Molecular Typing of Chikungunya Virus at a Regional Advanced Healthcare Facility in Central India: A Three-Year Prospective Study

Chikungunya virus (CHIKV) has emerged as a significant public health concern due to its tendency to re-emerge, causing massive outbreaks in India and globally. Recent outbreaks demonstrate the virus's ability to spread rapidly, evade the host's immune responses, and lead to debilitating illnesses. Despite advances in public health surveillance and vector control, the cyclical, unpredictable resurgence of CHIKV underscores gaps in our understanding of its molecular dynamics and epidemiological patterns that vary by region. This study investigates the molecular and phylogenetic characteristics of CHIKV infections from 2020 to 2023 at an advanced regional tertiary care facility in Central India. A total of 1,021 serum samples were collected from patients presenting exhibiting symptoms consistent with chikungunya infection. Of these, 178 tested positive for CHIKV IgM, and 16 were confirmed positive for CHIKV by reverse transcription-polymerase chain reaction (RT-PCR). The PCR-positive samples were then sequenced to analyze the entire viral genome. Genome annotation was performed using the Bacterial and Viral Bioinformatics Resource Center (BVBRC) database, and multiple sequence alignment (MSA) was performed using Molecular Evolutionary Genetics Analysis (MEGA) Version 11.0 (Pennsylvania State University, University Park, PA, United States). Phylogenetic analysis revealed that the circulating strains belonged to a single clade within the East-Central-South-African (ECSA) genotype. By comparing these strains with previously reported sequences from India, we identified notable mutations in the E1 region, such as S72N, K211E, M269V, D284E, A315V, and I317V, previously found strains from Central India and New Delhi. Mutations such as M31I, I54V, and S105T, as well as the A226V mutation previously reported in India, were absent, suggesting that the currently circulating CHIKV strains in our region are primarily transmitted through <i>Aedes aegypti</i> <i>.</i> In contrast, mutations previously observed in the nonstructural region before 2014, such as nsP2-E145D and nsP3-V376T, re-emerged in our isolates. These findings enhance our understanding of CHIKV's genetic diversity, delineating the evolution of local CHIKV clades and their implications for regional epidemiology and public health in Central India.