Contribution of RNA–RNA interactions mediated by the genome packaging signals for the selective genome packaging of influenza A virus

The influenza A virus genome is composed of eight single-stranded negative-sense RNA segments (vRNAs). The eight vRNAs are selectively packaged into each progeny virion. This process likely involves specific interactions between the vRNAs via segment-specific packaging signals located in both the 3' and 5' terminal regions of the respective vRNAs. To assess the importance of vRNA–vRNA interactions via packaging signals for selective genome packaging, we generated mutant viruses possessing silent mutations in the packaging signal region of the hemagglutinin (HA) vRNA. A mutant virus possessing silent mutations in nucleotides 1664 to 1676 resulted in defects in HA vRNA incorporation and showed a reduction in viral growth. After serial passage, the mutant virus acquired additional mutations in the 5' terminal packaging signal regions of both the HA and polymerase basic 2 (PB2) vRNAs. These mutations contributed to the recovery of viral growth and HA vRNA packaging efficiency. In addition, an RNA–RNA interaction between the 5' ends of HA and PB2 vRNAs was confirmed in vitro , and this interaction was disrupted following the introduction of silent mutations in the HA vRNA. Thus, our results demonstrated that RNA–RNA interactions between the packaging signal regions of HA vRNA and PB2 vRNA are important for selective genome packaging. Importance While numerous viral genomes comprise a single genome segment, the influenza A virus possesses eight segmented genomes. Influenza A virus can benefit from having a segmented genome because the segments can reassort with other strains of the influenza virus to create new genetically distinct strains. The influenza A virus efficiently incorporates one copy of each of its eight genomic segments per viral particle. However, the mechanism by which each segment is specifically selected is poorly understood. The genome segments contain RNA signals that facilitate the incorporation of segments into virus particles. These regions may facilitate specific interactions between the genome segments, creating an eight-segment complex, which can then be packaged into individual particles. In this study, we provide evidence that RNA signals contribute to specific interactions between two of the influenza virus genome segments.