Paleovirology

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Paleovirology is the study of viruses that existed in the past but are now extinct. In general, viruses cannot leave behind physical fossils, [1] therefore indirect evidence is used to reconstruct the past. For example, viruses can cause evolution of their hosts, and the signatures of that evolution can be found and interpreted in the present day. [2] Also, some viral genetic fragments which were integrated into germline cells of an ancient organism have been passed down to our time as viral fossils, [2] or endogenous viral elements (EVEs). [3] EVEs that originate from the integration of retroviruses are known as endogenous retroviruses, or ERVs, [4] and most viral fossils are ERVs. They may preserve genetic code from millions of years ago, hence the "fossil" terminology, although no one has detected a virus in mineral fossils. [2] The most surprising viral fossils originate from non-retroviral DNA and RNA viruses.

Contents

Terminology

Although there is no formal classification system for EVEs, they are categorised according to the taxonomy of their viral origin. Indeed, all known viral genome types and replication strategies, as defined by the Baltimore classification, have been found in the genomic fossil record. [5] [6] Acronyms have been designated to describe different types of viral fossil.

Other viral fossils originate from DNA viruses such as hepadnaviruses (a group that includes hepatitis B). [10]

Resurrection

Successful attempts to "resurrect" extinct viruses from the DNA fossils have been reported. [11] In addition, Pithovirus sibericum was revived from a 30,000-year-old ice core harvested from permafrost in Siberia, Russia. [12] [13]

See also

Related Research Articles

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 terms should not be used interchangeably. Unlike prophages, proviruses do not excise themselves from the host genome when the host cell is stressed.

<span class="mw-page-title-main">Retrovirus</span> Family of viruses

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. After invading a host cell's cytoplasm, the virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome, the reverse of the usual pattern, thus retro (backwards). The new DNA is then incorporated into the host cell genome by an integrase enzyme, at which point the retroviral DNA is referred to as a provirus. The host cell then treats the viral DNA as part of its own genome, transcribing and translating the viral genes along with the cell's own genes, producing the proteins required to assemble new copies of the virus. Many retroviruses cause serious diseases in humans, other mammals, and birds.

<span class="mw-page-title-main">Reverse transcriptase</span> Enzyme which generates DNA

A reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genomes, by retrotransposon mobile genetic elements to proliferate within the host genome, and by eukaryotic cells to extend the telomeres at the ends of their linear chromosomes. Contrary to a widely held belief, the process does not violate the flows of genetic information as described by the classical central dogma, as transfers of information from RNA to DNA are explicitly held possible.

<i>Mononegavirales</i> Order of viruses

Mononegavirales is an order of negative-strand RNA viruses which have nonsegmented genomes. Some members that cause human disease in this order include Ebola virus, human respiratory syncytial virus, measles virus, mumps virus, Nipah virus, and rabies virus. Important pathogens of nonhuman animals and plants are also in the group. The order includes eleven virus families: Artoviridae, Bornaviridae, Filoviridae, Lispiviridae, Mymonaviridae, Nyamiviridae, Paramyxoviridae, Pneumoviridae, Rhabdoviridae, Sunviridae, and Xinmoviridae.

Mouse mammary tumor virus (MMTV) is a milk-transmitted retrovirus like the HTL viruses, HI viruses, and BLV. It belongs to the genus Betaretrovirus. MMTV was formerly known as Bittner virus, and previously the "milk factor", referring to the extra-chromosomal vertical transmission of murine breast cancer by adoptive nursing, demonstrated in 1936, by John Joseph Bittner while working at the Jackson Laboratory in Bar Harbor, Maine. Bittner established the theory that a cancerous agent, or "milk factor", could be transmitted by cancerous mothers to young mice from a virus in their mother's milk. The majority of mammary tumors in mice are caused by mouse mammary tumor virus.

<i>Gammaretrovirus</i> Genus of viruses

Gammaretrovirus is a genus in the Retroviridae family. Example species are the murine leukemia virus and the feline leukemia virus. They cause various sarcomas, leukemias and immune deficiencies in mammals, reptiles and birds.

<span class="mw-page-title-main">Endogenous retrovirus</span> Inherited retrovirus encoded in an organisms genome

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.

<i>Jaagsiekte sheep retrovirus</i> Species of virus

Jaagsiekte sheep retrovirus (JSRV) is a betaretrovirus which is the causative agent of a contagious lung cancer in sheep, called ovine pulmonary adenocarcinoma.

The murine leukemia viruses are retroviruses named for their ability to cause cancer in murine (mouse) hosts. Some MLVs may infect other vertebrates. MLVs include both exogenous and endogenous viruses. Replicating MLVs have a positive sense, single-stranded RNA (ssRNA) genome that replicates through a DNA intermediate via the process of reverse transcription.

<span class="mw-page-title-main">Long terminal repeat</span> DNA sequence

A long terminal repeat (LTR) is a pair of identical sequences of DNA, several hundred base pairs long, which occur in eukaryotic genomes on either end of a series of genes or pseudogenes that form a retrotransposon or an endogenous retrovirus or a retroviral provirus. All retroviral genomes are flanked by LTRs, while there are some retrotransposons without LTRs. Typically, an element flanked by a pair of LTRs will encode a reverse transcriptase and an integrase, allowing the element to be copied and inserted at a different location of the genome. Copies of such an LTR-flanked element can often be found hundreds or thousands of times in a genome. LTR retrotransposons comprise about 8% of the human genome.

<span class="mw-page-title-main">ERV3</span> Protein-coding gene in the species Homo sapiens

HERV-R_7q21.2 provirus ancestral envelope (Env) polyprotein is a protein that in humans is encoded by the ERV3 gene.

<span class="mw-page-title-main">Syncytin-2</span> Protein-coding gene in the species Homo sapiens

Syncytin-2 also known as endogenous retrovirus group FRD member 1 is a protein that in humans is encoded by the ERVFRD-1 gene. This protein plays a key role in the implantation of human embryos in the womb.

Koala retrovirus (KoRV) is a retrovirus that is present in many populations of koalas. It has been implicated as the agent of koala immune deficiency syndrome (KIDS), an AIDS-like immunodeficiency that leaves infected koalas more susceptible to infectious disease and cancers. The virus is thought to be a recently introduced exogenous virus that is also integrating into the koala genome. Thus the virus can transmit both horizontally and vertically. The horizontal modes of transmission are not well defined but are thought to require close contact.

Retroviral matrix proteins are components of envelope-associated capsids of retroviruses. These proteins line the inner surface of viral envelopes and are associated with viral membranes.

Mason-Pfizer monkey virus (M-PMV), formerly Simian retrovirus (SRV), is a species of retroviruses that usually infect and cause a fatal immune deficiency in Asian macaques. The ssRNA virus appears sporadically in mammary carcinoma of captive macaques at breeding facilities which expected as the natural host, but the prevalence of this virus in feral macaques remains unknown. M-PMV was transmitted naturally by virus-containing body fluids, via biting, scratching, grooming, and fighting. Cross contaminated instruments or equipment (fomite) can also spread this virus among animals.

An endogenous viral element (EVE) is a DNA sequence derived from a virus, and present within the germline of a non-viral organism. EVEs may be entire viral genomes (proviruses), or fragments of viral genomes. They arise when a viral DNA sequence becomes integrated into the genome of a germ cell that goes on to produce a viable organism. The newly established EVE can be inherited from one generation to the next as an allele in the host species, and may even reach fixation.

Human endogenous retrovirus K (HERV-K) or Human teratocarcinoma-derived virus (HDTV) is a family of human endogenous retroviruses associated with malignant tumors of the testes. Phylogenetically, the HERV-K group belongs to the ERV2 or Class II or Betaretrovirus-like supergroup. Over the past several years, it has been found that this group of ERVs play an important role in embryogenesis, but their expression is silenced in most cell types in healthy adults. The HERV-K family, and particularly its subgroup HML-2, is the youngest and most transcriptionally active group and hence, it is the best studied among other ERVs. Reactivation of it or anomalous expression of HML-2 in adult tissues has been associated with various types of cancer and with neurodegenerative diseases such as amytrophic lateral sclerosis (ALS). Endogenous retrovirus K (HERV-K) is related to mammary tumor virus in mice. It exists in the human and cercopithecoid genomes. Human genome contains hundreds of copies of HERV-K and many of them possess complete open reading frames (ORFs) that are transcribed and translated, especially in early embryogenesis and in malignancies. One notable location of HERV-K is the C4 gene of RCCX module. HERV-K is also found in apes and Old World monkeys. It is uncertain how long ago in primate evolution the full-length HERV-K proviruses which are in the human genome today were created.

<i>Riboviria</i> Realm of viruses

Riboviria is a realm of viruses that includes all viruses that use a homologous RNA-dependent polymerase for replication. It includes RNA viruses that encode an RNA-dependent RNA polymerase, as well as reverse-transcribing viruses that encode an RNA-dependent DNA polymerase. RNA-dependent RNA polymerase (RdRp), also called RNA replicase, produces RNA from RNA. RNA-dependent DNA polymerase (RdDp), also called reverse transcriptase (RT), produces DNA from RNA. These enzymes are essential for replicating the viral genome and transcribing viral genes into messenger RNA (mRNA) for translation of viral proteins.

Gibbon-ape leukemia virus (GaLV) is an oncogenic, type C retrovirus that has been isolated from primate neoplasms, including the white-handed gibbon and woolly monkey. The virus was identified as the etiological agent of hematopoietic neoplasms, leukemias, and immune deficiencies within gibbons in 1971, during the epidemic of the late 1960s and early 1970s. Epidemiological research into the origins of GaLV has developed two hypotheses for the virus' emergence. These include cross-species transmission of the retrovirus present within a species of East Asian rodent or bat, and the inoculation or blood transfusion of a MbRV-related virus into captured gibbons populations housed at medical research institutions. The virus was subsequently identified in captive gibbon populations in Thailand, the US and Bermuda.

ERV-Fc was an endogenous retrovirus (ERV), or a genus or family of them, related to the modern murine leukemia virus. It was active and infectious among many species of mammals in several orders, jumping species more than 20 times between about 33 million and about 15 million years ago, in the Oligocene and early Miocene, in all large areas of the world except for Australia and Antarctica. After about 15 million years ago, it became extinct as an active infectious virus, perhaps due to its hosts developing inherited resistance to it, but inactive damaged copies and partial copies and fragments of its DNA survive as inclusions in the hereditary nuclear DNA of many species of mammals, some in different orders, including humans and other great apes. That has let interspecies jump routes of the spreading virus be tracked, and timed by the molecular clock in their extant descendants, but with gaps where trails were lost by passing through infected animals who left no extant descendants or by loss of the integrated sequence in some lineages.

References

  1. ↑ Laidler, J.R.; Stedman, K.M. (2010). "Virus Silicification under Simulated Hot Spring Conditions". Astrobiology. 10 (6): 569–576. Bibcode:2010AsBio..10..569L. doi:10.1089/ast.2010.0463. PMID   20735248. S2CID   7274625.
  2. 1 2 3 Emerman, M.; Malik, H.S. (2010). "Paleovirology – Modern Consequences of Ancient Viruses". PLOS Biology . 8 (2): e1000301. doi: 10.1371/journal.pbio.1000301 . PMC   2817711 . PMID   20161719.
  3. ↑ Katzourakis, Aris; Gifford, Robert J. (18 November 2010). "Endogenous Viral Elements in Animal Genomes". PLOS Genetics. 6 (11): e1001191. doi: 10.1371/journal.pgen.1001191 . PMC   2987831 . PMID   21124940.
  4. ↑ Weiss, RA (Oct 3, 2006). "The discovery of endogenous retroviruses". Retrovirology. 3: 67. doi: 10.1186/1742-4690-3-67 . PMC   1617120 . PMID   17018135.
  5. ↑ Pakorn Aiewsakun, Aris Katzourakis (2015). "Endogenous viruses: Connecting recent and ancient viral evolution". J. Virol. 479–480: 26–37. doi: 10.1016/j.virol.2015.02.011 . PMID   25771486.
  6. ↑ Aris Katzourakis, Robert J. Gifford (2010). "Endogenous Viral Elements in Animal Genomes". PLOS Genet. 6 (11): e1001191. doi: 10.1371/journal.pgen.1001191 . PMC   2987831 . PMID   21124940.
  7. ↑ Taylor, D. J.; J. Bruenn (2009). "The evolution of novel fungal genes from non-retroviral RNA viruses". BMC Biology. 7: 88. doi: 10.1186/1741-7007-7-88 . PMC   2805616 . PMID   20021636.
  8. ↑ Koonin, E. (2010). "Taming of the shrewd: novel eukaryotic genes from RNA viruses". BMC Biology. 8: 2. doi: 10.1186/1741-7007-8-2 . PMC   2823675 . PMID   20067611.
  9. ↑ Lida, Atsuo (2020). "Heritable endogenization of an RNA virus in a mammalian species" (PDF). bioRxiv. doi: 10.1101/2020.01.19.911933 .
  10. ↑ "Ancient "Fossil" Virus Shows Infection to Be Millions of Years Old", by Katherine Harmon, Scientific American, September 29, 2010
  11. ↑ "How to Resurrect an Extinct Retrovirus", Scientific American, November 2, 2006
  12. ↑ Yong, Ed (3 March 2014). "Giant virus resurrected from 69,000-year-old ice". Nature. doi:10.1038/nature.2014.14801. S2CID   87146458.
  13. ↑ Morelle, Rebecca (3 March 2014). "30,000-year-old giant virus 'comes back to life'". BBC News.
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