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Complete Genome Sequence of Herpes Simplex Virus 2 Strain G

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 stra...

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Autores principales: Chang, Weizhong, Jiao, Xiaoli, Sui, Hongyan, Goswami, Suranjana, Sherman, Brad T., Fromont, Caroline, Caravaca, Juan Manuel, Tran, Bao, Imamichi, Tomozumi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954253/
https://www.ncbi.nlm.nih.gov/pubmed/35336943
http://dx.doi.org/10.3390/v14030536
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author Chang, Weizhong
Jiao, Xiaoli
Sui, Hongyan
Goswami, Suranjana
Sherman, Brad T.
Fromont, Caroline
Caravaca, Juan Manuel
Tran, Bao
Imamichi, Tomozumi
author_facet Chang, Weizhong
Jiao, Xiaoli
Sui, Hongyan
Goswami, Suranjana
Sherman, Brad T.
Fromont, Caroline
Caravaca, Juan Manuel
Tran, Bao
Imamichi, Tomozumi
author_sort Chang, Weizhong
collection PubMed
description 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.
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spelling pubmed-89542532022-03-26 Complete Genome Sequence of Herpes Simplex Virus 2 Strain G Chang, Weizhong Jiao, Xiaoli Sui, Hongyan Goswami, Suranjana Sherman, Brad T. Fromont, Caroline Caravaca, Juan Manuel Tran, Bao Imamichi, Tomozumi Viruses Article 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. MDPI 2022-03-05 /pmc/articles/PMC8954253/ /pubmed/35336943 http://dx.doi.org/10.3390/v14030536 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Chang, Weizhong
Jiao, Xiaoli
Sui, Hongyan
Goswami, Suranjana
Sherman, Brad T.
Fromont, Caroline
Caravaca, Juan Manuel
Tran, Bao
Imamichi, Tomozumi
Complete Genome Sequence of Herpes Simplex Virus 2 Strain G
title Complete Genome Sequence of Herpes Simplex Virus 2 Strain G
title_full Complete Genome Sequence of Herpes Simplex Virus 2 Strain G
title_fullStr Complete Genome Sequence of Herpes Simplex Virus 2 Strain G
title_full_unstemmed Complete Genome Sequence of Herpes Simplex Virus 2 Strain G
title_short Complete Genome Sequence of Herpes Simplex Virus 2 Strain G
title_sort complete genome sequence of herpes simplex virus 2 strain g
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8954253/
https://www.ncbi.nlm.nih.gov/pubmed/35336943
http://dx.doi.org/10.3390/v14030536
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