Evolution of fitness values upon replication of viral populations is strongly influenced by the size of the virus population that participates in the infections. While large population passages often result in fitness gains, repeated plaque-to-plaque transfers result in average fitness losses. Here we develop a numerical model that describes fitness evolution of viral clones subjected to serial bottleneck events. The model predicts a biphasic evolution of fitness values in that a period of exponential decrease is followed by a stationary state in which fitness values display large fluctuations around an average constant value. This biphasic evolution is in agreement with experimental results of serial plaque-to-plaque transfers carried out with foot-and-mouth disease virus (FMDV) in cell culture. The existence of a stationary phase of fitness values has been further documented by serial plaque-to-plaque transfers of FMDV clones that had reached very low relative fitness values. The statistical properties of the stationary state depend on several parameters of the model, such as the probability of advantageous versus deleterious mutations, initial fitness, and the number of replication rounds. In particular, the size of the bottleneck is critical for determining the trend of fitness evolution. The initial steps in virus evolution are generation of diversity (through mutation, recombination, and genome segment reassortment in multipartite genomes), competition among the generated variants, and selection of those mutants showing the largest phenotypic advantage in a given environment (see overviews in references 9, 14, 17, 28, 30, and 40). Because of high mutation rates during viral RNA biosynthesis (2, 18), RNA viruses replicate as complex mutant swarms termed viral quasispecies (14, (21) (22) (23) (24) . The degree of adaptation of a viral quasispecies to a given environment is often quantitated by a relative fitness value, which measures the replication capacity of a viral population relative to a reference mutant distinguishable either genotypically or phenotypically (15, 26, 33, 37) . The long-term survival probability of a virus should consider parameters other than replication capacity (such as particle stability, transmissibility, etc. [11, 12, 15] ). Despite their limitations, relative fitness values, determined by growth competition experiments between two viral populations in cell culture and in vivo, are providing insights into basic features of quasispecies evolution as well as viral disease progression (5, 15, 49) . Because of the large variations in viral population size during infections in vivo, a focus of interest has been the study of the influence of virus population size on the evolution of fitness values (reviewed in reference 15). Experimental results with several RNA viruses have documented that large population passages often result in fitness gains (7, 26, 43, 45, 58) while repeated bottleneck events (serial plaque-to-plaque transfers being an extreme example) lead to average fitness losses (6, 19, 25, 27, 59, 60) , as predicted by the operation of Muller's ratchet (38, 41) . According to this mechanism, asexual populations of organisms will tend to accumulate deleterious mutations in an irreversible fashion unless accumulation is retarded by recombination. Studies with vesicular stomatitis virus (VSV) established that the size of the population bottleneck that led to either an increase, a decrease, or maintenance of a fitness value was determined by the initial fitness of the population (44). Consistent with this observation, exponential fitness gains observed upon large population passages were eventually limited by the population size, resulting in stochastic fitness variations (46). In a recent study of the fitness evolution of foot-and-mouth disease virus (FMDV) clones subjected to at least 100 successive plaque-to-plaque transfers, a linear accumulation of mutations together with a biphasic fitness decrease was observed (27). The second phase showed fitness fluctuations around a fitness mean value without perceivable fitness loss. This fact is remarkable since it could underlie a mechanism for low-fitness viral populations to elude extinction. For the present report we developed a numerical model that investigates fitness losses of fast-replicating genomes displaying high mutation rates and subjected to plaque-to-plaque transfers. The results with this new numerical model are in agreement with experimental results showing a biphasic fitness evolution of FMDV clones and fitness stability upon plaque transfers of very low fitness clones (27). The model predicts also the effect of transmission size on fitness evolution, as documented previously with experiments using VSV (44). Given its relevance to virus survival, the fitness stability of low-fitness clones has been further supported by 30 additional plaque-to-plaque transfers of highly debilitated FMDV clones. An essential feature of the model is the consideration of advantageous compensatory mutations as a molecular mechanism to cause fitness recovery, a feature adopted on the basis of experimental observations made with FMDV (1, 26) and also with unrelated systems such as human immu-* Corresponding author. Mailing address:
For example, Lazaro et al. REF present a time-stepping model with no explicit sequence structure; the model is used to study the evolution of fitness in the context of quasispecies theory.
Modeling Viral Genome Fitness Evolution Associated with Serial Bottleneck Events: Evidence of Stationary States of Fitness
Journal of virology
Journal of virology
Biology Medicine