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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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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