Influenza Virus Adaptation PB2-627K Modulates Nucleocapsid Inhibition by the Pathogen Sensor RIG-I

The cytoplasmic RNA helicase RIG-I mediates innate sensing of RNA viruses. The genomes of influenza A virus (FLUAV) are encapsidated by the nucleoprotein and associated with RNA polymerase, posing potential barriers to RIG-I sensing. We show that RIG-I recognizes the 5′-triphosphorylated dsRNA on FLUAV nucleocapsids but that polymorphisms at position 627 of the viral polymerase subunit PB2 modulate RIG-I sensing. Compared to mammalian-adapted PB2-627K, avian FLUAV nucleocapsids possessing PB2-627E are prone to increased RIG-I recognition, and RIG-I-deficiency partially restores PB2-627E virus infection of mammalian cells. Heightened RIG-I sensing of PB2-627E nucleocapsids correlates with previously established lower affinity of 627E-containing PB2 for nucleoprotein and is increased by further nucleocapsid instability. The effect of RIG-I on PB2-627E nucleocapsids is independent of antiviral signaling, suggesting that RIG-I-nucleocapsid binding alone can inhibit infection. These results indicate that RIG-I is a direct avian FLUAV restriction factor and highlight nucleocapsid disruption as an antiviral strategy. [Display omitted] •5′ppp dsRNA panhandle of incoming influenza virus nucleocapsids activates RIG-I•Human-adaptive mutation PB2-627K in the viral polymerase counteracts activation of RIG-I•RIG-I directly inhibits incoming nucleocapsids with the avian PB2-627E signature•Strength of polymerase binding to nucleocapsids determines RIG-I sensitivity RIG-I is a cytoplasmic pathogen recognition receptor that recognizes 5′ppp-dsRNA. Weber et al. show that RIG-I binds the “panhandle” promoter of incoming influenza A viruses and directly inhibits the onset of infection by destabilizing nucleocapsids. Strains with the mammalian-adapted polymerase subunit PB2-627K are more RIG-I resistant than those with avian-adapted PB2-627E.