Viral evolution is a subfield of evolutionary biology and virology that is specifically concerned with the evolution of viruses. Many viruses, in particular RNA viruses, have short generation times and relatively high mutation rates (on the order of one point mutation or more per genome per round of replication for RNA viruses). This elevated mutation rate, when combined with natural selection, allows viruses to quickly adapt to changes in their host environment.
Viral evolution is an important aspect of the epidemiology of viral diseases such as influenza (influenza virus), AIDS (HIV), and hepatitis (e.g. HCV). The rapidity of viral mutation also causes problems in the development of successful vaccines and antiviral drugs, as resistant mutations often appear within weeks or months after the beginning of the treatment. One of the main theoretical models to study viral evolution is the quasispecies model, as the viral quasispecies.
Viruses are ancient. Studies at the molecular level have revealed relationships between viruses infecting organisms from each of the three domains of life and viral proteins that pre-date the divergence of life and thus the last universal common ancestor. This indicates that some viruses emerged early in the evolution of life, and that viruses have probably arisen multiple times.
There are three classical hypotheses on the origins of viruses:
- Viruses may have once been small cells that parasitised larger cells (the degeneracy hypothesis or reduction hypothesis);
- some viruses may have evolved from bits of DNA or RNA that "escaped" from the genes of a larger organism (the vagrancy hypothesis or escape hypothesis);
- or viruses could have evolved from complex molecules of protein and nucleic acid at the same time as cells first appeared on earth (the virus-first hypothesis).
None of these hypotheses were fully accepted: the regressive hypothesis did not explain why even the smallest of cellular parasites do not resemble viruses in any way. The escape hypothesis did not explain the complex capsids and other structures on virus particles. The virus-first hypothesis was quickly dismissed because it contravened the definition of viruses, in that they require host cells. Virologists are, however, beginning to reconsider and re-evaluate all three hypotheses.
One of the problems for those studying viral origins and evolution is their high rate of mutation, particularly the case in RNA retroviruses like HIV/AIDS. A recent study based on comparisons of viral protein folding structures, however, is offering some new evidence. Fold Super Families (FSF's) are proteins that show similar folding structures independent of the actual sequence of amino acids, and have been found to show evidence of viral phylogeny. Thus viruses have been found to be capable of being divided into 4 FSFs; based upon the three realms of bacterioviruses, archaeoviruses, and eukaryoviruses, together with a fourth FSF that seems to indicate that it predated the separation of the three realms. Thus "viral proteomes retain traces of ancient evolutionary history that can be recovered using advanced bioinformatics approaches." Anshan Nasir and Gustavo Caetano-Anollés, "This implies the existence of ancient cellular lineages common to both cells and viruses before the appearance of the “last universal cellular ancestor” that gave rise to modern cells. According to our data, the prolonged pressure of genome and particle size reduction eventually reduced virocells into modern viruses (identified by the complete loss of cellular makeup), whereas other coexisting cellular lineages diversified into modern cells. " Furthermore, the long genetic distance between RNA and DNA FSF's suggests that the RNA world hypothesis may have new experimental evidence, with a long intermediary period in the evolution of cellular life.
Viruses do not form fossils in the traditional sense, because they are much smaller than the finest colloidal fragments forming sedimentary rocks that fossilize plants and animals. However, the genomes of many organisms contain endogenous viral elements (EVEs). These DNA sequences are the remnants of ancient virus genes and genomes that ancestrally 'invaded' the host germline. For example, the genomes of most vertebrate species contain hundreds to thousands of sequences derived from ancient retroviruses. These sequences are a valuable source of retrospective evidence about the evolutionary history of viruses, and have given birth to the science of paleovirology.
The evolutionary history of viruses can to some extent be inferred from analysis of contemporary viral genomes. The mutation rates for many viruses have been measured, and application of a molecular clock allows dates of divergence to be inferred.
Viruses evolve through changes in their RNA (or DNA), some quite rapidly, and the best adapted mutants quickly outnumber their less fit counterparts. In this sense their evolution is Darwinian. The way viruses reproduce in their host cells makes them particularly susceptible to the genetic changes that help to drive their evolution. The RNA viruses are especially prone to mutations. In host cells there are mechanisms for correcting mistakes when DNA replicates and these kick in whenever cells divide. These important mechanisms prevent potentially lethal mutations from being passed on to offspring. But these mechanisms do not work for RNA and when an RNA virus replicates in its host cell, changes in their genes are occasionally introduced in error, some of which are lethal. One virus particle can produce millions of progeny viruses in just one cycle of replication, therefore the production of a few "dud" viruses is not a problem. Most mutations are "silent" and do not result in any obvious changes to the progeny viruses, but others confer advantages that increase the fitness of the viruses in the environment. These could be changes to the virus particles that disguise them so they are not identified by the cells of the immune system or changes that make antiviral drugs less effective. Both of these changes occur frequently with HIV.
Many viruses (for example, influenza A virus) can "shuffle" their genes with other viruses when two similar strains infect the same cell. This phenomenon is called genetic shift, and is often the cause of new and more virulent strains appearing. Other viruses change more slowly as mutations in their genes gradually accumulate over time, a process known as genetic drift.
Through these mechanisms new viruses are constantly emerging and present a continuing challenge to attempts to control the diseases they cause. Most species of viruses are now known to have common ancestors, and although the "virus first" hypothesis has yet to gain full acceptance, there is little doubt that the thousands of species of modern viruses have evolved from less numerous ancient ones. The morbilliviruses, for example, are a group of closely related, but distinct viruses that infect a broad range of animals. The group includes measles virus, which infects humans and primates; canine distemper virus, which infects many animals including dogs, cats, bears, weasels and hyaenas; rinderpest, which infected cattle and buffalo; and other viruses of seals, porpoises and dolphins. Although it is not possible to prove which of these rapidly evolving viruses is the earliest, for such a closely related group of viruses to be found in such diverse hosts suggests the possibility that their common ancestor is ancient.
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