Abstract
Herpes simplex virus type 2 (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.
Highlights
Herpes simplex virus type 2 (HSV-2) is a member of the Alphaherpesvirinae subfamily of the Herpesviridae family [1]
Pacific Bioscience (PacBio) subreads were assembled into contigs using the PacBio de novo assembler Hierarchical Genome Assembly Process v4.0 (HGAP4) [32]
The contigs were aligned against the genome sequence of HSV-2 reference strain HG52 (NCBI Accession: NC_001798.2) [27] by BLASR (v2.0.0) [35] with default settings, and the contigs jointly covering the full length of the HG52 reference genome were merged into a draft sequence and improved by the PacBio genome resequencing pipeline (SMRT® Analysis v6.0) with default settings (Pacific Bioscience Inc.)
Summary
Weizhong Chang 1, *,† , Xiaoli Jiao 1,†,‡ , Hongyan Sui 1 , Suranjana Goswami 1 , Brad T. Sherman 1 , Caroline Fromont 2 , Juan Manuel Caravaca 2 , Bao Tran 2 and Tomozumi Imamichi 1, *. Current affiliation: RNAimmune, 401 Professional Drive #280, Gaithersburg, MD 20879, USA
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