Senecavirus-specific recombination assays reveal the intimate link between polymerase fidelity and RNA recombination

Chen Li, Haiwei Wang, Jiabao Shi, Decheng Yang, Guohui Zhou, Jitao Chang, Craig Eugene Cameron, Andrew Woodman, Li Yu

Research output: Contribution to journalArticle

Abstract

Senecavirus A (SVA) is a reemerging virus, and recent evidence has emphasized the importance of SVA recombination in vivo on virus evolution. In this study, we report the development of an infectious cDNA clone for the SVA/HLJ/CHA/2016 strain. We used this strain to develop a reporter virus expressing enhanced green fluorescent protein (eGFP), which we then used to screen for a recombination-deficient SVA by an eGFP retention assay. Sequencing of the virus that retained the eGFP following passage allowed us to identify the nonsynonymous mutations (S460L alone and I212V-S460L in combination) in the RNA-dependent RNA polymerase (RdRp) region of the genome. We developed a Senecavirus-specific cell culture-based recombination assay, which we used to elucidate the role of RdRp in SVA recombination. Our results demonstrate that these two polymerase variants (S460L and I212/S460L) have reduced recombination capacity. These results indicate that the RdRp plays a central role in SVA replicative recombination. Notably, our results showed that the two recombination-deficient variants have higher replication fidelity than the wild type (WT) and display decreased ribavirin sensitivity compared to the WT. In addition, these two mutants exhibited significantly increased fitness in vitro compared to the WT. These results demonstrate that recombination and mutation rates are intimately linked. Our results have important implications for understanding the crucial role of the RdRp in virus recombination and fitness, especially in the molecular mechanisms of SVA evolution and pathogenicity.

Original languageEnglish (US)
Article numbere00576-19
JournalJournal of virology
Volume93
Issue number13
DOIs
StatePublished - Jan 1 2019

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DNA-Directed RNA Polymerases
Genetic Recombination
RNA-directed RNA polymerase
RNA
RNA Replicase
assays
viruses
Viruses
green fluorescent protein
mutation
Senecavirus
Ribavirin
Mutation Rate
cell culture
pathogenicity
Virulence
clones
Complementary DNA
Clone Cells
Cell Culture Techniques

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Immunology
  • Insect Science
  • Virology

Cite this

Li, Chen ; Wang, Haiwei ; Shi, Jiabao ; Yang, Decheng ; Zhou, Guohui ; Chang, Jitao ; Cameron, Craig Eugene ; Woodman, Andrew ; Yu, Li. / Senecavirus-specific recombination assays reveal the intimate link between polymerase fidelity and RNA recombination. In: Journal of virology. 2019 ; Vol. 93, No. 13.
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abstract = "Senecavirus A (SVA) is a reemerging virus, and recent evidence has emphasized the importance of SVA recombination in vivo on virus evolution. In this study, we report the development of an infectious cDNA clone for the SVA/HLJ/CHA/2016 strain. We used this strain to develop a reporter virus expressing enhanced green fluorescent protein (eGFP), which we then used to screen for a recombination-deficient SVA by an eGFP retention assay. Sequencing of the virus that retained the eGFP following passage allowed us to identify the nonsynonymous mutations (S460L alone and I212V-S460L in combination) in the RNA-dependent RNA polymerase (RdRp) region of the genome. We developed a Senecavirus-specific cell culture-based recombination assay, which we used to elucidate the role of RdRp in SVA recombination. Our results demonstrate that these two polymerase variants (S460L and I212/S460L) have reduced recombination capacity. These results indicate that the RdRp plays a central role in SVA replicative recombination. Notably, our results showed that the two recombination-deficient variants have higher replication fidelity than the wild type (WT) and display decreased ribavirin sensitivity compared to the WT. In addition, these two mutants exhibited significantly increased fitness in vitro compared to the WT. These results demonstrate that recombination and mutation rates are intimately linked. Our results have important implications for understanding the crucial role of the RdRp in virus recombination and fitness, especially in the molecular mechanisms of SVA evolution and pathogenicity.",
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Senecavirus-specific recombination assays reveal the intimate link between polymerase fidelity and RNA recombination. / Li, Chen; Wang, Haiwei; Shi, Jiabao; Yang, Decheng; Zhou, Guohui; Chang, Jitao; Cameron, Craig Eugene; Woodman, Andrew; Yu, Li.

In: Journal of virology, Vol. 93, No. 13, e00576-19, 01.01.2019.

Research output: Contribution to journalArticle

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AU - Li, Chen

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