC-content In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases in a DNA or RNA molecule that are either guanine (G) or cytosine (C). This measure indicates the proportion of G and C bases out of ...

, similar to the ''Megaviridae'', in contrast to greater than 61% for pandoraviruses. 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.

Replication

The ''Alphapithovirus''

is one circular, double-stranded DNA ( dsDNA) chromosome of about 610,000

base pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...

s (bp), encoding approximately 467

open reading frame In molecular biology, reading frames are defined as spans of DNA sequence between the start and stop codons. Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible reading frames ...

s (ORFs), which translate into 467 different proteins. The genome encodes all the proteins needed to produce

mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA is ...

; these proteins are present in the purified virions. Viral entry is initiated by attachment of virions to cells, leading to internalization, and uncoating to release genetic material for replication and propagation.''Alphapithovirus'' therefore undergoes its entire replication cycle in its host's

cytoplasm The cytoplasm describes all the material within a eukaryotic or prokaryotic cell, enclosed by the cell membrane, including the organelles and excluding the nucleus in eukaryotic cells. The material inside the nucleus of a eukaryotic cell a ...

, rather than the more typical method of taking over the host's nucleus.

Discovery

''Alphapithovirus sibericum'' was discovered in a 30,000-year-old sample of

by Chantal Abergel and Jean-Michel Claverie of Aix-Marseille University. The virus was discovered buried below the surface of a late

Pleistocene The Pleistocene ( ; referred to colloquially as the ''ice age, Ice Age'') is the geological epoch (geology), epoch that lasted from to 11,700 years ago, spanning the Earth's most recent period of repeated glaciations. Before a change was fin ...

sediment. Called ''Pithovirus sibericum'', it belongs to a class of giant viruses that were discovered 10 years ago. It was found when riverbank samples collected in 2000 were exposed to amoebas. 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. The ''Alphapithovirus'' findings were published in the ''

Proceedings of the National Academy of Sciences ''Proceedings of the National Academy of Sciences of the United States of America'' (often abbreviated ''PNAS'' or ''PNAS USA'') is a peer-reviewed multidisciplinary scientific journal. It is the official journal of the National Academy of Scie ...

'' in March 2014. Although the virus is harmless to humans, its viability after being frozen for millennia has raised concerns that global

climate change Present-day climate change includes both global warming—the ongoing increase in Global surface temperature, global average temperature—and its wider effects on Earth's climate system. Climate variability and change, Climate change in ...

and

tundra In physical geography, a tundra () is a type of biome where tree growth is hindered by frigid temperatures and short growing seasons. There are three regions and associated types of tundra: #Arctic, Arctic, Alpine tundra, Alpine, and #Antarctic ...

drilling operations could lead to previously undiscovered and potentially pathogenic viruses being unearthed. However, other scientists dispute that this scenario poses a real threat. 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.

Evolution

The rate of mutation of the genome has been estimated to be 2.23 × 10⁻⁶ substitutions/site/year. 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.

References

External links