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

Abstract

During infection, the influenza A virus RNA polymerase produces both full-length and aberrant RNA molecules, such as defective viral genomes (DVG) and mini viral RNAs (mvRNA). Subsequent innate immune activation involves the binding of host pathogen receptor retinoic acid-inducible gene I (RIG-I) to viral RNAs. However, not all influenza A virus RNAs are strong RIG-I agonists. Here we show that potent innate immune activation by mvRNAs is determined by transient RNA structures, called template loops (t-loop) that stall the viral RNA polymerase and trigger aberrant RNA synthesis. The effect of t-loops depends on the formation of an RNA duplex near the template entry and exit channels of the RNA polymerase, and their effect is enhanced by mutation of the template exit path from the RNA polymerase active site. Overall, these findings provide a mechanism that links aberrant viral replication to the activation of the innate immune response.

Decoding the Role of Temperature in RNA Virus Infections

“…In vitro incubations of purified IAV RdRp at different temperatures showed that the dissociation rate of the RdRp is higher on the cRNA template than on the vRNA template, providing a putative molecular explanation for the reduced viral replication ( 48 ). Temperature may also affect the interaction of the IAV RdRp with secondary RNA structures in the viral RNA template, as illustrated by a recent study which showed that RNA duplexes can stall the RdRp and these structures may be less stable at higher temperatures ( 90 ) ( Fig. 1A ).…”