Picornavirus RNA Recombination Counteracts Error Catastrophe

Abstract

Template-dependent RNA replication mechanisms render picornaviruses susceptible to error catastrophe, an overwhelming accumulation of mutations incompatible with viability. Viral RNA recombination, in theory, provides a mechanism for viruses to counteract error catastrophe. We tested this theory by exploiting well-defined mutations in the poliovirus RNA-dependent RNA polymerase (RDRP), namely, a G64S mutation and an L420A mutation. Our data reveal two distinct mechanisms by which picornaviral RDRPs influence error catastrophe: fidelity of RNA synthesis and RNA recombination. A G64S mutation increased the fidelity of the viral polymerase and rendered the virus resistant to ribavirin-induced error catastrophe, but only when RNA recombination was at wild-type levels. An L420A mutation in the viral polymerase inhibited RNA recombination and exacerbated ribavirin-induced error catastrophe. Furthermore, when RNA recombination was substantially reduced by an L420A mutation, a high-fidelity G64S polymerase failed to make the virus resistant to ribavirin. These data indicate that viral RNA recombination is required for poliovirus to evade ribavirin-induced error catastrophe. The conserved nature of L420 within RDRPs suggests that RNA recombination is a common mechanism for picornaviruses to counteract and avoid error catastrophe. IMPORTANCE Positive-strand RNA viruses produce vast amounts of progeny in very short periods of time via template-dependent RNA replication mechanisms. Template-dependent RNA replication, while efficient, can be disadvantageous due to error-prone viral polymerases. The accumulation of mutations in viral RNA genomes leads to error catastrophe. In this study, we substantiate long-held theories regarding the advantages and disadvantages of asexual and sexual replication strategies among RNA viruses. In particular, we show that picornavirus RNA recombination counteracts the negative consequences of asexual template-dependent RNA replication mechanisms, namely, error catastrophe.

RNA-Dependent RNA Polymerase Speed and Fidelity are not the Only Determinants of the Mechanism or Efficiency of Recombination

“…There are known and unknown biochemical properties of the RdRp that determine recombination efficiency, and there are at least two distinct mechanisms of recombination. Without understanding the biochemical properties of the mutants under investigation, it is difficult to compare one study to another that may explain disparate observations made between laboratories [30,55]. Further analysis of the panel of mutants reported here may help to resolve the controversy but should illuminate how changes to the mechanism and efficiency of recombination impact viral evolution in a background of constant speed and fidelity.…”

Induced copy-back RNA synthesis as a novel therapeutic mechanism against RNA viruses

“…6H-J and Supplementary Fig. 6B) 40,43,44 . Altogether, our results define inducible intra-and intermolecular template switching (Fig.…”

“…Recombination is thought to provide a means to suppress the impact of deleterious mutations 40,43,44 . Our data would suggest that a balance between mutation and recombination must exist, because increasing the frequency of recombination exhibits antiviral activity ( Fig.…”

“…2) 19 . PV Y275H RdRp is one of the most robust, recombination-defective mutants described 19 , but the molecular basis for the defect is not known for this mutant or the others that have been reported in the PV system or other viral systems 20,43,44 . Here, we show that EV-A71 Y276H RdRp is equally robust and recombination defective in cells (Fig.…”

“…This level of detail for the mechanism of RdRp-mediated RNA recombination is unprecedented. Several recombinationdefective/impaired RdRp variants are known 43,44,47 , and it is possible that the mechanistic basis for the defects will be different. Therefore, evaluation of these derivatives may enable a genetic dissection of the mechanism of template switching and illumination of steps and/or intermediates masked by analyzing WT RdRp.…”