Differential Expression of Defensins and Other Innate Immune Effectors by Indian Isolates of Chikungunya Virus

Chikungunya virus (CHIKV) infection has been associated with heightened disease burden and fatality rate, especially post its resurgence in 2006, with presentation of various atypical symptoms. Its re-emergence and the subsequent periodic outbreaks indicate the constant evolution of the virus due to the incorporation of mutations in its genome. This can potentially elicit a differential induction of innate immune response of varying degrees, which has been poorly studied in the case of CHIKV. Leveraging an immunocompetent epithelial model cell line to define the varying internalization and replication of CHIKV and differential induction of innate immune response effectors, we demonstrate that CHIKV outbreak isolates (CHIKV 2006, 2016, 2022 and 2024 outbreak isolates) have differential internalization and replication dynamics and trigger expression of defensins, interferon lambda (IFN-λ), and microRNAs modulating CHIKV infection, in an isolate-dependent manner. We also observed that CHIKV 2024, despite having the highest internalization efficiency, shows delayed initiation of exponential replication, with an unusual "eclipse phase," spanning up to 18 h post-infection. While protein-protein interaction analysis suggested the potential interaction of DEFA5 and DEFB2 with CHIKV envelope glycoprotein, microRNA hybridization analysis revealed the differential hybridization pattern of microRNAs at the target sites of the genome of CHIKV outbreak isolates, with hsa-miR-214-3p showcasing increased yet sustained binding affinity to the post-2006 outbreak isolates of CHIKV. Overall, our study provides transcriptional insights regarding the isolate-dependent modulation of innate immune response by CHIKV, as a result of its evolutionary adaptation. This work also sheds light on the potential usage of human defensins and microRNAs modulating CHIKV infection as peptide-based and RNA-based therapeutics, respectively.