Aw Pauline Poh Kim, de Sessions Paola Florez, Wilm Andreas, Hoang Long Truong, Nagarajan Niranjan, Sessions October M, Hibberd Martin Lloyd
Genome Institute of Singapore, Singapore, Singapore.
Methods Mol Biol. 2014;1138:175-95. doi: 10.1007/978-1-4939-0348-1_12.
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.
RNA病毒以其能够迅速适应来自宿主免疫系统和/或抗病毒药物的选择压力而臭名昭著。这种适应性可能归因于其依赖RNA的RNA聚合酶易于出错的特性[1,2]。登革病毒是正链RNA病毒黄病毒科的成员，也具有这些易于出错的特性[3]。利用高通量、大规模平行测序方法，即下一代测序（NGS），我们现在能够准确地量化这些病毒群体，并追踪在单次感染过程中这些群体的变化。本章的目的有两个：描述测序前样本制备所需的方法，以及描述所得数据所需的生物信息学分析。
