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Open Access Highly Accessed Short report

Genetic characterization of Chikungunya virus from New Delhi reveal emergence of a new molecular signature in Indian isolates

Jatin Shrinet1, Shanu Jain1, Anil Sharma1, Shashi Shekhar Singh1, Kalika Mathur1, Vandita Rana1, Raj K Bhatnagar1, Bhupendra Gupta2, Rajni Gaind2, Monorama Deb2 and Sujatha Sunil1*

Author Affiliations

1 Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India

2 Vardhman Mahavir Medical College & Safdarjung Hospital, New Delhi, India

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Virology Journal 2012, 9:100  doi:10.1186/1743-422X-9-100

Published: 25 May 2012

Abstract

Background

Chikungunya (CHIK) is currently endemic in South and Central India and exist as co-infections with dengue in Northern India. In 2010, New Delhi witnessed an outbreak of CHIK in the months October-December. This was the first incidence of a dominant CHIK outbreak in Delhi and prompted us to characterize the Delhi virus strains. We have also investigated the evolution of CHIK spread in India.

Findings

Clinical samples were subjected to RT-PCR to detect CHIK viral RNA. The PCR amplified products were sequenced and the resulting sequences were genetically analyzed. Phylogenetic analysis based on partial sequences of the structural proteins E1 and E2 revealed that the viruses in the latest outbreak exhibited ECSA lineage. Two novel mutations, E1 K211E and E2 V264A were observed in all Delhi isolates. In addition, CHIKV sequences from eight states in India were analyzed along with Delhi sequences to map the genetic diversity of CHIKV within the country. Estimates of average evolutionary divergence within states showed varying divergence among the sequences both within the states and between the states. We identified distinct molecular signatures of the different genotypes of CHIKV revealing emergence of a new signature in the New Delhi clade. Statistical analyses and construction of evolutionary path of the virus within the country revealed gradual spread of one specific strain all over the country.

Conclusion

This study has identified unique mutations in the E1 and E2 genes and has revealed the presence of ancestral CHIKV population with maximum diversity circulating in Maharashtra. The study has further revealed the trend of CHIK spread in India since its first report in 1963 and its subsequent reappearance in 2005.

Keywords:
Chikungunya virus; India; Molecular signatures; ECSA lineage; Asian lineage