The 5′-end segment-specific noncoding region of influenza A virus regulates both competitive multi-segment RNA transcription and selective genome packaging during infection

Abstract

The 3′ and 5′ segment-specific noncoding regions (ssNCRs) of influenza A virus (IAV) have long been recognized as critical signals for selective genome packaging. However, their potential roles in other regulatory processes remain largely unexplored. We previously reported that the 3′-end H1-ssNCR, together with its adjacent coding region, primarily determines optimal HA vRNA accumulation in a multi-segment environment. In this study, we further demonstrate that the 5′-end ssNCR plays a dual role in regulating viral RNA transcription in a template-competitive manner and governing vRNA incorporation into progeny virions. These findings reveal previously underappreciated levels of complexity, highlighting that ssNCRs contribute not only to genome packaging but also to the fine-tuning of viral RNA synthesis in multi-segmented negative-strand RNA viruses.