Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Viruses. 2022 Mar 5;14(3):536. doi: 10.3390/v14030536.
Herpes simplex virus type (HSV-2) is a common causative agent of genital tract infections. Moreover, HSV-2 and HIV infection can mutually increase the risk of acquiring another virus infection. Due to the high GC content and highly repetitive regions in HSV-2 genomes, only the genomes of four strains have been completely sequenced (HG52, 333, SD90e, and MS). Strain G is commonly used for HSV-2 research, but only a partial genome sequence has been assembled with Illumina sequencing reads. In the current study, we de novo assembled and annotated the complete genome of strain G using PacBio long sequencing reads, which can span the repetitive regions, analyzed the 'α' sequence, which plays key roles in HSV-2 genome circulation, replication, cleavage, and packaging of progeny viral DNA, identified the packaging signals homologous to HSV-1 within the 'α' sequence, and determined both termini of the linear genome and cleavage site for the process of concatemeric HSV-2 DNA produced via rolling-circle replication. In addition, using Oxford Nanopore Technology sequencing reads, we visualized four HSV-2 genome isomers at the nucleotide level for the first time. Furthermore, the coding sequences of HSV-2 strain G have been compared with those of HG52, 333, and MS. Moreover, phylogenetic analysis of strain G and other diverse HSV-2 strains has been conducted to determine their evolutionary relationship. The results will aid clinical research and treatment development of HSV-2.
单纯疱疹病毒 2 型（HSV-2）是引起生殖道感染的常见病原体。此外，HSV-2 和 HIV 感染会相互增加感染另一种病毒的风险。由于 HSV-2 基因组中的 GC 含量高且高度重复，仅有四个株系的基因组被完全测序（HG52、333、SD90e 和 MS）。株系 G 常用于 HSV-2 研究，但仅使用 Illumina 测序数据组装了部分基因组序列。在本研究中，我们使用 PacBio 长读长从头组装并注释了株系 G 的完整基因组，这可以跨越重复区域，分析在 HSV-2 基因组循环、复制、切割和包装子代病毒 DNA 中起关键作用的 'α' 序列，鉴定了 'α' 序列内与 HSV-1 同源的包装信号，并确定了线性基因组的两端和用于滚环复制产生的串联 HSV-2 DNA 的切割位点。此外，我们首次使用 Oxford Nanopore Technology 测序数据在核苷酸水平可视化了四个 HSV-2 基因组异构体。此外，我们还比较了 HSV-2 株系 G 的编码序列与 HG52、333 和 MS 的编码序列。此外，还对 G 株系和其他不同 HSV-2 株系进行了系统发育分析，以确定它们的进化关系。研究结果将有助于 HSV-2 的临床研究和治疗发展。
