An endogenous viral element (EVE) is a DNA sequence derived from a

virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsk ...

, and present within the

germline In biology and genetics, the germline is the population of a multicellular organism's cells that pass on their genetic material to the progeny (offspring). In other words, they are the cells that form the egg, sperm and the fertilised egg. They ...

of a non-viral organism. EVEs may be entire viral genomes (

provirus A provirus is a virus genome that is integrated into the DNA of a host cell. In the case of bacterial viruses (bacteriophages), proviruses are often referred to as prophages. However, proviruses are distinctly different from prophages and these te ...

es), or fragments of viral genomes. They arise when a viral DNA sequence becomes integrated into the

genome In the fields of molecular biology and genetics, 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 ...

of a

germ cell Germ or germs may refer to: Science * Germ (microorganism), an informal word for a pathogen * Germ cell, cell that gives rise to the gametes of an organism that reproduces sexually * Germ layer, a primary layer of cells that forms during embr ...

that goes on to produce a viable organism. The newly established EVE can be inherited from one generation to the next as an

allele An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution. ::"The chrom ...

in the host species, and may even reach fixation.

Endogenous retrovirus Endogenous retroviruses (ERVs) are endogenous viral elements in the genome that closely resemble and can be derived from retroviruses. They are abundant in the genomes of jawed vertebrates, and they comprise up to 5–8% of the human genome ( ...

es and other EVEs that occur as proviruses can potentially remain capable of producing

infectious An infection is the invasion of tissues by pathogens, their multiplication, and the reaction of host tissues to the infectious agent and the toxins they produce. An infectious disease, also known as a transmissible disease or communicable dis ...

virus in their endogenous state. Replication of such 'active' endogenous viruses can lead to the proliferation of viral insertions in the germline. For most non-retroviral viruses, germline integration appears to be a rare, anomalous event, and the resulting EVEs are often only fragments of the parent virus genome. Such fragments are usually not capable of producing infectious virus, but may express

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...

or RNA and even

cell surface receptors Cell surface receptors (membrane receptors, transmembrane receptors) are receptors that are embedded in the plasma membrane of cells. They act in cell signaling by receiving (binding to) extracellular molecules. They are specialized integral m ...

Diversity and distribution

EVEs have been identified in

animal Animals are multicellular, eukaryotic organisms in the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, and go through an ontogenetic stage ...

plant Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae excl ...

s and

fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately fr ...

. In

vertebrate Vertebrates () comprise all animal taxa within the subphylum Vertebrata () ( chordates with backbones), including all mammals, birds, reptiles, amphibians, and fish. Vertebrates represent the overwhelming majority of the phylum Chordata, with ...

s EVEs derived from

retrovirus A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptas ...

es (

endogenous retrovirus Endogenous retroviruses (ERVs) are endogenous viral elements in the genome that closely resemble and can be derived from retroviruses. They are abundant in the genomes of jawed vertebrates, and they comprise up to 5–8% of the human genome ( ...

es) are relatively common. Because retroviruses integrate into the

nuclear genome Nuclear DNA (nDNA), or nuclear deoxyribonucleic acid, is the DNA contained within each cell nucleus of a eukaryotic organism. It encodes for the majority of the genome in eukaryotes, with mitochondrial DNA and plastid DNA coding for the rest. I ...

of the host cell as an inherent part of their replication cycle, they are predisposed to enter the host germline. In addition, EVEs related to

parvoviruses Parvoviruses are a family of animal viruses that constitute the family ''Parvoviridae''. They have linear, single-stranded DNA (ssDNA) genomes that typically contain two genes encoding for a replication initiator protein, called NS1, and the pr ...

filoviruses ''Filoviridae'' () is a family of single-stranded negative-sense RNA viruses in the order '' Mononegavirales''. Two members of the family that are commonly known are Ebola virus and Marburg virus. Both viruses, and some of their lesser known ...

, bornaviruses and circoviruses have been identified in vertebrate genomes. In plant genomes, EVEs derived from pararetroviruses are relatively common. EVEs derived from other, non-retrotranscribing virus families, such as ''

Geminiviridae ''Geminiviridae'' is a family of plant viruses that encode their genetic information on a circular genome of single-stranded (ss) DNA. There are 520 species in this family, assigned to 14 genera. Diseases associated with this family include: b ...

'', have also been identified in plants. Moreover, EVEs related to giant viruses (aka GEVEs) of

phylum In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below kingdom and above class. Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature ...

'' Nucleocytoviricota'' (NCLDV) similar to '' Aureococcus anophagefferens virus'' (AaV) have been found in 2019/2020.

Identification

EVEs are traditionally identified by similarity to known viruses. In 2021, it has been demonstrated that the

k-mer In bioinformatics, ''k''-mers are substrings of length k contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which ''k''-mers are composed of nucleotides (''i.e''. A, T, G ...

composition of endogenous RNA virus resemble that of their exogenous counterparts. As a result, it is now possible to identify novel groups of endogenous RNA viruses whose exogenous relatives have become extinct.

Use in paleovirology

EVEs are a rare source of retrospective information about ancient viruses. Many are derived from germline integration events that occurred millions of years ago, and can be viewed as viral

fossil A fossil (from Classical Latin , ) is any preserved remains, impression, or trace of any once-living thing from a past geological age. Examples include bones, shells, exoskeletons, stone imprints of animals or microbes, objects preserved ...

s. Such ancient EVEs are an important component of paleovirological studies that address the long-term

evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...

of viruses. Identification of orthologous EVE insertions enables the calibration of long-term evolutionary timelines for viruses, based on the estimated time since

divergence In vector calculus, divergence is a vector operator that operates on a vector field, producing a scalar field giving the quantity of the vector field's source at each point. More technically, the divergence represents the volume density of ...

of the ortholog-containing host species groups. This approach has provided minimum ages ranging from 30 to 93 million years for the '' Parvoviridae'', '' Filoviridae'', ''Bornaviridae'' and ''

Circoviridae ''Circoviridae'' is a family of DNA viruses. Birds and mammals serve as natural hosts. There are 101 species in this family, assigned to 2 genera. Diseases associated with this family include: PCV-2: postweaning multisystemic wasting syndrome; ...

'' families of viruses, >100 million years in the ''

Flaviviridae ''Flaviviridae'' is a family of enveloped positive-strand RNA viruses which mainly infect mammals and birds. They are primarily spread through arthropod vectors (mainly ticks and mosquitoes). The family gets its name from the yellow fever viru ...

'', and 12 million years for the

Lentivirus ''Lentivirus'' is a genus of retroviruses that cause chronic and deadly diseases characterized by long incubation periods, in humans and other mammalian species. The genus includes the human immunodeficiency virus (HIV), which causes AIDS. L ...

genus of the ''Retroviridae'' family. EVEs also facilitate the use of

molecular clock The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleo ...

-based approaches to obtain calibrations of viral evolution in

deep time Deep time is a term introduced and applied by John McPhee to the concept of geologic time in his book ''Basin and Range'' (1981), parts of which originally appeared in the '' New Yorker'' magazine. The philosophical concept of geological time ...

Co-option and exaptation by host species

EVEs can sometimes provide a selective advantage to the individuals in which they are inserted. For example, some protect against infection with related viruses. In some mammal groups, including higher primates, retroviral

envelope An envelope is a common packaging item, usually made of thin, flat material. It is designed to contain a flat object, such as a letter or card. Traditional envelopes are made from sheets of paper cut to one of three shapes: a rhombus, a ...

proteins have been exapted to produce a protein that is expressed in the

placenta The placenta is a temporary embryonic and later fetal organ that begins developing from the blastocyst shortly after implantation. It plays critical roles in facilitating nutrient, gas and waste exchange between the physically separate mate ...

syncytiotrophoblast Syncytiotrophoblast (from the Greek 'syn'- "together"; 'cytio'- "of cells"; 'tropho'- "nutrition"; 'blast'- "bud") is the epithelial covering of the highly vascular embryonic placental villi, which invades the wall of the uterus to establish nu ...

, and is involved in fusion of the

cytotrophoblast "Cytotrophoblast" is the name given to both the inner layer of the trophoblast (also called layer of Langhans) or the cells that live there. It is interior to the syncytiotrophoblast and external to the wall of the blastocyst in a developing embr ...

cells to form the syncytial layer of the placenta. In humans this protein is called

syncytin Syncytin-1 also known as enverin is a protein found in humans and other primates that is encoded by the ERVW-1 gene ( endogenous retrovirus group W envelope member 1). Syncytin-1 is a cell-cell fusion protein whose function is best characterized ...

, and is encoded by an

called ( ERVWE1) on chromosome seven. Remarkably, the capture of syncytin or syncytin-like genes has occurred independently, from different groups of endogenous retroviruses, in diverse mammalian lineages. Distinct, syncytin-like genes have been identified in

primates Primates are a diverse order of mammals. They are divided into the strepsirrhines, which include the lemurs, galagos, and lorisids, and the haplorhines, which include the tarsiers and the simians ( monkeys and apes, the latter including ...

rodent Rodents (from Latin , 'to gnaw') are mammals of the order Rodentia (), which are characterized by a single pair of continuously growing incisors in each of the upper and lower jaws. About 40% of all mammal species are rodents. They are n ...

lagomorph The lagomorphs are the members of the taxonomic order Lagomorpha, of which there are two living families: the Leporidae (hares and rabbits) and the Ochotonidae (pikas). The name of the order is derived from the Ancient Greek ''lagos'' (λαγ� ...

carnivore A carnivore , or meat-eater (Latin, ''caro'', genitive ''carnis'', meaning meat or "flesh" and ''vorare'' meaning "to devour"), is an animal or plant whose food and energy requirements derive from animal tissues (mainly muscle, fat and other s ...

s, and

ungulates Ungulates ( ) are members of the diverse clade Ungulata which primarily consists of large mammals with hooves. These include odd-toed ungulates such as horses, rhinoceroses, and tapirs; and even-toed ungulates such as cattle, pigs, giraffes, ca ...

, with integration dates ranging from 10 to 85 million years ago.

References

{{Organisms et al. Virology

Diversity and distribution

Identification

Use in paleovirology

Co-option and exaptation by host species

See also

References