Rawat Sumit K, Nema Ram Kumar, Nema Shashwati, Gupta Sudheer, Biswas Debasis
Microbiology, Bundelkhand Medical College, Sagar, IND.
Microbiology, All India Institute of Medical Sciences, Bhopal, IND.
Cureus. 2025 Mar 6;17(3):e80185. doi: 10.7759/cureus.80185. eCollection 2025 Mar.
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 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.
基孔肯雅病毒（CHIKV）因其有再次出现的趋势，在印度及全球引发大规模疫情，已成为一个重大的公共卫生问题。近期的疫情表明该病毒传播迅速、能逃避宿主免疫反应并导致使人衰弱的疾病。尽管在公共卫生监测和病媒控制方面取得了进展，但CHIKV周期性、不可预测的再度流行凸显了我们在理解其分子动态和因地区而异的流行病学模式方面存在的差距。本研究调查了2020年至2023年期间印度中部一家先进的地区三级医疗机构中CHIKV感染的分子和系统发育特征。共从出现与基孔肯雅感染相符症状的患者中采集了1021份血清样本。其中，178份CHIKV IgM检测呈阳性，16份通过逆转录聚合酶链反应（RT-PCR）确诊为CHIKV阳性。然后对PCR阳性样本进行测序以分析整个病毒基因组。使用细菌和病毒生物信息学资源中心（BVBRC）数据库进行基因组注释，并使用分子进化遗传学分析（MEGA）11.0版（美国宾夕法尼亚州立大学，大学公园分校）进行多序列比对（MSA）。系统发育分析表明，流行毒株属于东中非南非（ECSA）基因型内的一个单一分支。通过将这些毒株与印度先前报告的序列进行比较，我们在E1区域发现了显著突变，如S72N、K211E、M269V、D284E、A315V和I317V，这些突变在印度中部和新德里的先前毒株中也有发现。M31I、I54V和S105T等突变以及印度先前报告的A226V突变未出现，这表明我们地区目前流行的CHIKV毒株主要通过……传播。相比之下，2014年之前在非结构区域观察到的突变，如nsP2 - E145D和nsP3 - V376T，在我们的分离株中再次出现。这些发现加深了我们对CHIKV遗传多样性的理解，描绘了当地CHIKV分支的进化及其对印度中部地区流行病学和公共卫生的影响。
