The population genetics and evolutionary epidemiology of RNA viruses

The authors discuss the main mechanisms of RNA virus evolution — mutation, recombination, natural selection, genetic drift and migration, and how these interact to shape the genetic structure of populations.The quasispecies model of RNA virus evolution is explained and the question of whether this model provides an accurate description of RNA virus evolution is discussed.Experiments that can be carried out to test the basic principles of evolutionary theory are briefly described. The authors review what such experiments have told us about virus evolution and, more widely, what these experiments have revealed in terms of general evolutionary principles.RNA viruses evolve quickly, so a detailed reconstruction of their epidemiological history can be undertaken. The authors show how epidemiological patterns of viruses result from their evolution at two different levels: within individual hosts (and vectors) and among hosts at the population level.Using several examples, including HIV and SARS, the authors describe how studying RNA virus evolution could be used to understand virus emergence.Finally, the important topics of the evolution of virulence and resistance to drugs are discussed.