Arbovirus high fidelity variant loses fitness in mosquitoes and mice

Abstract

The error rate of RNA-dependent RNA polymerases (RdRp) affects the mutation frequency in a population of viral RNAs. Using chikungunya virus (CHIKV), we describe a unique arbovirus fidelity variant with a single C483Y amino acid change in the nsP4 RdRp that increases replication fidelity and generates populations with reduced genetic diversity. In mosquitoes, high fidelity CHIKV presents lower infection and dissemination titers than wild type. In newborn mice, high fidelity CHIKV produces truncated viremias and lower organ titers. These results indicate that increased replication fidelity and reduced genetic diversity negatively impact arbovirus fitness in invertebrate and vertebrate hosts. Studies with the first RNA-dependent RNA polymerase (RdRp) fidelity variant demonstrated that poliovirus RdRp error rate is a major contributor to population mutation frequency (1) and that reduced genetic diversity negatively impacts dissemination and pathogenesis in vivo (refs. 2-4; although the implications of these findings were limited by a relatively artificial model). The explanation for this reduced fitness is based on the idea that a diverse RNA virus population contains, by chance, more variants with potentially advantageous adaptive mutations, whereas a less diverse population is not as likely to possess such variants. Based on these observations, we hypothesized that RdRp fidelity of other RNA viruses can be modulated with similar fitness costs.Nucleoside analogs including ribavirin and 5-fluorouracil (5-FU) are mutagenic compounds that are misincorporated into viral genomes during RNA synthesis, resulting in deleterious mutations by mispairing in the following replication cycle (5-7). The consequent increase in the number of mutations places more genomic RNAs beyond a hypothetical error threshold: a mutation frequency at which the majority of the population harbors low fitness or lethal mutations (5,8). In this theoretical context, RNA virus populations lie close to this threshold-even moderate increases in mutation frequency could severely diminish infectivity. Increasing polymerase fidelity would potentially create a population farther from this error threshold that could better tolerate mutational input. Solid evidence supports this logic: DNA polymerase (9, 10) and reverse transcriptase (11-13) virus variants with antimutator phenotypes are linked to mutations that increase fidelity and reduce base analog incorporation. These observations present an interesting paradox: If point mutations in RNA viruses can increase RdRp fidelity, thereby decreasing replication mistakes, why is higher fidelity in RNA viruses not selected in nature? Is there a tradeoff between being error-prone but adaptable or being less adaptable but possessing higher fidelity? Does higher fidelity necessarily incur a phenotypic disadvantage in hosts, where a reduced ability to produce adaptive mutations impairs fitness, as was suggested by poliovirus studies?Arthropod borne (arbo-) viruses are unique among RNA viruses in that they obligatel...

Amino acid residues Ala283 and His421 in the RNA-dependent RNA polymerase of porcine reproductive and respiratory syndrome virus play important roles in viral ribavirin sensitivity and quasispecies diversity

“…3c). This indicated that the amino acid substitutions in nsp9 affected PRRSV fitness in vitro, a characteristic which was usually observed in some other RNA virus mutants containing high fidelity RdRp (Coffey et al, 2011;Van Slyke et al, 2015).…”

A Polymerase Mechanism-based Strategy for Viral Attenuation and Vaccine Development

“…Second, the enhanced fidelity reduces the frequency of genetic reversion to a wild-type, pathogenic phenotype (12). There is now evidence in several systems that RdRp fidelity is a determinant of viral pathogenesis and virulence (11)(12)(13)(14)(15)(16)(17)(18). Unfortunately, none of the mutations in the RdRp gene that lead to increased replication fidelity are at positions conserved across virus families, making it difficult to extrapolate attenuation by enhanced fidelity to other systems.…”

Genomic mutation rates that neutralize adaptive evolution and natural selection

“…A large increase in the mutation rate can create strong selection pressure for a lowered mutation rate, and a reduction in the mutation rate may thus evolve in short order. Our own work with a mutator strain of Escherichia coli and a nucleoside analogue mutagen, together with several previous mutagenesis studies using different viral systems, shows that resistance to mutagens at high doses can evolve rapidly and through a number of different mechanisms [76][77][78][79][80][81][82]. If one could increase the mutation rate to a level that is high enough to cause extinction, but not too high, selection for resistance could, in principle, be reduced considerably and the evolution of resistance might be prevented.…”