In order to understand the evolutionary mechanisms of persistence and diversification within the Caliciviridae, we have been exploiting endemic infection of feline calicivirus within five geographically distinct household groups of cats. By sequencing immunodominant and variable regions of the capsid gene, we identified the relative contribution of the different evolutionary processes employed by the virus to ensure its long-term survival in the host population. Such strategies included progressive evolution of a given variant of a strain through mutation accumulation within an individual, sequential reinfection with either a variant of the same strain or with a different strain, and mixed infection. Recombination between different strains in this study has been reported in detail elsewhere (K. P. Coyne et al., J. Gen. Virol. 87:921-926, 2006). Here, we provide evidence to suggest that true long-term persistent infection in individuals is relatively rare, with the majority of apparent viral carriers undergoing a combination of progressive evolution and cyclical reinfection. Progressive evolution at the individual level and variant reinfection at both the individual and population levels were associated with positive selection. Two measures of evolution rate were determined; for a virus progressively evolving within an individual (1.32 ؋ 10 ؊2 to 2.64 ؋ 10 ؊2 substitutions per nucleotide per year, i.e., no transmission) and for a strain circulating within a population (3.84 ؋ 10 ؊2 to 4.56 ؋ 10 ؊2 substitutions per nucleotide per year, i.e., including transmission). Reiteration of both progressive evolution and variant reinfection appeared to lead to a gradual increase in the diversity of a given strain of virus, both in the individual and in the population, until eventually new strains emerged.The Caliciviridae are an important group of human and animal RNA pathogens, causing a wide range of diseases, including acute outbreaks of gastroenteritis in humans (noroviruses and sapoviruses) and vesicular and other diseases in animals (vesiviruses and lagoviruses) (19). The Caliciviridae are a highly variable family of small positive-strand RNA viruses, demonstrating considerable antigenic and genetic diversity both between and within genera. Such variability has been associated with the emergence of highly transmissible globally dominant strains of human caliciviruses (36) and hypervirulent animal caliciviruses that are frequently lethal (9,33,39). Despite the obvious significance of such variation, the origins of this diversity and the evolutionary mechanisms by which new, and possibly more virulent strains evolve remain unclear.Feline calicivirus (FCV) belongs to the genus Vesivirus and is a highly infectious oral and respiratory pathogen of domestic cats (18). Following acute infection, some cats remain persistently infected with the virus (11,40,48,59). Such carriers appear to be relatively common in the general population, with prevalences ranging from 15 to 91%, and they play an important role in the epidemiolog...