ArticleGenome biology2021
PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed, 40 citations in OpenAlex.
- Immunophenotype and proviral landscape of HTLV-1c infection and pulmonary disease.EBioMedicine · 2026Article
- Omics-Level Approaches to Studying Gammaherpesvirus Infection.Pathogens (Basel, Switzerland) · 2026Review
- An active Helitron transposon family in wheat.Nature plants · 2026Article
- PRISM-Seq: An Ultra-sensitive Sequencing Approach For Mapping Lentiviral Integration Sites.bioRxiv : the preprint server for biology · 2026Article
- Tools to Quantify and Characterize the Persistent Reservoir in People with HIV-1: Focus on Non-B Subtypes.Viruses · 2026Review
- The Complexity of Bovine Leukemia Virus Oncogenesis.Viruses · 2025Review
- Novel protocol for mapping virus integration sites in genes involved in therapy resistance.Scientific reports · 2025Article
- Overview of Microorganisms: Bacterial Microbiome, Mycobiome, Virome Identified Using Next-Generation Sequencing, and Their Application to Ophthalmic Diseases.Microorganisms · 2025Review
- Novel Avenues for the Detection of Cancer-Associated Viral Genome Integrations Using Long-Read Sequencing Technologies.Cancers · 2025Review
- Ultra-sensitive detection of transposon insertions across multiple families by transposable element display sequencing.Genome biology · 2025Article
- Methodological landscape in the field of integration site identification of retroviruses and retroviral vectors.Frontiers in bioengineering and biotechnology · 2025Review
- Harnessing the evolving CRISPR/Cas9 for precision oncology.Journal of translational medicine · 2024Review
- Viral genome sequencing methods: benefits and pitfalls of current approaches.Biochemical Society transactions · 2024Review
- Immune targeting of HIV-1 reservoir cells: a path to elimination strategies and cure.Nature reviews. Microbiology · 2024Review
- GWAS reveals determinants of mobilization rate and dynamics of an active endogenous retrovirus of cattle.Nature communications · 2024Article
- HIV-PULSE: a long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization.Nucleic acids research · 2023Article
- Phenotypic characterization of single CD4+ T cells harboring genetically intact and inducible HIV genomes.Nature communications · 2023Article
- Clone Dynamics and Its Application for the Diagnosis of Enzootic Bovine Leukosis.Journal of virology · 2023Article
- Epigenetic silencing by the SMC5/6 complex mediates HIV-1 latency.Nature microbiology · 2022Article
- Extensive characterization of HIV-1 reservoirs reveals links to plasma viremia before and during analytical treatment interruption.Cell reports · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
20 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.
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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.