Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Viruses. 2021 Sep 19;13(9):1874. doi: 10.3390/v13091874.
HIV persists via integration of the viral DNA into the human genome. The HIV DNA pool within an infected individual is a complex population that comprises both intact and defective viral genomes, each with a distinct integration site, in addition to a unique repertoire of viral quasi-species. Obtaining an accurate profile of the viral DNA pool is critical to understanding viral persistence and resolving interhost differences. Recent advances in next-generation deep sequencing (NGS) technologies have enabled the development of two sequencing assays to capture viral near-full- genome sequences at single molecule resolution (FLIP-seq) or to co-capture full-length viral genome sequences in conjunction with its associated viral integration site (MIP-seq). This commentary aims to provide an overview on both FLIP-seq and MIP-seq, discuss their strengths and limitations, and outline specific chemistry and bioinformatics concerns when using these assays to study HIV persistence.
HIV 通过将病毒 DNA 整合到人类基因组中而持续存在。在受感染个体中，HIV DNA 池是一个复杂的群体，包含完整和缺陷的病毒基因组，每个基因组都有独特的整合位点，以及独特的病毒准种库。获得病毒 DNA 池的准确图谱对于理解病毒持续存在和解决宿主间差异至关重要。下一代深度测序（NGS）技术的最新进展使得开发两种测序检测方法成为可能，这些方法能够以单分子分辨率捕获病毒近全长基因组序列（FLIP-seq），或同时捕获全长病毒基因组序列及其相关的病毒整合位点（MIP-seq）。本评论旨在概述 FLIP-seq 和 MIP-seq，讨论它们的优缺点，并概述在使用这些检测方法研究 HIV 持续存在时的特定化学和生物信息学问题。
