Fidelity Variants and RNA Quasispecies

Abstract

By now, it is well established that the error rate of the RNA-dependent RNA polymerase (RdRp) that replicates RNA virus genomes is a primary driver of the mutation frequencies observed in RNA virus populations-the basis for the RNA quasispecies. Over the last 10 years, a considerable amount of work has uncovered the molecular determinants of replication fidelity in this enzyme. The isolation of high- and low-fidelity variants for several RNA viruses, in an expanding number of viral families, provides evidence that nature has optimized the fidelity to facilitate genetic diversity and adaptation, while maintaining genetic integrity and infectivity. This chapter will provide an overview of what fidelity variants tell us about RNA virus biology and how they may be used in antiviral approaches.

Fig. 1

Viral polymerase structures. a Coxsackie virus B3 structure depicting the positions of all viable low-fidelity mutants (blue) likely to favor or alter different conformational states of the polymerase active site. The locations of compensatory mutations are shown in red. Adapted from (Liu et al. 2013). b Structural homology model of the CHIK nsp4 core polymerase showing the predicted locations of C483 (green sphere) and two nearby residues (L368 and T370, shown as gold spheres) that are the structural equivalents of known fidelity-altering sites in Coxsackie virus polymerase (positions I230 and F232, respectively, panel a) (Liu et al. 2013). Adapted from (Gnädig et al. 2012). Three domains are depicted in this figure: (1) the polymerase palm domain (gray), where the fidelity-altering mutations are located, is modeled with fairly high confidence because of the large number of conserved polymerase sequence motifs (motifs A–D); (2) the thumb domain (purple); (3) the fingers (red). Domains where the modeling is weak are shown as semitransparent

Fig. 2

The five kinetic steps in the single-nucleotide addition cycle. ER, enzyme-template complex. *ER, active enzyme-template complex. PP, phosphodiester bond. Adapted from (Arnold and Cameron 2000, 2004)

Fig. 3

Schematic depicting the effects of viral diversity, due to viral polymerase fidelity changes, on mutagenic drug resistance and attenuation in vivo. The numbers in the viral diversity schematic are arbitrary illustrations meant to represent genetically inter-connected progeny genomes, comprising populations with low, normal, and high degrees of diversity