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Advanced Genetic Methodologies in Tracking Evolution and Spread of Chikungunya Virus

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Chikungunya Virus

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1426))

Abstract

Recent advances in genetic methodologies have substantially expanded our ability to track evolution and spatio-temporal distribution of rapidly evolving pathogens. The information gathered from such analyses can be used to decipher host adaptations that shape disease epidemiology. In this chapter, we demonstrate the utilization of freely available resources to track the evolution and spread of Chikungunya virus.

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References

  1. KariukiNjenga M, Nderitu L, Ledermann JP, Ndirangu A, Logue CH, Kelly CH, Sang R, Sergon K, Breiman R, Powers AM (2008) Tracking epidemic Chikungunya virus into the Indian Ocean from East Africa. J Gen Virol 89(Pt 11):2754–2760

    Article  CAS  Google Scholar 

  2. Schuffenecker I, Iteman I, Michault A, Murri S, Frangeul L, Vaney MC, Lavenir R, Pardigon N, Reynes JM, Pettinelli F, Biscornet L, Diancourt L, Michel S, Duquerroy S, Guigon G, Frenkiel MP, Brehin AC, Cubito N, Despres P, Kunst F, Rey FA, Zeller H, Brisse S (2006) Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med 3(7):e263

    Article  PubMed  PubMed Central  Google Scholar 

  3. Arankalle VA, Shrivastava S, Cherian S, Gunjikar RS, Walimbe AM, Jadhav SM, Sudeep AB, Mishra AC (2007) Genetic divergence of Chikungunya viruses in India (1963-2006) with special reference to the 2005-2006 explosive epidemic. J Gen Virol 88(Pt 7):1967–1976

    Article  CAS  PubMed  Google Scholar 

  4. Ng LC, Hapuarachchi HC (2010) Tracing the path of Chikungunya virus—evolution and adaptation. Infect Genet Evol 10(7):876–885

    Article  PubMed  Google Scholar 

  5. Hapuarachchi HC, Bandara KB, Sumanadasa SD, Hapugoda MD, Lai YL, Lee KS, Tan LK, Lin RT, Ng LF, Bucht G, Abeyewickreme W, Ng LC (2010) Re-emergence of Chikungunya virus in South-east Asia: virological evidence from Sri Lanka and Singapore. J Gen Virol 91(Pt 4):1067–1076

    Article  CAS  PubMed  Google Scholar 

  6. deLamballerie X, Leroy E, Charrel RN, Ttsetsarkin K, Higgs S, Gould EA (2008) Chikungunya virus adapts to tiger mosquito via evolutionary convergence: a sign of things to come? Virol J 5:33

    Article  Google Scholar 

  7. Tsetsarkin KA, Vanlandingham DL, McGee CE, Higgs S (2007) A single mutation in chikungunya virus affects vector specificity and epidemic potential. PLoS Pathog 3(12):e201

    Article  PubMed  PubMed Central  Google Scholar 

  8. Vazeille M, Moutailler S, Coudrier D, Rousseaux C, Khun H, Huerre M, Thiria J, Dehecq JS, Fontenille D, Schuffenecker I, Despres P, Failloux AB (2007) Two Chikungunya isolates from the outbreak of La Reunion (Indian Ocean) exhibit different patterns of infection in the mosquito, Aedesalbopictus. PLoS One 2(11), e1168

    Article  PubMed  PubMed Central  Google Scholar 

  9. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16(1):37–48

    Article  CAS  PubMed  Google Scholar 

  10. Lemey P, Rambaut A, Drummond AJ, Suchard MA (2009) Bayesian phylogeography finds its roots. PLoS Comput Biol 5(9):e1000520

    Article  PubMed  PubMed Central  Google Scholar 

  11. Lemey P, Rambaut A, Welch JJ, Suchard MA (2010) Phylogeography takes a relaxed random walk in continuous space and time. Mol Biol Evol 27(8):1877–1885

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947–2948

    Article  CAS  PubMed  Google Scholar 

  13. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acid Symp Ser 41:95–98

    CAS  Google Scholar 

  15. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10(4):e1003537

    Article  PubMed  PubMed Central  Google Scholar 

  17. Bielejec F, Rambaut A, Suchard MA, Lemey P (2011) SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics 27(20):2910–2912

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Bloomquist EW, Lemey P, Suchard MA (2010) Three roads diverged? Routes to phylogeographic inference. Trends Ecol Evol 25(11):626–632

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgement

We acknowledge original developers of software described in this section for their expertise contribution to the advancement of phylogenetic analyses. Their efforts to constantly improve existing software and to make them freely available are greatly appreciated.

Author information

Authors and Affiliations

  1. Environmental Health Institute, National Environment Agency, 11, BioPolis Way, Helios #06-05/08, Singapore, 138667, Singapore

    Hapuarachchige Chanditha Hapuarachchi

  2. School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Block 83, #04-00, 535 Clementi Road, Singapore, 599489, Singapore

    Kim-Sung Lee

Authors
  1. Hapuarachchige Chanditha Hapuarachchi
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  2. Kim-Sung Lee
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Corresponding authors

Correspondence to Hapuarachchige Chanditha Hapuarachchi or Kim-Sung Lee .

Editor information

Editors and Affiliations

  1. Dept of Microbiology and Immunology, National University of Singapore, Singapore, Singapore

    Justin Jang Hann Chu

  2. Dept of Microbiology and Immunology, National University of Singapore, Singapore, Singapore

    Swee Kim Ang

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© 2016 Springer Science+Business Media New York

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Hapuarachchi, H.C., Lee, KS. (2016). Advanced Genetic Methodologies in Tracking Evolution and Spread of Chikungunya Virus. In: Chu, J., Ang, S. (eds) Chikungunya Virus. Methods in Molecular Biology, vol 1426. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3618-2_3

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  • DOI: https://doi.org/10.1007/978-1-4939-3618-2_3

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3616-8

  • Online ISBN: 978-1-4939-3618-2

  • eBook Packages: Springer Protocols

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