The role of chikungunya virus capsid-viral RNA interactions in programmed ribosomal frameshifting

Chikungunya virus (CHIKV) is a globally significant arthropod-borne virus that causes outbreaks in tropical and subtropical regions and is rapidly expanding in geographical range. Infection can lead to acute febrile illness with debilitating joint pain that may persist as chronic arthritis. Efficient CHIKV replication and virion assembly rely on coordinated interactions between viral RNA and the capsid protein, a structural component essential for particle formation. In addition to its well-established structural role, the alphavirus capsid protein has been shown in Sindbis virus to bind viral RNA and stabilize the genome, while in New World alphaviruses, it contributes to immune evasion through inhibition of host gene expression. However, its potential regulatory functions in viral RNA processes remain less understood. Here, we show that CHIKV capsid modulates programmed ribosomal frameshifting (PRF) within the 6K/Transframe (TF) region, influencing the balance between structural protein synthesis and TF production. Using a previously engineered CHIKV mutant (9900), which contains silent mutations that reduce capsid binding within 6K/TF, we demonstrate that diminished capsid-vRNA interaction correlates with increased PRF efficiency. This is associated with enhanced viral replication in immune-competent cells, yet this enhanced replication is not further improved by JAK-STAT inhibition, indicating that capsid binding already modulates immune response pathways. These findings identify CHIKV capsid as a potential modulator of PRF, expanding our understanding of alphavirus gene expression and RNA-protein interactions.

The multifunctional roles of the chikungunya virus (CHIKV) capsid protein-particularly its RNA-binding properties and potential to influence translation-represent important aspects of viral replication and pathogenesis. This study focuses on the CHIKV capsid's influence on PRF, a key step in viral protein synthesis. Similar capsid-vRNA binding regions have been described in other alphaviruses, such as Venezuelan equine encephalitis virus (B. D. Carey, I. Akhrymuk, B. Dahal, C. L. Pinkham, et al., PLOS Pathogens 16:e1008282, 2020, https://doi.org/10.1371/journal.ppat.1008282), suggesting that capsid-mediated modulation of translation may represent a partially conserved mechanism across the alphavirus genus. By elucidating a role for capsid in PRF modulation, this study highlights a previously unrecognized layer of gene regulation in alphaviruses with broad implications for immune evasion, viral fitness, and translational control.