Resistance of virus to extinction on bottleneck passages: Study of a decaying and fluctuating pattern of fitness loss

Abstract

RNA viruses display high mutation rates and their populations replicate as dynamic and complex mutant distributions, termed viral quasispecies. Repeated genetic bottlenecks, which experimentally are carried out through serial plaque-to-plaque transfers of the virus, lead to fitness decrease (measured here as diminished capacity to produce infectious progeny). Here we report an analysis of fitness evolution of several low fitness foot-and-mouth disease virus clones subjected to 50 plaque-to-plaque transfers. Unexpectedly, fitness decrease, rather than being continuous and monotonic, displayed a fluctuating pattern, which was influenced by both the virus and the state of the host cell as shown by effects of recent cell passage history. The amplitude of the fluctuations increased as fitness decreased, resulting in a remarkable resistance of virus to extinction. Whereas the frequency distribution of fitness in control (independent) experiments follows a log-normal distribution, the probability of fitness values in the evolving bottlenecked populations fitted a Weibull distribution. We suggest that multiple functions of viral genomic RNA and its encoded proteins, subjected to high mutational pressure, interact with cellular components to produce this nontrivial, fluctuating pattern. RNA viruses mutate at rates in the range of 10 Ϫ3 to 10 Ϫ5 base substitutions per nucleotide copied (1, 2). These values are several orders of magnitude larger than those normally encountered during replication of viral DNA and many orders of magnitude greater than that of cellular DNA (3, 4). One of the consequences of these high mutation rates is that RNA virus populations are composed of ensembles of closely related, nonidentical genomes that are known as viral quasispecies (5-10). Viral quasispecies evolve as a result of competition, selection, and random sampling events acting on continuously arising mutant genomes. A viral quasispecies is generally dominated by one or several most-fit genomes surrounded by a mutant spectrum whose components rank according to their relative fitness in the environment in which replication takes place (7, 9, 10). Fitness is defined here as the relative replication capacity of viruses measured in growth competition experiments (11,12).Alterations in population size have a decisive effect in the evolution of fitness of viral quasispecies. Large population passages of RNA viruses often result in fitness gains (13-16). In contrast to this finding, repeated bottleneck passages (experimentally carried out by plaque-to-plaque transfers of a virus; compare Fig. 1) are known to result in average fitness losses of a number of different . Such losses have been interpreted as an accentuation of Muller's ratchet (21), or accumulation of deleterious mutations predicted to occur in asexual populations of organisms when no compensatory mechanisms such as sex or recombination operate (17-25). In the case of the important viral pathogen foot-and-mouth disease virus (FMDV), a representative of the RNA family of virus ter...

Genetic and Phenotypic Variation of Foot-and-Mouth Disease Virus during Serial Passages in a Natural Host

“…In contrast to the observed resistance to extinction of FMDV subjected to plaque-to-plaque in vitro transfers (15,25), animal-to-animal transmission in nature may lead to virus extinction. Under conditions of natural host transmission, a number of viral phenotypic functions are likely involved in virus-host interactions and an unknown number of bottlenecks lead to a continuous purification of the population, narrowing the mutant spectrum composition of the quasispecies in such a way that it is unable to successfully retain its fitness.…”

Rate and effects of spontaneous mutations that affect fitness in mutatorEscherichia coli

“…We note that the increases in fitness observed involved different lines from those of the previous experiment, and that it is difficult to rule out possible variation of the environment in the fitness assays, which could have caused lower estimates of fitness at bottleneck 20. It has been suggested that the number of compensatory mutations may increase during the accumulation of deleterious mutations (Lazaro et al 2003;Gordo & Dionisio 2005;Silander et al 2007). In fact for some viruses undergoing strong bottlenecks, stabilization in their fitness was observed after an initial fitness decline (Lazaro et al 2003;Silander et al 2007).…”

Mutagenesis-Induced, Large Fitness Variations with an Invariant Arenavirus Consensus Genomic Nucleotide Sequence

“…In the first passage without FU, the capacity to produce progeny, which is taken as an estimate of relative viral fitness (33,47), was impaired. However, two to three passages in the absence of mutagens allowed LCMV to regain the capacity to produce progeny at levels comparable to those of LCMV not subjected to mutagenic treatment (Fig.…”