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Dengue pp 175–195Cite as

Next-Generation Whole Genome Sequencing of Dengue Virus

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1138))

Abstract

RNA viruses are notorious for their ability to quickly adapt to selective pressure from the host immune system and/or antivirals. This adaptability is likely due to the error-prone characteristics of their RNA-dependent, RNA polymerase [1, 2]. Dengue virus, a member of the Flaviviridae family of positive-strand RNA viruses, is also known to share these error-prone characteristics [3]. Utilizing high-throughput, massively parallel sequencing methodologies, or next-generation sequencing (NGS), we can now accurately quantify these populations of viruses and track the changes to these populations over the course of a single infection. The aim of this chapter is twofold: to describe the methodologies required for sample preparation prior to sequencing and to describe the bioinformatics analyses required for the resulting data.

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Abbreviations

TBE:

Tris–Borate–EDTA

EtBr:

Ethidium bromide

PCR:

Polymerase chain reaction

RT-PCR:

Reverse transcriptase polymerase chain reaction

cDNA:

Complementary DNA

DNA:

Deoxyribonucleic acid

RNA:

Ribonucleic acid

dNTP:

Deoxyribonucleotide triphosphate

kb:

Kilobase

bp:

Base pairs

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Author information

Authors and Affiliations

  1. Genome Institute of Singapore, Singapore, Singapore

    Pauline Poh Kim Aw, Paola Florez de Sessions, Andreas Wilm, Long Truong Hoang, Niranjan Nagarajan & Martin Lloyd Hibberd

  2. Emerging Infectious Diseases Program, Duke-NUS Graduate Medical School, Singapore, Singapore

    October M. Sessions

Authors
  1. Pauline Poh Kim Aw
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  2. Paola Florez de Sessions
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  3. Andreas Wilm
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  4. Long Truong Hoang
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  5. Niranjan Nagarajan
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  6. October M. Sessions
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  7. Martin Lloyd Hibberd
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Corresponding author

Correspondence to October M. Sessions .

Editor information

Editors and Affiliations

  1. Georgetown University Medical Center Dept. of Microbiology and Immunology, Washington, District of Columbia, USA

    Radhakrishnan Padmanabhan

  2. Duke-NUS GMS Singapore Emerging Infectious Diseases, Singapore, Singapore

    Subhash G. Vasudevan

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Aw, P.P.K. et al. (2014). Next-Generation Whole Genome Sequencing of Dengue Virus. In: Padmanabhan, R., Vasudevan, S. (eds) Dengue. Methods in Molecular Biology, vol 1138. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0348-1_12

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  • DOI: https://doi.org/10.1007/978-1-4939-0348-1_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0347-4

  • Online ISBN: 978-1-4939-0348-1

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