Next-generation whole genome sequencing of dengue virus.
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.
Genome Institute of Singapore, Singapore, Singapore.
Pauline Poh Kim
PP
Aw
Paola Florez
PF
de Sessions
Andreas
A
Wilm
Long Truong
LT
Hoang
Niranjan
N
Nagarajan
October M
OM
Sessions
Martin Lloyd
ML
Hibberd
D020029:Base Pairing / Q000235:genetics; D019295:Computational Biology; D018076:DNA, Complementary / Q000096:biosynthesis; D004279:DNA, Viral / Q000235:genetics / Q000302:isolation & purification; D003716:Dengue Virus / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D016133:Polymerase Chain Reaction; D012313:RNA / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics / Q000302:isolation & purification; D012984:Software
D018076:DNA, Complementary; D004279:DNA, Viral; C034477:RNA primers; D012367:RNA, Viral; D012313:RNA