A Small RNA Enhancer of Viral Polymerase Activity.

Influenza A virus is an unremitting virus that results in significant morbidity and mortality worldwide. Key to the viral life cycle is the RNA-dependent RNA-polymerase, a heterotrimeric complex responsible for both transcription and replication of the segmented genome. Here we demonstrate that the viral polymerase utilizes a small RNA enhancer to regulate enzymatic activity and maintain stoichiometric balance of the viral genome. We demonstrate that IAV synthesizes small viral RNAs (svRNAs) that interact with the viral RdRp in order to promote genome replication in a segment-specific manner. svRNAs localize to the nucleus, the site of IAV replication, are synthesized from the positive sense genomic intermediate, and interact within a novel RNA binding channel of the PA polymerase subunit. Synthetic svRNAs promote polymerase activity in vitro, while loss of svRNA inhibits viral RNA synthesis in a segment-specific manner. Taken together, we mechanistically define svRNA as a small regulatory enhancer RNA, which functions to promote genome replication and maintain segment balance through allosteric modulation of polymerase activity.