Academic
Publications
Genetic characterization of 2006–2008 isolates of Chikungunya virus from Kerala, South India, by whole genome sequence analysis

Genetic characterization of 2006–2008 isolates of Chikungunya virus from Kerala, South India, by whole genome sequence analysis,10.1007/s11262-009-041

Genetic characterization of 2006–2008 isolates of Chikungunya virus from Kerala, South India, by whole genome sequence analysis   (Citations: 3)
BibTex | RIS | RefWorks Download
Chikungunya virus (CHIKV), a positive-stranded alphavirus, causes epidemic febrile infections characterized by severe and prolonged arthralgia. In the present study, six CHIKV isolates (2006 RGCB03, RGCB05; 2007 RGCB80, RGCB120; 2008 RGCB355, RGCB356) from three consecutive Chikungunya outbreaks in Kerala, South India, were analyzed for genetic variations by sequencing the 11798 bp whole genome of the virus. A total of 37 novel mutations were identified and they were predominant in the 2007 and 2008 isolates among the six isolates studied. The previously identified E1 A226V critical mutation, which enhances mosquito adaptability, was present in the 2007 and 2008 samples. An important observation was the presence of two coding region substitutions, leading to nsP2 L539S and E2 K252Q change. These were identified in three isolates (2007 RGCB80 and RGCB120; 2008 RGCB355) by full-genome analysis, and also in 13 of the 31 additional samples (42%), obtained from various parts of the state, by sequencing the corresponding genomic regions. These mutations showed 100% co-occurrence in all these samples. In phylogenetic analysis, formation of a new genetic clade by these isolates within the East, Central and South African (ECSA) genotypes was observed. Homology modeling followed by mapping revealed that at least 20 of the identified mutations fall into functionally significant domains of the viral proteins and are predicted to affect protein structure. Eighteen of the identified mutations in structural proteins, including the E2 K252Q change, are predicted to disrupt T-cell epitope immunogenicity. Our study reveals that CHIK virus with novel genetic changes were present in the severe Chikungunya outbreaks in 2007 and 2008 in South India.
Journal: Virus Genes , vol. 40, no. 1, pp. 14-27, 2010
Cumulative Annual
View Publication
The following links allow you to view full publications. These links are maintained by other sources not affiliated with Microsoft Academic Search.
    • ...Kerala, in South India, was one among the worst affected states [11-14]...
    • ...Recent studies carried out in CHIKV from Kerala [11,12,14] have revealed novel genetic changes in the virus isolates from 2006-2008 outbreaks...
    • ...Single-step RT PCR was done using 10 μl of the isolated RNA from all the samples using Fidelitaq RT-PCR kit (USB, Cleveland, Ohio), as previously described [14]...
    • ...PCR primers (Table 1; Figure 2) for CHIKV detection PCR were designed based on earlier reports [16] and on the conserved genomic regions of local strains of CHIKV [14]...
    • ...Selected regions of the CHIKV genome (nucleotide position, with respect to S27 reference sequence AF369024: nsP2 3134-3636; E2 8832-9332; E1 10246-10539; Table 1; Figure 2) were amplified by RT PCR as described above using new sets of primers (Table1; Figure 2). These specific regions were chosen as they showed nucleotide variability and novel mutations in our previous study with the local strains of CHIKV [14], making them suitable for ...
    • ...flasks, as per standardized protocols [14]...
    • ...Analysis of the partial nucleotide sequences of nsP2 (378 bp; position 3246-3623), E1 (position 10427-10931) and E2 (position 8893- 9320) revealed a few random nucleotide changes in the CHKV isolates studied (Additional File 1) with respect to the corresponding sequences of the previous isolates from Kerala [14]...
    • ...The E1 sequence of all the strains had the C10670T substitution resulting in the A226V mutation identified in the recent isolates of CHIKV [3,14]...
    • ...The gene sequences of CHIKV obtained from mosquito and patient samples formed a close cluster, distinct from the strains isolated previously from Kerala [14], rest of India and other parts of the world...
    • ...Both the mutations were present in the isolates in this study and also in the recent Indian isolates [10,12,14] (Figure 5). Interestingly, the novel mutation in E2 (L210Q) that was detected exclusively in these 2009 CHIKV strains was adjacent to the E2-211 position...
    • ...The results from this study, along with the previous observations [11,12,14], indicate a constant genomic evolution of the CHIKV strains circulating in Kerala...

    Kudukkil P Niyaset al. Molecular characterization of Chikungunya virus isolates from clinical...

Sort by: