Virus Evolution

Abstract

Viruses are transmissible deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) genetic elements that require a cell for multiplication. Viruses are diverse and ubiquitous in nature. They evolve in continuous interaction with their host cells and organisms, following Darwinian principles: genetic variation, competition among variant forms, selection of the most fit variants in a given environment, and random drift of genomes favoured by bottleneck events. Viruses probably had an ancient origin and survived as agents of gene transfer and promoters of cell variation. Disease is a side effect of virus‐host interactions. RNA viruses and some DNA viruses can evolve very rapidly, fuelled by limited template‐copying fidelity of the polymerases that catalyse their replication. Their populations are extremely complex mutant clouds termed viral quasispecies, with a continuously changing mutant composition. Interactions of cooperation or interference can be established among genomes and their expression products within a mutant spectrum, giving rise to new phenotypic traits. Adaptability mediated by quasispecies dynamics represents a problem for disease prevention and control, but it has inspired new strategies to combat viral disease, such as new vaccine designs, recognition of the need of combination therapies in antiviral pharmacology and the development of lethal mutagenesis or viral extinction driven by an excess of mutations. Key Concepts Virions are the virus particles produced upon completion of the intracellular replication cycle. Cells can be infected via different entry pathways, and by single virions or multiple particles through vesicles or cell‐to‐cell contacts. Inter‐host transmission of virions can give rise to disease outbreaks, epidemics or pandemics (worldwide epidemics). Deep sequencing methodology has unveiled great diversity of viruses during infection, as well as in natural habitats. The ensemble of viruses in our biosphere is termed the ‘virosphere’. The total number of virus particles in the biosphere at any given point in time is estimated from 10 31 to 10 32 , 10 times more than cells. Mutation, recombination, segment reassortment, and gene transfers between cells and viruses contribute to virus diversity. Several theories of virus origins have been proposed. A currently favoured view is that viruses have an ancestral origin and have contributed to shape the cellular world mainly through gene transfers. RNA viruses and some DNA viruses are replicated by low‐fidelity polymerases (with a propensity to introduce mutations). As a consequence, such viruses constitute mutant spectra (swarms or clouds) termed viral quasispecies. There is an arms race between viruses and the host response to prevent infection. Some proteins that play physiological functions in cells can be recruited as part of the innate immunity against viruses. Viral fitness measures the relative replicative capacity of a virus in a given environment. Population bottlenecks may alter viral fitness and influence evolutionary outcomes. The adaptive potential of viral quasispecies has encouraged research in new strategies for viral disease prevention and control.