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


RESULTS
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.


CONCLUSIONS
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.
Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
Jatin
J
Shrinet
Shanu
S
Jain
Anil
A
Sharma
Shashi Shekhar
SS
Singh
Kalika
K
Mathur
Vandita
V
Rana
Raj K
RK
Bhatnagar
Bhupendra
B
Gupta
Rajni
R
Gaind
Monorama
M
Deb
Sujatha
S
Sunil
D018354:Alphavirus Infections / Q000453:epidemiology* / Q000821:virology*; D002646:Chikungunya virus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D016000:Cluster Analysis; D004196:Disease Outbreaks; D014644:Genetic Variation; D006801:Humans; D007194:India / Q000453:epidemiology; D020125:Mutation, Missense; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D015678:Viral Structural Proteins / Q000235:genetics
D012367:RNA, Viral; D015678:Viral Structural Proteins