Low-Fidelity Polymerases of Alphaviruses Recombine at Higher Rates To Overproduce Defective Interfering Particles

Poirier, Enzo Z.; Mounce, Bryan C.; Rozen-Gagnon, Kathryn; Hooikaas, Peter Jan; Stapleford, Kenneth A.; Moratorio, Gonzalo; Vignuzzi, Marco

doi:10.1128/jvi.02921-15

Cited by 61 publications

(79 citation statements)

References 39 publications

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“…In addition, recombination in RNA viruses is not a result of natural selection that in itself creates an advantageous genotype, but rather an effect of a low-fidelity polymerase and high replication rates producing occasional beneficial combinations283435. Recombination is also linked to the production of defective interfering particles (with similar truncated viral genomes as seen here) which propagates and accumulates at high MOIs and attenuates the virus142536. Our findings do not corroborate this.…”

Section: Discussionmentioning

confidence: 56%

Experimental piscine alphavirus RNA recombination in vivo yields both viable virus and defective viral RNA

Petterson

Guo

Evensen

et al. 2016

Sci Rep

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RNA recombination in non-segmented RNA viruses is important for viral evolution and documented for several virus species through in vitro studies. Here we confirm viral RNA recombination in vivo using an alphavirus, the SAV3 subtype of Salmon pancreas disease virus. The virus causes pancreas disease in Atlantic salmon and heavy losses in European salmonid aquaculture. Atlantic salmon were injected with a SAV3 6K-gene deleted cDNA plasmid, encoding a non-viable variant of SAV3, together with a helper cDNA plasmid encoding structural proteins and 6K only. Later, SAV3-specific RNA was detected and recombination of viral RNA was confirmed. Virus was grown from plasmid-injected fish and shown to infect and cause pathology in salmon. Subsequent cloning of PCR products confirming recombination, documented imprecise homologous recombination creating RNA deletion variants in fish injected with cDNA plasmid, corresponding with deletion variants previously found in SAV3 from the field. This is the first experimental documentation of alphavirus RNA recombination in an animal model and provides new insight into the production of defective virus RNA.

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Section: Discussionmentioning

confidence: 56%

Experimental piscine alphavirus RNA recombination in vivo yields both viable virus and defective viral RNA

Petterson

Guo

Evensen

et al. 2016

Sci Rep

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“…The recombination frequency varies as well, for example, being relatively high in nidoviruses (442)(443)(444)(445) and rather low in flaviviruses (185,446). Like the situation with picornaviruses, this frequency in other RNA viruses depends on the fidelity of the RdRP (381). On the one hand, low error and recombination rates endow viral genomes with a greater stability, but on the other hand, they diminish their capacity for recovery in the case of damage.…”

Section: Some Additional Lessons From Other Rna Viruses Positive-stramentioning

confidence: 99%

Emergency Services of Viral RNAs: Repair and Remodeling

Agol

Gmyl

2018

Microbiol Mol Biol Rev

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Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements. This conservatism stems from genetic robustness or mutational tolerance, which is largely due to the functional degeneracy of many protein and RNA elements as well as to negative selection. Another relevant mechanism is the capacity to restore fitness after genetic damages, also based on replicative infidelity. Conversely, error-prone replication is a major tool that ensures viral evolvability. The potential for changes in debilitated genomes is much higher in small populations, because in the absence of stronger competitors low-fit genomes have a choice of various trajectories to wander along fitness landscapes. Thus, low-fit populations are inherently unstable, and it may be said that to run ahead it is useful to stumble. In this report, focusing on picornaviruses and also considering data from other RNA viruses, we review the biological relevance and mechanisms of various alterations of viral RNA genomes as well as pathways and mechanisms of rehabilitation after loss of fitness. The relationships among mutational robustness, resilience, and evolvability of viral RNA genomes are discussed.

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“…We and others have observed correlations between RdRp fidelity and recombination efficiency, with higher fidelity suppressing recombination and vice versa [19][20][21][22][23][24]. An unexpected outcome of this study was the observation that IF-KH and PS-KH PVs exhibit substantially different propensities for recombination in cells ( Figure 3B), in spite of very similar speed and fidelity phenotypes in cells ( Figures 1C and 2C) and in vitro ( Figure 2D).…”

Section: Discussionmentioning

confidence: 52%

“…Further complicating the fidelity-versus-speed question are the recent observations that changes to fidelity also have consequence for the efficiency of recombination [19][20][21][22][23][24]. Increased RdRp fidelity decreases recombination efficiency and vice versa [19][20][21][22][23][24]. It will likely be impossible to attribute a single biochemical property of the RdRp to biological outcome.The most extensively studied PV fidelity mutants encode RdRps with amino acid substitutions at sites remote from the active site.…”

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confidence: 99%

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

Kim

Ellis

Woodman

et al. 2019

Genes

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Using the RNA-dependent RNA polymerase (RdRp) from poliovirus (PV) as our model system, we have shown that Lys-359 in motif-D functions as a general acid in the mechanism of nucleotidyl transfer. A K359H (KH) RdRp derivative is slow and faithful relative to wild-type enzyme. In the context of the KH virus, RdRp-coding sequence evolves, selecting for the following substitutions: I331F (IF, motif-C) and P356S (PS, motif-D). We have evaluated IF-KH, PS-KH, and IF-PS-KH viruses and enzymes. The speed and fidelity of each double mutant are equivalent. Each exhibits a unique recombination phenotype, with IF-KH being competent for copy-choice recombination and PS-KH being competent for forced-copy-choice recombination. Although the IF-PS-KH RdRp exhibits biochemical properties within twofold of wild type, the virus is impaired substantially for recombination in cells. We conclude that there are biochemical properties of the RdRp in addition to speed and fidelity that determine the mechanism and efficiency of recombination. The interwoven nature of speed, fidelity, the undefined property suggested here, and recombination makes it impossible to attribute a single property of the RdRp to fitness. However, the derivatives described here may permit elucidation of the importance of recombination on the fitness of the viral population in a background of constant polymerase speed and fidelity.broad-spectrum therapeutics [2-4] and a target for function/mechanism-based strategies for viral attenuation [5-10]. One function/mechanism of the RdRp that has been targeted most is that required for faithful incorporation of nucleotides [5][6][7][8][9][10]. Changing RdRp fidelity decreases or increases the genetic variation of the viral population, which, in turn, decreases fitness and virulence of the viral population [11][12][13][14][15][16].Known RdRp variants exhibiting a high-fidelity phenotype can also exhibit a reduced speed of nucleotide incorporation, at least at the biochemical level [17]. Replication speed is also a determinant of viral fitness and virulence [18]. So, is it the increased fidelity or decreased speed of nucleotide addition that gives rise to the attenuated phenotype? Further complicating the fidelity-versus-speed question are the recent observations that changes to fidelity also have consequence for the efficiency of recombination [19][20][21][22][23][24]. Increased RdRp fidelity decreases recombination efficiency and vice versa [19][20][21][22][23][24]. It will likely be impossible to attribute a single biochemical property of the RdRp to biological outcome.The most extensively studied PV fidelity mutants encode RdRps with amino acid substitutions at sites remote from the active site. Constructing equivalent substitutions conferring equivalent phenotypes in RdRps other than PV is difficult if not impossible. Our laboratory has therefore pursued active-site-based strategies to manipulate the fidelity, speed, and/or recombination efficiency of the RdRp [25]. We have shown that a lysine (Lys-359 in PV) present in ...

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Low-Fidelity Polymerases of Alphaviruses Recombine at Higher Rates To Overproduce Defective Interfering Particles

Cited by 61 publications

References 39 publications

Experimental piscine alphavirus RNA recombination in vivo yields both viable virus and defective viral RNA

Experimental piscine alphavirus RNA recombination in vivo yields both viable virus and defective viral RNA

Emergency Services of Viral RNAs: Repair and Remodeling

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

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