Skip to main content

Molecular Epidemiology of Chikungunya Virus by Sequencing

  • Protocol
  • First Online:
Chikungunya Virus

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

  • 1983 Accesses

Abstract

Molecular surveillance of Chikungunya virus (CHIKV) is important as it provides data on the circulating CHIKV genotypes in endemic countries and enabling activation of measures to be taken in the event of a pending outbreak. Molecular surveillance is carried out by first detecting CHIKV in susceptible humans or among field-caught mosquitoes. This is followed by sequencing a selected region of the virus which will provide evidence on the source of the virus and possible association of the virus to increased cases of Chikungunya infections.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Singh RK, Tiwari S, Mishra VK, Tiwari R, Dhole TN (2012) Molecular epidemiology of Chikungunya virus: mutation in E1 gene region. J Virol Methods 185:213–220

    Article  CAS  PubMed  Google Scholar 

  2. Powers AM, Brault AC, Tesh RB, Weaver SC (2000) Re-emergence of Chikungunya and O’nyong-nyong viruses: evidence for distinct geographical lineages and distinct evolutionary relationships. J Gen Virol 81:471–479

    Article  CAS  PubMed  Google Scholar 

  3. Schuffenecker I, Iteman I, Michault A, Murri Frangeul S, Vaney L et al (2006) Genome microevolution of Chikungunya viruses causing the Indian Ocean outbreak. PloS Med 3, e263

    Article  PubMed  PubMed Central  Google Scholar 

  4. Powers AM, Logue CH (2007) Changing patterns of Chikungunya virus: re emergence of a zoonotic arbovirus. J Gen Virol 88:2363–2377

    Article  CAS  PubMed  Google Scholar 

  5. Laksmipathy DT, Dhanasekaran D (2008) Molecular epidemiology of Chikungunya virus in Vellore District, Tamilnadu, India in 2006. East Afr J Public Health 5(2):122–125

    Google Scholar 

  6. Chem YK, Zainah S, Beremdam SJ, Tengku Rogayah TAR, Khairul AH, Chua KB (2010) Molecular epidemiology of Chikungunya virus in Malaysia since its first emergence in 1998. Med J Malaysia 5(1):31–35

    Google Scholar 

  7. Noridah O, Paranthaman V, Nayar SK, Masliza M, Ranjit K, Norizah I, Chem YK, Mustafa B, Kumarasamy V, Chua KB (2007) Outbreak of Chikungunya due to virus of Central/East African Genotype 1 in Malaysia. Med J Malaysia 62(4):323–328

    CAS  PubMed  Google Scholar 

  8. Bortel WV, Dorleans F, Rosine J, Blateau A, Rousset D, Matheus S, Leparc-Goffart I, Flusin O et al (2014) Chikungunya outbreak in the Caribbean region, December 2013 to March 2014, and the significance for Europe. Euro Surveill 19(13):pii: 20759

    Article  Google Scholar 

  9. Laurent P, Roux KL, Grivard P, Bertil G, Naze F, Picard M, Staikowsky F, Barau G, Schuffenecker I, Michault A (2007) Development of a sensitive real time reverse transcriptase PCR assay with an internal control to detect and quantify Chikungunya virus. Clin Chem 53(8):1408–1414

    Article  CAS  PubMed  Google Scholar 

  10. Santhosh SR, Dash PL, Parida MM, Khan M, Tiwari M, Lakshmana Rao PV (2008) Comparative full genome analysis revealed E1: A226V shift in 2007 Indian Chikungunya virus isolates. Virus Res 135:36–41

    Article  CAS  PubMed  Google Scholar 

  11. Rianthavorn P, Prianantathavorn K, Wuttirattanakowit N, Theamboonlers A, Poovorawan Y (2010) An outbreak of Chikungunya in southern Thailand from 2008-2009 caused by African strains with A226V mutation. Int J Infect Dis 145:161–165

    Article  Google Scholar 

  12. Pongsiri P, Praianantathavorn K, Theamboonlers A, Payungporn S, Poorawan Y (2012) Multiplex real time Rt-PCR for detecting Chikungunya virus and dengue virus. Asian Pac J Trop Dis 5(5):342–346

    Article  CAS  Google Scholar 

  13. Apandi YM, Lau SK, Norfaezah A, Nur Izmawati AR, Liyana AZ, Khairul Izwan H, Zainah S (2011) Epidemiology and molecular characterization of Chikungunya virus involved in the 2008 and 2009 outbreak in Malaysia. J Gen Mol Virol 3(2):35–42

    Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ravindran Thayan .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media New York

About this protocol

Cite this protocol

Thayan, R., Yusof, M.A., Saat, Z., Sekaran, S.D., Wang, S.M. (2016). Molecular Epidemiology of Chikungunya Virus by Sequencing. 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_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-3618-2_2

  • 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

Publish with us

Policies and ethics