Molecular Characterisation of Clinical Isolates of Chikungunya Virus: A Study from Tertiary Care Hospitals in Southern India

Abstract

Introduction: Indian ocean islands and India have experienced massive severe Chikungunya outbreak from 2005 up till now and then Chikungunya became epidemic in India. The mutations that occurred in E1 gene were responsible for increased infectivity, virulence and host adaptability. It is important to find out the genotype and its probable evolvement and novel mutations in the E1 gene reported during 2006-2009 from the current isolates, which may affect the local protein structure.

Aim: To perform Molecular diagnosis and Molecular Characterisation of Chikungunya virus isolates.

Materials and methods: A total of 33 samples were included in the study. RNA was isolated from 33 serum samples and Real time PCR was carried out. Further, Nested PCR and E1 partial gene sequencing was performed. Phylogenetic analysis, mutational analysis and protein modelling studies were carried out.

Results: Out of 33 samples tested, 31 were found positive for CHIK RNA. Phylogenetic analysis showed that isolates belongs to ECSA genotype and E1K211E, E1M269V and E1D284E mutations were observed from all the isolates.

Conclusion: The isolates may have evolved from ECSA Reunion island strains and identified unique mutations in E1 gene were maintained. These mutations have not affected local protein structure.

Keywords: E1 gene; Mutational analysis; Phylogenetic analysis.

[Table/Fig-1]:

Structure of Chikungunya virus whole genome with arrangement of structural and non structural genes. The location primers marked in E1 gene.

[Table/Fig-4]:

Phylogenetic analysis based on Partial E1 nucleotide sequences and relationship with reference strains. Gene bank accession number for reference strain labelled.

[Table/Fig-6]:

Mapping of mutations positions in E1 gene.