scholarly journals Viral replication modes in single-peak fitness landscapes: a dynamical systems analysis

2017 ◽  
Author(s):  
Joan Forners ◽  
J. Tomás Lázaro ◽  
Tomás Alarcón ◽  
Santiago F. Elena ◽  
Josep Sardanyés
Keyword(s):  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Rna Viruses ◽  
Viral Rna ◽  
Mutation Rates ◽  
Single Peak ◽  
Lethal Mutagenesis ◽  
Error Catastrophe ◽  
Degradation Rates ◽  
Transcritical Bifurcations

Positive-sense, single-stranded RNA viruses are important pathogens infecting almost all types of organisms. Experimental evidences from mutant distributions and amplification kinetics of viral RNA suggest that these pathogens may follow different RNA replication modes, ranging from the stamping machine replication (SMR) to the geometric replication (GR) modes. Despite previous theoretical works have focused on the evolutionary dynamics of RNA viruses amplifying their genomes with different strategies, few is known in terms of the bifurcations and transitions involving error thresholds (mutation-induced dominance of mutants) and lethal mutagenesis (mutation-induced extinction of all sequences). Here we analyze a dynamical system describing the intracellular amplification of viral RNA genomes evolving on a single-peak fitness landscape focusing on three cases considering neutral, deleterious, and lethal mutants spectra. In our model, the different replication modes are introduced with parameter α: with α ≳ 0 for the SMR and α = 1 for the GR. We analytically derive the critical mutation rates causing lethal mutagenesis and error catastrophe, governed by transcritical bifurcations that depend on parameters α, k1 (replicative fitness of mutants), and on the spontaneous degradation rates of the sequences, ϵ. For the lethal case the critical mutation rate involving lethal mutagenesis is . Here, the SMR involves lower critical mutation rates, being the system more robust to lethal mutagenesis replicating closer to the GR mode. This result is also found for the neutral and deleterious cases, but for these later cases lethal mutagenesis can shift to the error catastrophe once the replication mode surpasses a threshold given by .

scholarly journals Noise-induced bistability in the quasineutral coexistence of viral RNA under different replication modes

2018 ◽  
Author(s):  
Josep Sardanyés ◽  
Andreu Arderiu ◽  
Santiago F. Elena ◽  
Tomás Alarcón
Keyword(s):  
Viral Replication ◽  
Evolutionary Dynamics ◽  
Rna Viruses ◽  
Initial Conditions ◽  
Rna Replication ◽  
Viral Rna ◽  
Stochastic Simulations ◽  
Strong Impact ◽  
Deterministic Models ◽  
The Impact

Evolutionary and dynamical investigations on real viral populations indicate that RNA replication can range between two extremes given by so-called stamping machine replication (SMR) and geometric replication (GR). The impact of asymmetries in replication for single-stranded, (+) sense RNA viruses has been up to now studied with deterministic models. However, viral replication should be better described by including stochasticity, since the cell infection process is typically initiated with a very small number of RNA macromolecules, and thus largely influenced by intrinsic noise. Under appropriate conditions, deterministic theoretical descriptions of viral RNA replication predict a quasineutral coexistence scenario, with a line of fixed points involving different strands’ equilibrium ratios depending on the initial conditions. Recent research on the quasineutral coexistence in two competing populations reveals that stochastic fluctuations fundamentally alters the mean-field scenario, and one of the two species outcompetes the other one. In this manuscript we study this phenomenon for RNA viral replication modes by means of stochastic simulations and a diffusion approximation. Our results reveal that noise has a strong impact on the amplification of viral RNA, also causing the emergence of noise-induced bistability. We provide analytical criteria for the dominance of (+) sense strands depending on the initial populations on the line of equilibria, which are in agreement with direct stochastic simulation results. The biological implications of this noise-driven mechanism are discussed within the framework of the evolutionary dynamics of RNA viruses with different modes of replication.

scholarly journals Noise-induced bistability in the quasi-neutral coexistence of viral RNAs under different replication modes

2018 ◽  
Vol 15 (142) ◽  
pp. 20180129 ◽  
Author(s):  
Josep Sardanyés ◽  
Andreu Arderiu ◽  
Santiago F. Elena ◽  
Tomás Alarcón
Keyword(s):  
Evolutionary Dynamics ◽  
Rna Viruses ◽  
Initial Conditions ◽  
Rna Replication ◽  
Viral Rna ◽  
Stochastic Simulations ◽  
Strong Impact ◽  
Deterministic Models ◽  
Viral Rnas ◽  
The Impact

Evolutionary and dynamical investigations into real viral populations indicate that RNA replication can range between the two extremes represented by so-called ‘stamping machine replication’ (SMR) and ‘geometric replication’ (GR). The impact of asymmetries in replication for single-stranded (+) sense RNA viruses has been mainly studied with deterministic models. However, viral replication should be better described by including stochasticity, as the cell infection process is typically initiated with a very small number of RNA macromolecules, and thus largely influenced by intrinsic noise. Under appropriate conditions, deterministic theoretical descriptions of viral RNA replication predict a quasi-neutral coexistence scenario, with a line of fixed points involving different strands' equilibrium ratios depending on the initial conditions. Recent research into the quasi-neutral coexistence in two competing populations reveals that stochastic fluctuations fundamentally alter the mean-field scenario, and one of the two species outcompetes the other. In this article, we study this phenomenon for viral RNA replication modes by means of stochastic simulations and a diffusion approximation. Our results reveal that noise has a strong impact on the amplification of viral RNAs, also causing the emergence of noise-induced bistability. We provide analytical criteria for the dominance of (+) sense strands depending on the initial populations on the line of equilibria, which are in agreement with direct stochastic simulation results. The biological implications of this noise-driven mechanism are discussed within the framework of the evolutionary dynamics of RNA viruses with different modes of replication.

scholarly journals Epistatic interactions within the influenza virus polymerase complex mediate mutagen resistance and replication fidelity

2017 ◽  
Author(s):  
Matthew D. Pauly ◽  
Daniel M. Lyons ◽  
Adam S. Lauring
Keyword(s):  
Genetic Diversity ◽  
Drug Resistance ◽  
Influenza Virus ◽  
Mutation Rate ◽  
Rna Viruses ◽  
Nucleoside Analogs ◽  
Mutation Rates ◽  
Epistatic Interactions ◽  
Polymerase Complex ◽  
Lethal Mutagenesis

AbstractLethal mutagenesis is a broad-spectrum antiviral strategy that employs mutagenic nucleoside analogs to exploit the high mutation rate and low mutational tolerance of many RNA viruses. Studies of mutagen-resistant viruses have identified determinants of replicative fidelity and the importance of mutation rate to viral population dynamics. We have previously demonstrated the effective lethal mutagenesis of influenza virus using three nucleoside analogs as well as the virus’s high genetic barrier to mutagen resistance. Here, we investigate the mutagen-resistant phenotypes of mutations that were enriched in drug-treated populations. We find that PB1 T123A has higher replicative fitness than the wild type, PR8, and maintains its level of genome production during 5-fluorouracil treatment. Surprisingly, this mutagen-resistant variant also has an increased baseline rate of C to U and G to A mutations. A second drug-selected mutation, PA T97I, interacts epistatically with PB T123A to mediate high-level mutagen resistance, predominantly by limiting the inhibitory effect of nucleosides on polymerase activity. Consistent with the importance of epistatic interactions in the influenza polymerase, we find that nucleoside analog resistance and replication fidelity are strain dependent. Two previously identified ribavirin-resistance mutations, PB1 V43I and PB1 D27N, do not confer drug resistance in the PR8 background, and the PR8-PB1 V43I polymerase exhibits a normal baseline mutation rate. Our results highlight the genetic complexity of the influenza virus polymerase and demonstrate that increased replicative capacity is a mechanism by which an RNA virus can counter the negative effects of elevated mutation rates.ImportanceRNA viruses exist as genetically diverse populations. This standing genetic diversity gives them the potential to adapt rapidly, evolve resistance to antiviral therapeutics, and evade immune responses. Viral mutants with altered mutation rates or mutational tolerance have provided insights into how genetic diversity arises and how it affects the behavior of RNA viruses. To this end, we identified variants within the polymerase complex of influenza virus that are able tolerate drug-mediated increases in viral mutation rates. We find that drug resistance is highly dependent on interactions among mutations in the polymerase complex. In contrast to other viruses, influenza virus counters the effect of higher mutation rates primarily by maintaining high levels of genome replication. These findings suggest the importance of maintaining large population sizes for viruses with high mutation rates and show that multiple proteins can affect both mutation rate and genome synthesis.

scholarly journals Structure-Function Relationships Underlying the Replication Fidelity of Viral RNA-Dependent RNA Polymerases

2014 ◽  
Vol 89 (1) ◽  
pp. 275-286 ◽  
Author(s):  
Grace Campagnola ◽  
Seth McDonald ◽  
Stéphanie Beaucourt ◽  
Marco Vignuzzi ◽  
Olve B. Peersen
Keyword(s):  
Rna Viruses ◽  
Viral Rna ◽  
Mutation Rates ◽  
Rapid Adaptation ◽  
Replication Fidelity ◽  
Virus Growth ◽  
Polymerase Structure ◽  
Positive Strand Rna

ABSTRACTViral RNA-dependent RNA polymerases are considered to be low-fidelity enzymes, providing high mutation rates that allow for the rapid adaptation of RNA viruses to different host cell environments. Fidelity is tuned to provide the proper balance of virus replication rates, pathogenesis, and tissue tropism needed for virus growth. Using our structures of picornaviral polymerase-RNA elongation complexes, we have previously engineered more than a dozen coxsackievirus B3 polymerase mutations that significantly altered virus replication rates andin vivofidelity and also provided a set of secondary adaptation mutations after tissue culture passage. Here we report a biochemical analysis of these mutations based on rapid stopped-flow kinetics to determine elongation rates and nucleotide discrimination factors. The data show a spatial separation of fidelity and replication rate effects within the polymerase structure. Mutations in the palm domain have the greatest effects onin vitronucleotide discrimination, and these effects are strongly correlated with elongation rates andin vivomutation frequencies, with faster polymerases having lower fidelity. Mutations located at the top of the finger domain, on the other hand, primarily affect elongation rates and have relatively minor effects on fidelity. Similar modulation effects are seen in poliovirus polymerase, an inherently lower-fidelity enzyme where analogous mutations increase nucleotide discrimination. These findings further our understanding of viral RNA-dependent RNA polymerase structure-function relationships and suggest that positive-strand RNA viruses retain a unique palm domain-based active-site closure mechanism to fine-tune replication fidelity.IMPORTANCEPositive-strand RNA viruses represent a major class of human and animal pathogens with significant health and economic impacts. These viruses replicate by using a virally encoded RNA-dependent RNA polymerase enzyme that has low fidelity, generating many mutations that allow the rapid adaptation of these viruses to different tissue types and host cells. In this work, we use a structure-based approach to engineer mutations in viral polymerases and study their effects onin vitronucleotide discrimination as well as virus growth and genome replication fidelity. These results show that mutation rates can be drastically increased or decreased as a result of single mutations at several key residues in the polymerase palm domain, and this can significantly attenuate virus growthin vivo. These findings provide a pathway for developing live attenuated virus vaccines based on engineering the polymerase to reduce virus fitness.

Viral Quasispecies and Lethal Mutagenesis

2016 ◽  
Vol 24 (1) ◽  
pp. 39-48 ◽  
Author(s):  
Esteban Domingo ◽  
Celia Perales
Keyword(s):  
Nucleotide Sequence ◽  
Genetic Information ◽  
Rna Viruses ◽  
Viral Disease ◽  
Mutation Rates ◽  
Current Status ◽  
Viral Quasispecies ◽  
Lethal Mutagenesis ◽  
Dna And Rna ◽  
A Genome

Virology has undergone a profound transformation with the incorporation of quasispecies theory to the understanding of the composition and dynamics of viral populations as they cause disease. RNA viral populations do not consist of a genome class with a defined nucleotide sequence but of a cloud or swarm or related mutants due to high mutation rates (number of incorrect nucleotides introduced per nucleotide copied) during replication. DNA and RNA viruses whose multiplication is catalysed by a low fidelity polymerase replicate close to an error threshold for maintenance of their genetic information. This means that modest increases in mutation rate jeopardize their genetic stability. Realization of this important corollary of quasispecies theory has opened new approaches to combating viral disease. One of these approaches is lethal mutagenesis that consists of forcing virus extinction by an excess of mutations evoked by virus-specific mutagenic agents. This article summarizes the origin and current status of this new antiviral approach.

scholarly journals Fitness landscape analysis reveals that the wild type allele is sub-optimal and mutationally robust

2021 ◽  
Author(s):  
Tzahi Gabzi ◽  
Yitzhak Tzachi Pilpel ◽  
Tamar Friedlander
Keyword(s):  
Mutation Rate ◽  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Fitness Landscape ◽  
Mutation Rates ◽  
Wild Type Allele ◽  
Wild Type ◽  
Type Allele ◽  
Landscape Mapping ◽  
Evolutionary Trajectories

Fitness landscape mapping and the prediction of evolutionary trajectories on these landscapes are major tasks in evolutionary biology research. Evolutionary dynamics is tightly linked to the landscape topography, but this relation is not straightforward. Models predict different evolutionary outcomes depending on mutation rates: high-fitness genotypes should dominate the population under low mutation rates and lower-fitness, mutationally robust (also called 'flat') genotypes - at higher mutation rates. Yet, so far, flat genotypes have been demonstrated in very few cases, particularly in viruses. The quantitative conditions for their emergence were studied only in simplified single-locus, two-peak landscapes. In particular, it is unclear whether within the same genome some genes can be flat while the remaining ones are fit. Here, we analyze a previously measured fitness landscape of a yeast tRNA gene. We found that the wild type allele is sub-optimal, but is mutationally robust ('flat'). Using computer simulations, we estimated the critical mutation rate in which transition from fit to flat allele should occur for a gene with such characteristics. We then used a scaling argument to extrapolate this critical mutation rate for a full genome, assuming the same mutation rate for all genes. Finally, we propose that while the majority of genes are still selected to be fittest, there are a few mutation hot-spots like the tRNA, for which the mutationally robust flat allele is favored by selection.

scholarly journals Picornavirus RNA Recombination Counteracts Error Catastrophe

2019 ◽  
Vol 93 (14) ◽  
Author(s):  
Brian J. Kempf ◽  
Colleen L. Watkins ◽  
Olve B. Peersen ◽  
David J. Barton
Keyword(s):  
Rna Viruses ◽  
Rna Replication ◽  
Viral Rna ◽  
Common Mechanism ◽  
Negative Consequences ◽  
Rna Recombination ◽  
Viral Polymerase ◽  
Advantages And Disadvantages ◽  
Error Catastrophe ◽  
Positive Strand Rna

ABSTRACTTemplate-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.IMPORTANCEPositive-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.

scholarly journals Phylogenetic Evidence for the Rapid Evolution of Human B19 Erythrovirus

2006 ◽  
Vol 80 (7) ◽  
pp. 3666-3669 ◽  
Author(s):  
Laura A. Shackelton ◽  
Edward C. Holmes
Keyword(s):  
Host Cell ◽  
Evolutionary Dynamics ◽  
Rna Viruses ◽  
Rapid Evolution ◽  
Evolutionary Change ◽  
High Rate ◽  
Mutation Rates ◽  
Genome Replication ◽  
Nucleotide Substitutions ◽  
Viral Pathogen

ABSTRACT Human B19 erythrovirus is a ubiquitous viral pathogen, commonly infecting individuals before adulthood. As with all autonomous parvoviruses, its small single-stranded DNA genome is replicated with host cell machinery. While the mechanism of parvovirus genome replication has been studied in detail, the rate at which B19 virus evolves is unknown. By inferring the phylogenetic history and evolutionary dynamics of temporally sampled B19 sequences, we observed a surprisingly high rate of evolutionary change, at approximately 10−4 nucleotide substitutions per site per year. This rate is more typical of RNA viruses and suggests that high mutation rates are characteristic of the Parvoviridae.

scholarly journals Viral RNA Mutations Are Region Specific and Increased by Ribavirin in a Full-Length Hepatitis C Virus Replication System

2002 ◽  
Vol 76 (17) ◽  
pp. 8505-8517 ◽  
Author(s):  
Ana Maria Contreras ◽  
Yoichi Hiasa ◽  
Wenping He ◽  
Adam Terella ◽  
Emmett V. Schmidt ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Rna Viruses ◽  
Full Length ◽  
Mutation Rates ◽  
Hcv Rna ◽  
Nucleotide Substitutions ◽  
Replication System ◽  
Error Catastrophe

ABSTRACT High rates of genetic variation ensure the survival of RNA viruses. Although this variation is thought to result from error-prone replication, RNA viruses must also maintain highly conserved genomic segments. A balance between conserved and variable viral elements is especially important in order for viruses to avoid “error catastrophe.” Ribavirin has been shown to induce error catastrophe in other RNA viruses. We therefore used a novel hepatitis C virus (HCV) replication system to determine relative mutation frequencies in variable and conserved regions of the HCV genome, and we further evaluated these frequencies in response to ribavirin. We sequenced the 5′ untranslated region (5′ UTR) and the core, E2 HVR-1, NS5A, and NS5B regions of replicating HCV RNA isolated from cells transfected with a T7 polymerase-driven full-length HCV cDNA plasmid containing a cis-acting hepatitis delta virus ribozyme to control 3′ cleavage. We found quasispecies in the E2 HVR-1 and NS5B regions of untreated replicating viral RNAs but not in conserved 5′ UTR, core, or NS5A regions, demonstrating that important cis elements regulate mutation rates within specific viral segments. Neither T7-driven replication nor sequencing artifacts produced these nucleotide substitutions in control experiments. Ribavirin broadly increased error generation, especially in otherwise invariant regions, indicating that it acts as an HCV RNA mutagen in vivo. Similar results were obtained in hepatocyte-derived cell lines. These results demonstrate the potential utility of our system for the study of intrinsic factors regulating genetic variation in HCV. Our results further suggest that ribavirin acts clinically by promoting nonviable HCV RNA mutation rates. Finally, the latter result suggests that our replication model may be useful for identifying agents capable of driving replicating virus into error catastrophe.

scholarly journals Favipiravir elicits antiviral mutagenesis during virus replication in vivo

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Armando Arias ◽  
Lucy Thorne ◽  
Ian Goodfellow
Keyword(s):  
Cell Culture ◽  
Viral Load ◽  
Infectious Virus ◽  
Viral Infections ◽  
Rna Viruses ◽  
Mutation Rates ◽  
Lethal Mutagenesis ◽  
Antiviral Nucleoside ◽  
Proof Of Principle

Lethal mutagenesis has emerged as a novel potential therapeutic approach to treat viral infections. Several studies have demonstrated that increases in the high mutation rates inherent to RNA viruses lead to viral extinction in cell culture, but evidence during infections in vivo is limited. In this study, we show that the broad-range antiviral nucleoside favipiravir reduces viral load in vivo by exerting antiviral mutagenesis in a mouse model for norovirus infection. Increased mutation frequencies were observed in samples from treated mice and were accompanied with lower or in some cases undetectable levels of infectious virus in faeces and tissues. Viral RNA isolated from treated animals showed reduced infectivity, a feature of populations approaching extinction during antiviral mutagenesis. These results suggest that favipiravir can induce norovirus mutagenesis in vivo, which in some cases leads to virus extinction, providing a proof-of-principle for the use of favipiravir derivatives or mutagenic nucleosides in the clinical treatment of noroviruses.

Sign in / Sign up

Export Citation Format

Share Document