Virus Genes

, 40:14 | Cite as

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

  • E. Sreekumar
  • Aneesh Issac
  • Sajith Nair
  • Ramkumar Hariharan
  • M. B. Janki
  • D. S. Arathy
  • R. Regu
  • Thomas Mathew
  • M. Anoop
  • K. P. Niyas
  • M. R. Pillai


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.


Alphavirus Positive-stranded RNA Lineage Virulence Mutations Epitope 



The work was funded by Department of Biotechnology, Govt. of India (Grant No. BT/PR9101/MED/29/04/2007). The authors are thankful to Prof. C.C. Kartha, Professor of Eminence, Cardiovascular Disease Biology, RGCB for critical suggestions. Authors are grateful to the Indian Medical Association, Thiruvananthapuram, and the Department of Health, Govt. of Kerala, for the help rendered during the study.

Supplementary material

11262_2009_411_MOESM1_ESM.pdf (37 kb)
(PDF 36 kb)


  1. 1.
    A.M. Powers, C.H. Logue, J. Gen. Virol. 88, 2363 (2007)CrossRefPubMedGoogle Scholar
  2. 2.
    N. Vasilakis, S.C. Weaver, Adv. Virus. Res. 72, 1 (2008)CrossRefPubMedGoogle Scholar
  3. 3.
    E.A. Gould, T. Solomon, Lancet 371, 500 (2008)CrossRefPubMedGoogle Scholar
  4. 4.
    I. Schuffenecker, I. Iteman, A. Michault, S. Murri, L. Frangeul, M.C. Vaney, R. Lavenir, N. Pardigon, J.M. Reynes, F. Pettinelli, L. Biscornet, L. Diancourt, S. Michel, S. Duquerroy, G. Guigon, M.P. Frenkiel, A.C. Brehin, N. Cubito, P. Despres, F. Kunst, F.A. Rey, H. Zeller, S. Brisse, PLoS Med. 3, e263 (2006)CrossRefPubMedGoogle Scholar
  5. 5.
    G. Rezza, L. Nicoletti, R. Angelini, R. Romi, A.C. Finarelli, M. Panning, P. Cordioli, C. Fortuna, S. Boros, F. Magurano, G. Silvi, P. Angelini, M. Dottori, M.G. Ciufolini, G.C. Majori, A. Cassone, Lancet 370, 1840 (2007)CrossRefPubMedGoogle Scholar
  6. 6.
    S.R. Santhosh, P.K. Dash, M.M. Parida, M. Khan, M. Tiwari, P.V. Lakshmana Rao, Virus Res. 135, 36 (2008)CrossRefPubMedGoogle Scholar
  7. 7.
    K.V. Shah, C.J. Gibbs Jr., G. Banerjee, Indian J. Med. Res. 52, 676 (1964)PubMedGoogle Scholar
  8. 8.
    K. Pavri, Trans. R Soc. Trop. Med. Hyg. 80, 491 (1986)CrossRefPubMedGoogle Scholar
  9. 9.
    D.T. Mourya, J.R. Thakare, M.D. Gokhale, A.M. Powers, S.L. Hundekar, P.C. Jayakumar, V.P. Bondre, Y.S. Shouche, V.S. Padbidri, Acta Virol. 45, 305 (2001)PubMedGoogle Scholar
  10. 10.
    P.N. Yergolkar, B.V. Tandale, V.A. Arankalle, P.S. Sathe, A.B. Sudeep, S.S. Gandhe, M.D. Gokhle, G.P. Jacob, S.L. Hundekar, A.C. Mishra, Emerg. Infect. Dis. 12, 1580 (2006)PubMedGoogle Scholar
  11. 11.
    V.A. Arankalle, S. Shrivastava, S. Cherian, R.S. Gunjikar, A.M. Walimbe, S.M. Jadhav, A.B. Sudeep, A.C. Mishra, J. Gen. Virol. 88, 1967 (2007)CrossRefPubMedGoogle Scholar
  12. 12.
    N.P. Kumar, R. Joseph, T. Kamaraj, P. Jambulingam, J. Gen. Virol. 89, 1945 (2008)CrossRefPubMedGoogle Scholar
  13. 13.
    M. Kannan, R. Rajendran, I.P. Sunish, R. Balasubramaniam, N. Arunachalam, R. Paramsivan, S.C. Tewari, P.P. Samuel, B.K. Tyagi, Indian J. Med. Res. 129, 311 (2009)PubMedGoogle Scholar
  14. 14.
    M. Kielian, M.R. Klimjack, S. Ghosh, W.A. Duffus, J. Cell Biol. 134, 863 (1996)CrossRefPubMedGoogle Scholar
  15. 15.
    J.K. Fazakerley, A. Boyd, M.L. Mikkola, L. Kaariainen, J. Virol. 76, 392 (2002)CrossRefPubMedGoogle Scholar
  16. 16.
    Mayuri, T.W. Geders, J.L. Smith, R.J. Kuhn, J. Virol. 82, 7284 (2008)CrossRefPubMedGoogle Scholar
  17. 17.
    M. Vazeille, S. Moutailler, D. Coudrier, C. Rousseaux, H. Khun, M. Huerre, J. Thiria, J.S. Dehecq, D. Fontenille, I. Schuffenecker, P. Despres, A.B. Failloux, PLoS One 2, e1168 (2007)CrossRefPubMedGoogle Scholar
  18. 18.
    K.A. Tsetsarkin, D.L. Vanlandingham, C.E. McGee, S. Higgs, PLoS Pathog. 3, e201 (2007)CrossRefPubMedGoogle Scholar
  19. 19.
    F. Hasebe, M.C. Parquet, B.D. Pandey, E.G. Mathenge, K. Morita, V. Balasubramaniam, Z. Saat, A. Yusop, M. Sinniah, S. Natkunam, A. Igarashi, J. Med. Virol. 67, 370 (2002)CrossRefPubMedGoogle Scholar
  20. 20.
    T.A. Hall, Nucleic Acids Symp. Ser. 41, 95 (1999)Google Scholar
  21. 21.
    S. Kumar, K. Tamura, M. Nei, Brief Bioinform. 5, 150 (2004)CrossRefPubMedGoogle Scholar
  22. 22.
    N. Guex, M.C. Peitsch, Electrophoresis 18, 2714 (1997)CrossRefPubMedGoogle Scholar
  23. 23.
    L. Willard, A. Ranjan, H. Zhang, H. Monzavi, R.F. Boyko, B.D. Sykes, D.S. Wishart, Nucleic Acids Res. 31, 3316 (2003)CrossRefPubMedGoogle Scholar
  24. 24.
    I.A. Doytchinova, P. Guan, D.R. Flower, BMC Bioinformatics 7, 131 (2006)CrossRefPubMedGoogle Scholar
  25. 25.
    A.B. Sudeep, D. Parashar, J. Biosci. 33, 443 (2008)CrossRefPubMedGoogle Scholar
  26. 26.
    F. Talarmin, F. Staïkowsky, P. Schoenlaub, A. Risbourg, X. Nicolas, A. Zagnoli, P. Boyer, Med. Trop. 67, 167 (2007)Google Scholar
  27. 27.
    J.J. Valamparmpil, S. Chirakkarot, S. Letha, C. Jayakumar, K.M. Gopinathan, Ind. J. Paediatr. 76, 151 (2009)CrossRefGoogle Scholar
  28. 28.
    S.S. Cherian, A.M. Walimbe, S.M. Jadhav, S.S. Gandhe, S.L. Hundekar, A.C. Mishra, V.A. Arankalle, Infect. Genet. Evol. 9, 16 (2009)CrossRefPubMedGoogle Scholar
  29. 29.
    N. Garmashova, R. Gorchakov, E. Frolova, I. Frolov, J. Virol. 80, 5686 (2006)CrossRefPubMedGoogle Scholar
  30. 30.
    K. Tamm, A. Merits, I. Sarand, J. Gen. Virol. 89, 676 (2008)CrossRefPubMedGoogle Scholar
  31. 31.
    A. Golubtsov, L. Kaariainen, J. Caldentey, FEBS Lett. 580, 1502 (2006)CrossRefPubMedGoogle Scholar
  32. 32.
    W. Zhang, S. Mukhopadhyay, S.V. Pletnev, T.S. Baker, R.J. Kuhn, M.G. Rossmann, J. Virol. 76, 11645 (2002)CrossRefPubMedGoogle Scholar
  33. 33.
    S. Mukhopadhyay, W. Zhang, S. Gabler, P.R. Chipman, E.G. Strauss, J.H. Strauss, T.S. Baker, R.J. Kuhn, M.G. Rossmann, Structure 14, 63 (2006)CrossRefPubMedGoogle Scholar
  34. 34.
    M. Kielian, Virology 344, 38 (2006)CrossRefPubMedGoogle Scholar
  35. 35.
    M. Kielian, F.A. Rey, Nat. Rev. Microbiol. 4, 67 (2006)CrossRefPubMedGoogle Scholar
  36. 36.
    T.P. Hopp, K.R. Woods, Proc. Natl Acad. Sci. USA 78, 3824 (1981)CrossRefPubMedGoogle Scholar
  37. 37.
    T.J. Smith, R.H. Cheng, N.H. Olson, P. Peterson, E. Chase, R.J. Kuhn, T.S. Baker, Proc. Natl Acad. Sci. USA 92, 10648 (1995)CrossRefPubMedGoogle Scholar
  38. 38.
    T.A. Wilkinson, T.L. Tellinghuisen, R.J. Kuhn, C.B. Post, Biochemistry 44, 2800 (2005)CrossRefPubMedGoogle Scholar
  39. 39.
    J. West, R. Hernandez, D. Ferreira, D.T. Brown, J. Virol. 80, 4458 (2006)CrossRefPubMedGoogle Scholar
  40. 40.
    J.H. Strauss, E.G. Strauss, Microbiol. Rev. 58, 491 (1994)PubMedGoogle Scholar
  41. 41.
    A.H. Khan, K. Morita, M.C. Parquet, F. Hasebe, E.G.M. Mathenge, A. Igarashi, J. Gen. Virol. 83, 3075 (2002)PubMedGoogle Scholar
  42. 42.
    D. Middleton, F. Williams, Methods Mol. Biol. 210, 67 (2003)PubMedGoogle Scholar
  43. 43.
    J. Sidney, H.M. Grey, S. Southwood, E. Celis, P.A. Wentworth, M.F. del Guercio, R.T. Kubo, R.W. Chesnut, A. Sette, Hum. Immunol. 45, 79 (1996)CrossRefPubMedGoogle Scholar
  44. 44.
    G. Pialoux, B.A. Gauzere, S. Jaureguiberry, M. Strobel, Lancet Infect. Dis. 7, 319 (2007)CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • E. Sreekumar
    • 1
  • Aneesh Issac
    • 1
  • Sajith Nair
    • 1
  • Ramkumar Hariharan
    • 2
  • M. B. Janki
    • 2
  • D. S. Arathy
    • 1
  • R. Regu
    • 3
  • Thomas Mathew
    • 4
  • M. Anoop
    • 1
  • K. P. Niyas
    • 1
  • M. R. Pillai
    • 2
  1. 1.Molecular Virology LaboratoryRajiv Gandhi Centre for Biotechnology (RGCB)ThiruvananthapuramIndia
  2. 2.Translational Cancer Research LaboratoryRajiv Gandhi Centre for Biotechnology (RGCB)ThiruvananthapuramIndia
  3. 3.National Institute of Communicable Diseases (NICD)KozhikkodeIndia
  4. 4.Department of Community MedicineT.D. Medical CollegeAlappuzhaIndia

Personalised recommendations