ArticlePloS one2016
De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 49 citations in OpenAlex.
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- Decoding and Unravelling Mpox, Herpes, and Syphilis Infections: A State of Art Review.Current pharmaceutical biotechnology · 2025Review
- Combined use of pritelivir with acyclovir or foscarnet suppresses evolution of HSV-1 drug resistance.Virus evolution · 2024Article
- Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly.Microbial genomics · 2022Article
- Capturing Structural Variants of Herpes Simplex Virus Genome in Full Length by Oxford Nanopore Sequencing.Microbiology spectrum · 2022Article
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- MinION nanopore sequencing and assembly of a complete human papillomavirus genome.Journal of virological methods · 2021Article
- Combination of long- and short-read sequencing fully resolves complex repeats of herpes simplex virus 2 strain MS complete genome.Microbial genomics · 2021Article
- Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection.Retrovirology · 2020Article
- Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses.Virus evolution · 2020Article
- SEQU-INTO: Early detection of impurities, contamination and off-targets (ICOs) in long read/MinION sequencing.Computational and structural biotechnology journal · 2020Article
- Hinge Region in DNA Packaging Terminase pUL15 of Herpes Simplex Virus: A Potential Allosteric Target for Antiviral Drugs.Biomolecules · 2019Article
- Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion.Pathogens (Basel, Switzerland) · 2019Review
- NanoPipe-a web server for nanopore MinION sequencing data analysis.GigaScience · 2019Article
- Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing.PloS one · 2019Article
- Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection.Viruses · 2018Article
- Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations.BMC genomics · 2018Article
- Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO.Scientific reports · 2018Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from <1% to 53% of amino acids in each gene exhibiting at least one substitution within the pool of samples. The UL23 gene had one of the highest genetic variabilities at 35.2% in keeping with its role in development of drug resistance. The assembly of accurate, full-length HHV-1 genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal.
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