Isolation of fidelity variants of RNA viruses and characterization of virus mutation frequency

Stéphanie Beaucourt, Antonio V. Bordería, Lark L Schneider, Nina F. Gnädig, Marta Sanz-Ramos, Yasnee Beeharry, Marco Vignuzzi

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

RNA viruses use RNA dependent RNA polymerases to replicate their genomes. The intrinsically high error rate of these enzymes is a large contributor to the generation of extreme population diversity that facilitates virus adaptation and evolution. Increasing evidence shows that the intrinsic error rates, and the resulting mutation frequencies, of RNA viruses can be modulated by subtle amino acid changes to the viral polymerase. Although biochemical assays exist for some viral RNA polymerases that permit quantitative measure of incorporation fidelity, here we describe a simple method of measuring mutation frequencies of RNA viruses that has proven to be as accurate as biochemical approaches in identifying fidelity altering mutations. The approach uses conventional virological and sequencing techniques that can be performed in most biology laboratories. Based on our experience with a number of different viruses, we have identified the key steps that must be optimized to increase the likelihood of isolating fidelity variants and generating data of statistical significance. The isolation and characterization of fidelity altering mutations can provide new insights into polymerase structure and function1-3. Furthermore, these fidelity variants can be useful tools in characterizing mechanisms of virus adaptation and evolution4-7.

Original languageEnglish (US)
Article numbere2953
JournalJournal of Visualized Experiments
Issue number52
DOIs
StatePublished - Jun 2011
Externally publishedYes

Fingerprint

RNA Viruses
Mutation Rate
RNA
Viruses
RNA Replicase
Mutation
Viral RNA
DNA-Directed RNA Polymerases
Genome
Amino Acids
Enzymes
Population
Amino acids
Assays
Genes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemical Engineering(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)

Cite this

Beaucourt, S., Bordería, A. V., Schneider, L. L., Gnädig, N. F., Sanz-Ramos, M., Beeharry, Y., & Vignuzzi, M. (2011). Isolation of fidelity variants of RNA viruses and characterization of virus mutation frequency. Journal of Visualized Experiments, (52), [e2953]. https://doi.org/10.3791/2953

Isolation of fidelity variants of RNA viruses and characterization of virus mutation frequency. / Beaucourt, Stéphanie; Bordería, Antonio V.; Schneider, Lark L; Gnädig, Nina F.; Sanz-Ramos, Marta; Beeharry, Yasnee; Vignuzzi, Marco.

In: Journal of Visualized Experiments, No. 52, e2953, 06.2011.

Research output: Contribution to journalArticle

Beaucourt, Stéphanie ; Bordería, Antonio V. ; Schneider, Lark L ; Gnädig, Nina F. ; Sanz-Ramos, Marta ; Beeharry, Yasnee ; Vignuzzi, Marco. / Isolation of fidelity variants of RNA viruses and characterization of virus mutation frequency. In: Journal of Visualized Experiments. 2011 ; No. 52.
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