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Complete Genome Sequence of Herpes Simplex Virus 2 Strain G
Authors:Weizhong Chang  Xiaoli Jiao  Hongyan Sui  Suranjana Goswami  Brad T Sherman  Caroline Fromont  Juan Manuel Caravaca  Bao Tran  Tomozumi Imamichi
Institution:1.Laboratory of Human Retrovirology and lmmunoinformatics, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.J.); (H.S.); (S.G.); (B.T.S.);2.Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (C.F.); (J.M.C.); (B.T.)
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.
Keywords:HSV-2  complete genome sequence    α    sequence  packaging signals  genome termini  strain G
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