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

Abstract

BackgroundChikungunya (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.FindingsClinical 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.ConclusionThis 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.

Molecular characterization of dengue and chikungunya virus strains circulating in New Delhi, India

“…With reference to the Indian strains GQ996372/08 and HM159390/09, nucleotide divergence of 1% and 0.5% and protein divergence of up to 1% were detected. The mutations identified in the analyzed sequences were Lys211Glu, Met296Val, As-p284Glu and Val322Ala, all of which have previously been reported (22).…”

Chikungunya Fever Outbreak, Bhutan, 2012

“…Amino acid sequence analyses showed that all 6 Bhutan isolates lack the E1 gene mutations, which led to the A226V E1 protein change found in the Réunion Island 06.49 strain and which are closely associated with a higher transmission rate (Figure 2) ( 10 ). In addition, the 2012 Bhutan strain still retained the E211 amino acid, which is also found in the India 2010 strain ( 11 ). …”

High Efficiency of Temperate Aedes albopictus to Transmit Chikungunya and Dengue Viruses in the Southeast of France

“…In India, circulating CHIKV genotypes belong to the newly introduced ECSA lineage [2]. Two specific mutations, E1-K211E and E2-V264A, were detected in CHIKV strains isolated from New-Delhi revealing the emergence of a new signature in this clade [32]. Thus, other positions in the CHIKV genome exert strong epistatic effects on the E1-A226V substitution responsible for a significant increase in CHIKV transmission by Ae.…”