Chikungunya virus (CHIKV), an arthropod-borne Alphavirus is responsible for chikungunya disease. Arthralgia and arthritis are the major symptom. Some patients recover early while others for a very long time. This study provides, epidemiology and molecular characterization of three whole-genome sequences of CHIKV and assessed phylogenetic analysis, physiological properties, antigenicity, and B-cell epitope prediction by in silico. We report the clinical epidemiology of 325 suspected patients. Of these, 118 (36.30%) were confirmed CHIKV positive by either PCR or ELISA. Clinical analysis showed joint pain, joint swelling and headache were frequent and significant features. Phylogenie analysis showed the currently circulating strain is in close clustring to Africa, Uganda, and Singapore CHIKV strains. Molecular characterization by WGS was done. Thirty eight amino acid changes in the nonstructural proteins were found with respect to the S27 (ECSA) strain. Of these five located in nsP2. Similarly, 34 amino acid changes in structural proteins were observed. The major change was notice; in E3 protein hydropathicity −0.281 to −0.362, in E2 isoelectric point (pI) 8.24 to 8.37, instability index 66.08 to 71.062, aliphatic index varied from 74.69 to 68.59 and E3 75.79 to 70.05. In nsP1 protein pI varies from 6.62 to 8.04, while no other change was observed in structural and nonstructural protein. The linear B-cell epitopes, position, and number varied with the mutation. The molecular characterizations of WGS demonstrate the observation of protein, antigenicity with respect to the mutation.

中文翻译：

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2016 年印度北部人类病例中基孔肯雅病毒的流行病学和分子特征

基孔肯雅病毒 (CHIKV) 是一种节肢动物传播的甲病毒，是基孔肯雅病的罪魁祸首。关节痛和关节炎是主要症状。一些患者恢复得早，而另一些则恢复很长时间。本研究提供了 CHIKV 的三个全基因组序列的流行病学和分子特征，并通过计算机模拟评估了系统发育分析、生理特性、抗原性和 B 细胞表位预测. 我们报告了 325 名疑似患者的临床流行病学。其中，118 (36.30%) 例经 PCR 或 ELISA 证实为 CHIKV 阳性。临床分析显示关节痛、关节肿胀和头痛是常见且显着的特征。系统发育分析表明，目前流行的毒株与非洲、乌干达和新加坡的 CHIKV 毒株密切相关。通过 WGS 进行分子表征。在 S27 (ECSA) 菌株的非结构蛋白中发现了 38 个氨基酸变化。这五个位于nsP2 中。类似地，观察到结构蛋白中的 34 个氨基酸变化。主要的变化是通知；在E3蛋白质亲水性 -0.281 至 -0.362，在E2等电点 (pI) 8.24 至 8.37，不稳定性指数 66.08 至 71.062，脂肪族指数从 74.69 至 68.59不等，E3 75.79 至 70.05。在nsP1蛋白中，pI 从 6.62 到 8.04 不等，而在结构和非结构蛋白中没有观察到其他变化。线性 B 细胞表位、位置和数量随突变而变化。WGS 的分子特征证明了对突变的蛋白质、抗原性的观察。