Title

Genetic characterization of Chikungunya virus 2009 isolates from South India

Authors

Gopalsamy Sarangan¹, Seema A Nayar², Monika Mani¹, Sudharasana Sundarrajan³, Sathish Sankar⁴, Gunasekaran Palani⁵, Gracy Fathima Selvaraj⁵, Jayachandran Damodharan⁶, Karuppaiah Muthumani⁷, Padma Srikanth^1*

Affiliation

¹Department of Microbiology, Sri Ramachandra Medical College and Research Institute, Chennai, India;

²Department of Microbiology, Trivandrum Medical College, Trivandrum, India;

³Department of Biotechnology, Vellore Institute of Technology, Vellore, India;

⁴Sri Sakthi Amma Institute of Biomedical Research Sri Narayani Hospital and Research Centre, Sripuram, India;

⁵Department of Virology, King Institute of Preventive Medicine, India;

⁶Saveetha Institute of Medical and Technical Sciences, Chennai, India;

⁷The Wistar Institute, Philadelphia, USA.

Email

srikanth_padma@rediffmail.com;

Article Type

Hypothesis

Date

Received February 5, 2018; Revised March 6, 2018; Accepted March 6, 2018; Published March 31, 2018

Chikungunya Virus (CHIKV) is a single stranded positive sense enveloped RNA virus. Re-emergence of CHIKV caused a massive outbreak with severe clinical manifestation affecting multiple organs. The genetic diversity of CHIKV, which caused recurring outbreaks in India, was studied. Blood samples were collected from suspected human cases of CHIKV infection in Chennai, Tamil Nadu and three Northern districts of Kerala in Southern India during the CHIKV outbreak in 2009. A partial E2 gene segment was amplified by RT-PCR. Among 119 samples 37 samples were positive for CHIKV by RT-PCR. Phylogenetic analysis revealed that the isolated sequences belonged to Indian Ocean Lineage (IOL) of ECSA genotype. The mutational analysis revealed the presence of substitutions such as S299N, T312M, A344T, S375T, V386G, W339R and S375P in the current study. In addition, a novel mutation V386G was observed in all the sequences. Two isolates found with unique substitutions W339R and S375P are reported. The structural analysis of the wild type and mutant proteins revealed that the structural changes are accompanied by modification in the intraprotein interactions.

Keywords

Chikungunya virus, partial E2 gene, RT-PCR, substitutions, selection pressure.

Citation

Sarangan et al. Bioinformation 14(3): 106-112 (2018)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.