Generation and characterization of infectious clones of chikungunya virus from an Indian strain as a resource towards chikungunya vaccine research

India has witnessed several devastating chikungunya virus (CHIKV) epidemics since 2005. Developing a stable reverse genetic system using Indian CHIKV strains will be paramount to studying the molecular mechanism of CHIKV pathogenesis. We generated the first infectious clone (IC) of an Indian isolate of CHIKV and described the procedure in the present report. The IC was constructed directly using the isolate's RNA/cDNA and was further characterized after rescuing the virus. The IC exhibited characteristics similar to those of the natural isolate, such as cytopathic effect (CPE), plaque morphology, replication kinetics, and neutralization behavior. Using the same isolate, we also developed a stable IC with a reporter gene (mCherry) between double sub-genomic promoters. We further evaluated the feasibility of using this IC to test neutralization potential of CHIKV sera in 97 samples and observed that CHIKV patients' samples from India were able to neutralize this IC significantly better than an Asian genotype IC. With an impetus on vaccine and therapeutics development for CHIKV in recent years, the ICs generated through our study offer a powerful tool for evaluating several aspects of CHIKV pathogenicity and vaccine efficacy.