ArticleScientific reports2019
HIV-1 DNA-capture-seq is a useful tool for the comprehensive characterization of HIV-1 provirus.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Circulating Cell-Free DNA of Bovine Leukemia Virus: A Promising Biomarker for Enzootic Bovine Leukosis.Microbiology and immunology · 2025Article
- Transgene Mapping in Animals: What to Choose?International journal of molecular sciences · 2025Review
- Robust HPV-16 Detection Workflow for Formalin-Fixed Cancer Tissue and Its Application for Oral Squamous Cell Carcinoma.Cancer medicine · 2025Article
- Viral genome sequencing methods: benefits and pitfalls of current approaches.Biochemical Society transactions · 2024Review
- HPV, HBV, and HIV-1 Viral Integration Site Mapping: A Streamlined Workflow from NGS to Genomic Insights of Carcinogenesis.Viruses · 2024Article
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- HIV-Tocky system to visualize proviral expression dynamics.Communications biology · 2024Article
- Clone Dynamics and Its Application for the Diagnosis of Enzootic Bovine Leukosis.Journal of virology · 2023Article
- Article
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- Simultaneous monitoring of HIV viral load and screening of SARS-CoV-2 employing a low-cost RT-qPCR test workflow.The Analyst · 2022Article
- Probe Capture Enrichment Methods for HIV and HCV Genome Sequencing and Drug Resistance Genotyping.Pathogens (Basel, Switzerland) · 2022Review
- Article
- Emerging Single-cell Approaches to Understand HIV in the Central Nervous System.Current HIV/AIDS reports · 2022Review
- The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.F1000Research · 2022Article
- Jurkat-Derived (J-Lat, J1.1, and Jurkat E4) and CEM-Derived T Cell Lines (8E5 and ACH-2) as Models of Reversible Proviral Latency.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Review
- Sequencing Ultrarare Targets with Compound Nucleic Acid Cytometry.Analytical chemistry · 2021Article
- PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads.Genome biology · 2021Article
- A target enrichment high throughput sequencing system for characterization of BLV whole genome sequence, integration sites, clonality and host SNP.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Regardless of recent advances in the development of anti-retroviral drugs, it is still extremely difficult to eradicate HIV-1 from infected individuals. The characterization of the HIV-1 provirus, a type of viral reservoir, with a high resolution is key to HIV-1 cure research. Here, we demonstrate that DNA-capture-seq is a powerful tool to obtain comprehensive information on the HIV-1 provirus. We use biotinylated DNA probes targeting the entire HIV-1 sequence to capture fragments containing HIV-1 sequences from DNA-seq libraries prepared for high throughput sequencing. We demonstrate that the protocol provided the entire proviral sequence from the beginning of the 5' LTR to the end of the 3' LTR. Since HIV-1 DNA-probes can hybridize not only viral fragments but also virus-host chimeric ones, the viral integration site information can also be obtained. We verify the efficiency of the protocol by using latently infected cell lines, such as ACH-2 and J1.1, and newly generated ones. The results reveal that the 2 new clones that we analyse harbour one copy of replication-competent provirus, suggesting that latency is not caused by genetic mutations or deletions of the provirus. In conclusion, HIV-1 DNA-capture-seq is a powerful tool to characterize the HIV-1 provirus at a single nucleotide resolution and therefore might be useful for various experiments aiming for an HIV-1 cure.
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