Contingent Neutrality in Competing Viral Populations

Abstract

The replicative fitness of a genetically marked (MARM-C) population of vesicular stomatitis virus was examined in competition assays in BHK-21 cells. In standard fitness assays involving up to eight competition passages of the mixed populations, MARM-C competes equally with the wild type (wt), but very prolonged competitions always led to the wt gaining dominance over MARM-C in a very slowed, nonlinear manner (J. Quer et al., J. Mol. Biol. 264: [465][466][467][468][469][470][471] 1996). In the present study we show that a number of quite unrelated environmental perturbations, which decreased virus replication during competitions, all led to an accelerated dominance of the wt over MARM-C. These perturbations were (i) the presence of added (or endogenously generated) defective interfering particles, (ii) the presence of the chemical mutagen 5-fluorouracil (5-FU), or (iii) an increase in temperature to 40.5°C. Thus, the "neutral fitness" of the MARM-C population is contingent. We have determined the entire genomic consensus sequence of MARM-C and have identified only six mutations. Clearly, some or all of these mutations allowed the MARM-C quasispecies population to compete equally with wt in a defined constant host environment, but the period of neutrality was shortened when the environment was perturbed during competitions. Interestingly, when four passages of each population were carried out independently in the presence of 5-FU (but in the absence of competition), no significant differences were detected in the fitness changes of wt and MARM-C, nor was there a difference in their subsequent abilities to compete with each other in a standard fitness assay. We propose a model for this contingent neutrality. The conditions employed to generate the MARM-C quasispecies population selected a small number of mutations in the consensus sequence. It appears that the MARM-C quasispecies population has moved into a segment of sequence space in which the average fitness value is neutral but, under environmental stress, beneficial mutations cannot be generated rapidly enough to compete with those being generated concurrently by competing wt virus quasispecies populations.

Mutagenesis versus Inhibition in the Efficiency of Extinction of Foot-and-Mouth Disease Virus

“…It was unexpected that REDpt60 could be extinguished with FU (200 g/ml) alone while C-S8c1, of comparable fitness, could not (35,52). This difference may relate to mutations present in REDpt60 that, although not impairing fitness under standard culture conditions, may render this genome less tolerant to environmental perturbations, as previously described for VSV (43). In the case of MARLS (5,31,33), a clone with a relative fitness 130-fold higher than that of C-S8c1, only treatments in which FU was present in combination with inhibitors were successful in driving the virus to extinction (Fig.…”

“…REDpt60 could be extinguished with FU in four passages under the same conditions in which C-S8c1 was not extinguished (52). The phenomenon underlying the sensitivity to extinction of REDpt60 could be contingent neutrality of accumulated mutations, first described with a VSV mutant that, despite showing fitness equal to that of the wild type under standard cell culture conditions, manifested a selective disadvantage when a number of environmental perturbations intervened during viral replication (43). Theoretical studies have also suggested the advantage of replicons with increased robustness against mutations (56).…”

Quasispecies Theory in Virology

“…The consensus sequence need not be identical to the dominant or master sequence. Direct fitness measurements of components of mutant spectra provide little evidence of strict neutrality (14,15,30). In the absence of evidence of a clonal origin, virologists sometimes infer a quasispecies structure, and this indeed is not a rigorous use of the concept (17).…”

Modeling Viral Genome Fitness Evolution Associated with Serial Bottleneck Events: Evidence of Stationary States of Fitness

“…Furthermore, recent evidence has shown that a corrected ratio of nonsynonymous to synonymous mutations may be taken as indicative of positive selection in an experimental setting in which positive selection is impossible (56), making quantifications of neutral sites on the basis of the ratio of nonsynonymous to synonymous mutations questionable. Given also the contingent nature of some neutral mutations (48), it is likely that the number of truly neutral sites in RNA genomes with compact genetic information is limited, albeit the number is unknown and difficult to estimate. This uncertainty should not affect the numerical model proposed here, since one of its basic quantitative features is that the combined number of deleterious and neutral mutations largely exceeds the number of advantageous mutations, irrespective of the proportion of deleterious to neutral mutations.…”