Minimal Polymerase-Containing Precursor Required for Chikungunya Virus RNA Synthesis

Alphaviruses pose a growing global health threat, with Chikungunya virus (CHIKV) epidemics ongoing. Although several CHIKV vaccine candidates have progressed to late-stage clinical evaluation, none have yet achieved licensure or widespread availability. The CHIKV nonstructural proteins nsP2 and nsP4 encode essential enzymatic activities that represent key targets for antiviral development, yet the biochemical basis of nsP4 RNA-dependent RNA polymerase (RdRp) activity remains poorly understood. Here, we identify a minimal, functional precursor form of nsP4 derived from the nsP3-nsP4 polyprotein (P34) that is active in a cell-based RNA replicon system. Using synthetic, capped mRNAs, we show that cleavage of P34 by the nsP2 protease is required for robust reporter expression, and that a truncated form retaining only the C-terminal 50 residues of nsP3 (CT50-P34) supports near-wild-type replication. Unexpectedly, ubiquitin-nsP4 fusions failed to substitute for P34, likely reflecting the transient expression supported by our RNA-based system. We propose that precursor forms of nsP4 interact with the nsP1 dodecamer at the site of genome replication, where cleavage activates the RdRp and localization within the nsP1 dodecamer maintains nsP4 in its active conformation. Dissociation from the nsP1 dodecamer triggers a conformational switch to an inactive state. Together, these findings establish a tractable framework for interrogation of the assembly, activation, and regulation of the alphavirus polymerase.