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Viruses have been referred to since ancient times. However, the exact origin of these tiny organisms that carry only the genetic information in a protein coat is still unknown.
The main problem is no fossils of viruses have ever been detected. So the exact origins are difficult to speculate. These particles are too small and too fragile for the process of fossilisation or even for preservation of nucleic acid sequences in leaf tissues or insects in amber.
Thus viral origin studies rely upon viruses that are isolated in the present, or from material that is at most a few decades old.
The new branch of virus molecular systematics helps in understanding the distant relationships of and origins of many important groups of viruses. The researchers have now sequenced all or part of the DNA and/or RNA of the known varieties of viruses, including the largest (pox- and herpesviruses) and the smallest (gemini- and other ssDNA viruses). The cellular sequences help in understanding the evolution of viruses over centuries.
For example, Geminiviruses are a diverse group of viruses and each of the subtypes have different genes and genome components. The differences however may be traced back to a common origin when considering geographical diversity, and genetic divergence of the vehicles or hosts that carry the viruses.
Similarly Potyviruses are an ancient family of viruses and the genomes vary among the subtypes and are not shared by all members. These are transmitted by aphids while rymo- and triticiviruses are mite-transmitted, and ipomoviruses are whitefly-transmitted. These have been found to have descended from a fungal virus.
Tracing back evolution the descent of the viruses could be speculated to be from a single ancestor containing RNA functions or from cellular organisms (containing DNA in cases of DNA viruses). Retroviruses like the HIV virus, as well as pararetroviruses, retrotransposons and retroposons share a common origin of the reverse transcription function. This means these viruses have the enzyme that switches the RNA-based genetics to DNA-based heredity.
In addition some animal viruses - like picornaviruses and alphaviruses - have origins in plant viruses which do not have same structure, genome components, organisation or number of genes. The small spherical picornaviruses (ssRNA, 1 genome component, infects animals) has relations with comoviruses (small spherical, 2 genome components, infects plants) and Potyviridae (filamentous, 1 or two genome components, infects plants).
From the evolutionary studies it is apparent that there can have been no single origin of viruses as organisms. Thus, there can be no simple "family tree" for viruses. Their only common feature is their role as an obligate parasite that needs a host to propagate.
Evolution may have begun from the beginning of life in water, as well as the timeline of colonisation of dry land by organisms. Viruses of nearly all the major classes of organisms - animals, plants, fungi and bacteria/archaea - probably evolved with their hosts in the seas and the viruses emerged from the waters with their different hosts.
Most viruses of land plants are probably evolved from those in the green algae that emerged +/- 1000 Million years ago.
There are three main hypotheses regarding the origins of viruses:
According to this hypothesis viruses originated through a progressive process. The mobile of movable pieces of genetic material capable of moving within a genome, gained the ability to exit one cell and enter another.
Some virologists feel viruses may have originated via a regressive, or reductive, process. Certain bacteria that are obligate intracellular parasites, like Chlamydia and Rickettsia species, evolved from free-living ancestors. Viruses thus could have evolved from more complex, possibly free-living organisms that lost genetic information over time as these became parasitic in their replication. Viruses of nucleocytoplasmic large DNA viruses (NCLDVs) illustrate this hypothesis.
This hypothesis suggests that viruses existed before cells. Koonin and Martin (2005) hypothesized that viruses existed in a pre-cellular world as self-replicating units.
None of the hypothesis may be correct. To date, no clear explanation for the origin(s) of viruses exists. And so viruses could have arisen from mobile genetic elements that gained the ability to move between cells or they may have descended from previously free-living organisms that adapted a parasitic replication strategy or may have existed before, and led to the evolution of, cellular life.