ArticleBMC genomics2018
Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed, 28 citations in OpenAlex.
- Detection and characterization of neonatal cytomegalovirus through nanopore sequencing using flongle flow cells: Pilot study in Philadelphia, Pennsylvania.Journal of virological methods · 2026Article
- Microtubule mechanotransduction refines cytomegalovirus interactions with and remodeling of host chromatin.Nature communications · 2025Article
- High-fidelity long-read sequencing of an avian herpesvirus reveals extensive intrapopulation diversity in tandem repeat regions.PLoS pathogens · 2025Article
- Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization fromMicrobiology spectrum · 2025Article
- Determination of whole genome sequence of human cytomegalovirus circulating in Japan and discovery of geographic genome structure in UL148 gene.Virus research · 2025Article
- Embracing Complexity: What Novel Sequencing Methods Are Teaching Us About Herpesvirus Genomic Diversity.Annual review of virology · 2024Review
- Direct Nanopore Sequencing of Human Cytomegalovirus Genomes from High-Viral-Load Clinical Samples.Viruses · 2023Article
- Strain-Dependent Restriction of Human Cytomegalovirus by Zinc Finger Antiviral Proteins.Journal of virology · 2023Article
- Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly.Microbial genomics · 2022Article
- Article
- Viral gene drive in herpesviruses.Nature communications · 2020Article
- 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
- Metagenomic Nanopore Sequencing of Influenza Virus Direct from Clinical Respiratory Samples.Journal of clinical microbiology · 2019Article
- Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion.Pathogens (Basel, Switzerland) · 2019Review
- The emerging role of human cytomegalovirus infection in human carcinogenesis: a review of current evidence and potential therapeutic implications.Oncotarget · 2019Review
- Human cytomegalovirus genomics and transcriptomics through the lens of next-generation sequencing: revision and future challenges.Virus genes · 2019Review
- Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundHuman cytomegalovirus (HCMV) has a double-stranded DNA genome of approximately 235 Kbp that is structurally complex including extended GC-rich repeated regions. Genomic recombination events are frequent in HCMV cultures but have also been observed in vivo. Thus, the assembly of HCMV whole genomes from technologies producing shorter than 500 bp sequences is technically challenging. Here we improved the reconstruction of HCMV full genomes by means of a hybrid, de novo genome-assembly bioinformatics pipeline upon data generated from the recently released MinION MkI B sequencer from Oxford Nanopore Technologies.
resultsThe MinION run of the HCMV (strain TB40/E) library resulted in ~ 47,000 reads from a single R9 flowcell and in ~ 100× average read depth across the virus genome. We developed a novel, self-correcting bioinformatics algorithm to assemble the pooled HCMV genomes in three stages. In the first stage of the bioinformatics algorithm, long contigs (N50 = 21,892) of lower accuracy were reconstructed. In the second stage, short contigs (N50 = 5686) of higher accuracy were assembled, while in the final stage the high quality contigs served as template for the correction of the longer contigs resulting in a high-accuracy, full genome assembly (N50 = 41,056). We were able to reconstruct a single representative haplotype without employing any scaffolding steps. The majority (98.8%) of the genomic features from the reference strain were accurately annotated on this full genome construct. Our method also allowed the detection of multiple alternative sub-genomic fragments and non-canonical structures suggesting rearrangement events between the unique (UL /US) and the repeated (T/IRL/S) genomic regions.
conclusionsThird generation high-throughput sequencing technologies can accurately reconstruct full-length HCMV genomes including their low-complexity and highly repetitive regions. Full-length HCMV genomes could prove crucial in understanding the genetic determinants and viral evolution underpinning drug resistance, virulence and pathogenesis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.