Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses

Richard Janissen, Andrew Woodman, Djoshkun Shengjuler, Thomas Vallet, Kuo Ming Lee, Louis Kuijpers, Ibrahim M. Moustafa, Fiona Fitzgerald, Nynke H. Dekker, More Authors

Research output: Contribution to journalArticleScientificpeer-review

7 Citations (Scopus)
38 Downloads (Pure)


Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics during RNA synthesis using magnetic tweezers, we identify the “backtracked” state as an intermediate used by the RdRp for copy-back RNA synthesis and homologous recombination. Cell-based assays and RNA sequencing (RNA-seq) experiments further demonstrate that the pyrazine-carboxamide ribonucleotide stimulates these processes during infection. These results suggest that pyrazine-carboxamide ribonucleotides do not induce lethal mutagenesis or chain termination but function by promoting template switching and formation of defective viral genomes. We conclude that RdRp-catalyzed intra- and intermolecular template switching can be induced by pyrazine-carboxamide ribonucleotides, defining an additional mechanistic class of antiviral ribonucleotides with potential for broad-spectrum activity.

Original languageEnglish
Pages (from-to)4467-4480.e7
JournalMolecular Cell
Issue number21
Publication statusPublished - 2021

Bibliographical note

Accepted Author Manuscript


  • backtracking
  • copy-back RNA synthesis
  • enterovirus A71
  • favipiravir
  • poliovirus
  • pyrazine-carboxamide analogue
  • recombination
  • RNA-dependent RNA polymerase
  • T-1106
  • template switching


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