ArticlePloS one2014
A method enabling high-throughput sequencing of human cytomegalovirus complete genomes from clinical isolates.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 26 citations in OpenAlex.
- Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome.Nucleic acids research · 2024Article
- Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance.Applied microbiology and biotechnology · 2024Review
- Genomic and geographical structure of human cytomegalovirus.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Common Polymorphisms in the Glycoproteins of Human Cytomegalovirus and Associated Strain-Specific Immunity.Viruses · 2021Review
- GRACy: A tool for analysing human cytomegalovirus sequence data.Virus evolution · 2021Article
- Evolution and Genetic Diversity of Primate Cytomegaloviruses.Microorganisms · 2020Review
- Review
- Human Cytomegalovirus Interleukin 10 Homologs: Facing the Immune System.Frontiers in cellular and infection microbiology · 2020Review
- Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection.BMC infectious diseases · 2019Article
- Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion.Pathogens (Basel, Switzerland) · 2019Review
- Human Cytomegalovirus Genomes Sequenced Directly From Clinical Material: Variation, Multiple-Strain Infection, Recombination, and Gene Loss.The Journal of infectious diseases · 2019Article
- Human cytomegalovirus genomics and transcriptomics through the lens of next-generation sequencing: revision and future challenges.Virus genes · 2019Review
- Genome-Wide Sequence Analysis of Kaposi Sarcoma-Associated Herpesvirus Shows Diversification Driven by Recombination.The Journal of infectious diseases · 2018Article
- Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations.BMC genomics · 2018Article
- Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples.Microbiome · 2017Article
- Deep Lessons From the Uncultured.The Journal of infectious diseases · 2017Article
- Modulation of the Host Environment by Human Cytomegalovirus with Viral Interleukin 10 in Peripheral Blood.The Journal of infectious diseases · 2017Article
- Genome Sequences of Diverse Human Cytomegalovirus Strains with Utility in Drug Screening and Vaccine Evaluation.Genome announcements · 2017Article
- Next-generation sequencing in clinical virology: Discovery of new viruses.World journal of virology · 2015Review
- High-throughput analysis of human cytomegalovirus genome diversity highlights the widespread occurrence of gene-disrupting mutations and pervasive recombination.Journal of virology · 2015Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous virus that can cause serious sequelae in immunocompromised patients and in the developing fetus. The coding capacity of the 235 kbp genome is still incompletely understood, and there is a pressing need to characterize genomic contents in clinical isolates. In this study, a procedure for the high-throughput generation of full genome consensus sequences from clinical HCMV isolates is presented. This method relies on low number passaging of clinical isolates on human fibroblasts, followed by digestion of cellular DNA and purification of viral DNA. After multiple displacement amplification, highly pure viral DNA is generated. These extracts are suitable for high-throughput next-generation sequencing and assembly of consensus sequences. Throughout a series of validation experiments, we showed that the workflow reproducibly generated consensus sequences representative for the virus population present in the original clinical material. Additionally, the performance of 454 GS FLX and/or Illumina Genome Analyzer datasets in consensus sequence deduction was evaluated. Based on assembly performance data, the Illumina Genome Analyzer was the platform of choice in the presented workflow. Analysis of the consensus sequences derived in this study confirmed the presence of gene-disrupting mutations in clinical HCMV isolates independent from in vitro passaging. These mutations were identified in genes RL5A, UL1, UL9, UL111A and UL150. In conclusion, the presented workflow provides opportunities for high-throughput characterization of complete HCMV genomes that could deliver new insights into HCMV coding capacity and genetic determinants of viral tropism and pathogenicity.
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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 OpenQuestion graph.