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Genetic divergence of Chikungunya virus plaque variants from the Comoros Island (2005)

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Abstract

Chikungunya virus (CHIKV) from a human sample collected during the 2005 Chikungunya outbreak in the Comoros Island, showed distinct and reproducible large (L2) and small (S7) plaques which were characterized in this study. The parent strain and plaque variants were analysed by in vitro growth kinetics in different cell lines and their genetic similarity assessed by whole genome sequencing, comparative sequence alignment and phylogenetic analysis. In vitro growth kinetic assays showed similar growth patterns of both plaque variants in Vero cells but higher viral titres of S7 compared to L2 in C6/36 cells. Amino acids (AA) alignments of the CHIKV plaque variants and S27 African prototype strain, showed 30 AA changes in the non-structural proteins (nsP) and 22 AA changes in the structural proteins. Between L2 and S7, only two AAs differences were observed. A missense substitution (C642Y) of L2 in the nsP2, involving a conservative AA substitution and a nonsense substitution (R524X) of S7 in the nsP3, which has been shown to enhance O’nyong-nyong virus infectivity and dissemination in Anopheles mosquitoes. The phenotypic difference observed in plaque size could be attributed to one of these AA substitutions. Phylogenetic analysis showed that the parent strain and its variants clustered closely together with each other and with Indian Ocean CHIKV strains indicating circulation of isolates with close evolutionary relatedness in the same outbreak. These observations pave way for important functional studies to understand the significance of the identified genetic changes in virulence and viral transmission in mosquito and mammalian hosts.

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References

  1. K. Sergon, C. Njuguna, R. Kalani, V. Ofula, C. Onyango, L.S. Konongoi, S. Bedno, H. Burke, A.M. Dumilla, J. Konde, M.K. Njenga, R. Sang, R.F. Breiman, Seroprevalence of Chikungunya virus (CHIKV) infection on Lamu Island, Kenya, October 2004. Am. J. Trop. Med. Hyg. 78, 333–337 (2008)

    PubMed  Google Scholar 

  2. K. Sergon, A.A. Yahaya, J. Brown, S.A. Bedja, M. Mlindasse, N. Agata, Y. Allaranger, M.D. Ball, A.M. Powers, V. Ofula, C. Onyango, L.S. Konongoi, R. Sang, M.K. Njenga, R.F. Breiman, Seroprevalence of Chikungunya virus infection on Grande Comore Island, union of the Comoros Island, 2005. Am. J. Trop. Med. Hyg. 76, 1189–1193 (2007)

    PubMed  Google Scholar 

  3. A.M. Powers, Genomic evolution and phenotypic distinctions of Chikungunya viruses causing the Indian Ocean outbreak. Exper. Biol. Med. 236, 909–914 (2011)

    Article  CAS  Google Scholar 

  4. C.K. Lim, T. Nishibori, K. Watanabe, M. Ito, A. Kotaki, K. Tanaka, I. Kurane, T. Takasaki, Chikungunya virus isolated from a returnee to Japan from Sri Lanka: isolation of two sub-strains with different characteristics. Am. J. Trop. Med. Hyg. 81, 865–868 (2009)

    Article  PubMed  Google Scholar 

  5. E. Warner, J. Garcia-Diaz, G. Balsamo, S. Shranatan, A. Bergmann, L. Blauwet, M. Sohail, L. Baddour, C. Reed, Chikungunya fever diagnosed among international travellers—United States, 2005–2006. MMWR Morb. Mortal. Wkly. Rep. 55, 1040–1042 (2006)

    Google Scholar 

  6. H.C. Hapuarachchi, K.B. Bandara, S.D. Sumanadasa, M.D. Hapugoda, Y.L. Lai, K.S. Lee, L.K. Tan, R.T. Lin, L.F. Ng, G. Bucht, W. Abeyewickreme, L.C. Ng, Re-emergence of Chikungunya virus in South-east Asia: virological evidence from Sri Lanka and Singapore. J. Gen. Virol. 91, 1067–1076 (2010)

    Article  CAS  PubMed  Google Scholar 

  7. K.A. Tsetsarkin, D.L. Vanlandingham, C.E. McGee, S. Higgs, A single mutation in chikungunya virus affects vector specificity and epidemic potential. PLoS Pathog. 3, e201 (2007)

    Article  PubMed Central  PubMed  Google Scholar 

  8. 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, Two Chikungunya isolates from the outbreak of La Reunion (Indian Ocean) exhibit different patterns of infection in the mosquito, Aedes albopictus. PLoS. One. 2, e1168 (2007)

    Article  PubMed Central  PubMed  Google Scholar 

  9. I. Nagata, Y. Kimura, T. Matsumoto, K. Maeno, S. Yoshii, Y. Nagai, M. Iinuma, Plaque variants by Sindbis virus. Arch. Gesamte. Virusforsch. 22, 78–86 (1967)

    Article  CAS  PubMed  Google Scholar 

  10. N.M. Tauraso, Identification of two plaque variants of Guaroa virus. Arch. Virol. 28, 212–218 (1969)

    CAS  Google Scholar 

  11. C. Odhiambo, M. Venter, K. Limbaso, R. Swanepoel, R. Sang, Genome sequence analysis of in vitro and in vivo phenotypes of Bunyamwera and Ngari Virus isolates from Northern Kenya. PLoS One 9, e105446 (2014)

    Article  PubMed Central  PubMed  Google Scholar 

  12. H. Kinoshita, E.G. Mathenge, N.T. Hung, V.T. Huong, A. Kumatori, F. Yu, M.C. Parquet, S. Inoue, R.R. Matias, F.F. Natividad, K. Morita, F. Hasebe, Isolation and characterization of two phenotypically distinct dengue type-2 virus isolates from the same dengue hemorrhagic fever patient. Jpn. J. Infect. Dis. 62, 343–350 (2009)

    CAS  PubMed  Google Scholar 

  13. Y.G. Li, U. Siripanyaphinyo, U. Tumkosit, N. Noranate, A. Nuegoonpipat, R. Tao, T. Kurosu, K. Ikuta, N. Takeda, S. Anantapreecha, Chikungunya virus induces a more moderate cytopathic effect in mosquito cells than in mammalian cells. Intervirology 56, 6–12 (2013)

    Article  PubMed  Google Scholar 

  14. N. Wikan, P. Sakoonwatanyoo, S. Ubol, S. Yoksan, D.R. Smith, Chikungunya virus infection of cell lines: analysis of the East, Central and South African lineage. PLoS One 7, e31102 (2012)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  15. K.B. Sundstrom, M. Stoltz, N. Lagerqvist, A. Lundkvist, K. Nemirov, J. Klingstrom, Characterization of two substrains of Puumala virus that show phenotypes that are different from each other and from the original strain. J. Virol. 85, 1747–1756 (2011)

    Article  PubMed Central  PubMed  Google Scholar 

  16. I. Schuffenecker, I. Iteman, A. Michault, S. Murri, L. Frangeul, M.C. Vaney, R. Lavenir, N. Pardigon, J.M. Reynes, F. Ppettinelli, L. Biscornet, L. Diancourt, S. Michael, S. Duquerroy, G. Guegon, M.P. Frenkiel, A.C. Breihen, N. Cubito, P. Despres, F. Kunst, F. Rey, H. Zeller, S. Brisse, Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med. 3, e263 (2006)

    Article  PubMed Central  PubMed  Google Scholar 

  17. E.G. Strauss, R. Levinson, C.M. Rice, J. Dalrymple, J.H. Strauss, Nonstructural proteins nsP3 and nsP4 of Ross River and O’Nyong-nyong viruses: sequence and comparison with those of other alphaviruses. J. Virol. 164, 265–274 (1988)

    Article  CAS  Google Scholar 

  18. K. Myles, C. Kelly, J. Ledermann, A. Powers, Effects of an opal termination codon preceding the nsP4 gene sequence in the O’Nyong-Nyong virus genome on Anopheles gambiae infectivity. J. Virol. 80, 4992–4997 (2006)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. A.M. Powers, A.C. Brault, R.B. Tesh, S.C. Weaver, Re-emergence of Chikungunya and O’nyong-nyong viruses: evidence for distinct geographical lineages and distant evolutionary relationships. J. Gen. Virol. 81, 471–479 (2000)

    Article  CAS  PubMed  Google Scholar 

  20. M. Enserink, Chikungunya: no longer a third world disease. Science 318, 1860–1861 (2007)

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The project was funded by the Consortium for National Health Research (CNHR), Kenya (Project Number RLG09-001/031). This study was also supported with reagents and equipment by JICA-JSPS Project and JICA-JST-SATREPS Project. We acknowledge the Biosciences Eastern and Central Africa - International Livestock Research Institute’s (BecA-ILRI-Hub) genomics platform for supporting the sequencing work. We also appreciate the support given by the Government of the Comoros Island. This work was submitted with the permission of the Director, KEMRI, Nairobi, Kenya.

Author contributions

CW, SI contributed in the laboratory work, data analysis and drafted the manuscript. CR, GM participated in sequencing the variants and data analysis; JK and JO contributed in study design and data analysis. RS and LM contributed to study design, data analysis, overall supervision, implementation and management of the project. All authors reviewed and approved the final manuscript.

Disclaimers

The views expressed are not to be considered as official, or as reflecting the views of USAMRU-K, the Walter Reed Army Institute of Research or the United States Departments of the Army or Defence.

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Authors and Affiliations

  1. Department of Biochemistry, University of Nairobi, P. O. Box 30197-00100, Nairobi, Kenya

    Caroline Wasonga

  2. Arbovirus/Viral Haemorrhagic Fever Laboratory, Kenya Medical Research Institute (KEMRI), P. O. Box 54840-00200, Nairobi, Kenya

    Caroline Wasonga & Rosemary Sang

  3. Production Department, Kenya Medical Research Institute (KEMRI), P. O. Box 54840-00200, Nairobi, Kenya

    James Kimotho

  4. Department of Virology, Institute of Tropical Medicine, Nagasaki University, 1-12-4, Sakamoto, Nagasaki, 852-8523, Japan

    Shingo Inoue

  5. Department of Biological Sciences, International Livestock Research Institute, P. O. Box 3079- 00100, Nairobi, Kenya

    Cecilia Rumberia & George Michuki

  6. Medical Laboratory Sciences Department, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya

    Juliette R. Ongus

  7. Molecular Biology and Bioinformatics Unit, International Centre of Insect Physiology and Ecology, P. O. Box 30772 - 00100, Nairobi, Kenya

    Juliette R. Ongus

  8. Department of Emerging Infectious Diseases, United States Army Medical Research Unit - Kenya, P. O. Box 606 - 00621, Village Market, Nairobi, Kenya

    Lillian Musila

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  1. Caroline Wasonga
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  2. Shingo Inoue
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  3. Cecilia Rumberia
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  4. George Michuki
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  6. Juliette R. Ongus
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  7. Rosemary Sang
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Correspondence to Caroline Wasonga.

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Edited by Keizo Tomonaga.

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Wasonga, C., Inoue, S., Rumberia, C. et al. Genetic divergence of Chikungunya virus plaque variants from the Comoros Island (2005). Virus Genes 51, 323–328 (2015). https://doi.org/10.1007/s11262-015-1243-4

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  • DOI: https://doi.org/10.1007/s11262-015-1243-4

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