Virus population dynamics during infection

During RNA virus infection of a host, error-prone viral replication will give rise to a cloud of genetically-linked mutants, as well as truncated, defective genomes. In this review, we describe the dynamics of viral diversity during infection, illustrating that the viral population fluctuates greatly in number of genomes and composition of mutants, in relation with the existence of physical barriers or immune pressures. We illustrate the importance of generating diversity by analyzing the case of fidelity variants, largely attenuated in vivo. Recombination is also considered in its various roles: redistribution of mutations on full-length genomes, and production of highly-immunostimulatory defective genomes. We cover these notions by underlining, when they exist, the differences between acute and persistent infections.