Epidemiology and molecular characterization of chikungunya virus from human cases in North India, 2016

Abstract

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.

Spread of a Novel Indian Ocean Lineage Carrying E1-K211E/E2-V264A of Chikungunya Virus East/Central/South African Genotype across the Indian Subcontinent, Southeast Asia, and Eastern Africa

“…At first, the earliest E1-K211E/E2-V264A IOL strain sparsely circulated in Delhi, Mumbai, and Kerala in India since 2010 [25]. Then, the wide expansion of IOL sub-lineage E1-K211E/E2-V264A occurred after the virus acquired the mutation of E1-I317V associated with the later outbreaks.…”

“…Although IK-b Kenya strains were most closely related to the Indian strains 2014 (KX619422and KX619423), they shared E1-K211E and E2-V264A in common, the long branch between IK-b and New Delhi 2014 suggested possible missing sampling of circulating strains in this gap. In addition, there were nonsynonymous mutations (nsP1-V139I, nsP2-V793I, E1-I344M, E3-T23S) specific to the IK-b clade, indicating a unique evolution of the Kenya 2016 viruses[25].…”

Expression, Purification, and Refolding of Chikungunya Virus Full-Length Envelope E2 Protein along with B-Cell and T-Cell Epitope Analyses Using Immuno-Informatics Approaches

“…Using a bacteriophage Qβ viruslike particle (VLP) platform, Basu et al reported that epitopes spanning 1–18 and 226–259 aa elicited high-titer antibodies and the C-terminal epitope (spanning 378–411 aa) was the least reactive, possibly due to the truncated E2 protein fragment used in this study . In an in silico B-cell epitope prediction study, the epitope residues at 386 and 388 aa positions were predicted to evoke significant immune response . Of note, an immuno-informatics study by Hasan et al reported the peptide region spanning 9 aa from 397 to 405 aa as the most potential B-cell epitope, along with epitopes identified in the N-terminal region (1–29 aa) .…”

“…57 In an in silico B-cell epitope prediction study, the epitope residues at 386 and 388 aa positions were predicted to evoke significant immune response. 58 Of note, an immuno-informatics study by Hasan et al reported the peptide region spanning 9 aa from 397 to 405 aa as the most potential B-cell epitope, along with epitopes identified in the N-terminal region (1−29 aa). 59 Rodriguez et al also predicted B-cell epitopes located in the N-terminal (spanning 14−22 and 27−35 aa) and C-terminal (spanning 367−389 aa) regions, suggesting that the presence of these amino acids in the CHIKV E2-FL protein may be contributing in its increased immunogenicity.…”

Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil

“…The E2-L248F from clade I has been reported in Asian lineage sequences from Colombia (2014-2015) and Philippines (2012) 45,46 . Isolates from Thailand, Indonesia, Lao PDR, Cameroon and India also presented the 6K-I54V mutation observed in clade I 44,[47][48][49][50] .…”