Transient RNA structures cause aberrant influenza virus replication and innate immune activation

Hollie French, Emmanuelle Pitré, Michael S. Oade, Elizaveta Elshina, Karishma Bisht, Alannah King, David L.V. Bauer, Aartjan J.W. te Velthuis

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


During infection, the influenza A virus RNA polymerase produces both full-length and aberrant RNA molecules, such as defective viral genomes (DVGs) and mini viral RNAs (mvRNAs). Subsequent innate immune activation involves the binding of host pathogen receptor retinoic acid–inducible gene I (RIG-I) to viral RNAs. However, it is not clear what factors determine which influenza A virus RNAs are RIG-I agonists. Here, we provide evidence that RNA structures, called template loops (t-loops), stall the viral RNA polymerase and contribute to innate immune activation by mvRNAs during influenza A virus infection. Impairment of replication by t-loops depends on the formation of an RNA duplex near the template entry and exit channels of the RNA polymerase, and this effect is enhanced by mutation of the template exit path from the RNA polymerase active site. Overall, these findings are suggestive of a mechanism involving polymerase stalling that links aberrant viral replication to the activation of the innate immune response.

Original languageEnglish (US)
Article numbereabp8655
JournalScience Advances
Issue number36
StatePublished - Sep 2022

All Science Journal Classification (ASJC) codes

  • General


Dive into the research topics of 'Transient RNA structures cause aberrant influenza virus replication and innate immune activation'. Together they form a unique fingerprint.

Cite this