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This study provides, epidemiology and molecular characterization of three whole\u2010genome sequences of CHIKV and assessed phylogenetic analysis, physiological properties, antigenicity, and B\u2010cell epitope prediction by <jats:italic>in silico<\/jats:italic>. 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 <jats:italic>nsP2<\/jats:italic>. Similarly, 34 amino acid changes in structural proteins were observed. The major change was notice; in <jats:italic>E3<\/jats:italic> protein hydropathicity \u22120.281 to \u22120.362, in <jats:italic>E2<\/jats:italic> 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 <jats:italic>E3<\/jats:italic> 75.79 to 70.05. In <jats:italic>nsP1<\/jats:italic> protein pI varies from 6.62 to 8.04, while no other change was observed in structural and nonstructural protein. The linear B\u2010cell epitopes, position, and number varied with the mutation. The molecular characterizations of WGS demonstrate the observation of protein, antigenicity with respect to the mutation.<\/jats:p>","DOI":"10.1111\/1348-0421.12869","type":"journal-article","created":{"date-parts":[[2020,12,22]],"date-time":"2020-12-22T13:15:50Z","timestamp":1608642950000},"page":"290-301","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Epidemiology and molecular characterization of chikungunya virus from human cases in North India, 2016"],"prefix":"10.1111","volume":"65","author":[{"given":"Naushad","family":"Khan","sequence":"first","affiliation":[{"name":"Department of Biotechnology Jamia Hamdard  New Delhi India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruchika","family":"Bhat","sequence":"additional","affiliation":[{"name":"Department of Chemistry Indian Institute of Technology Delhi  New Delhi 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