ArticlePloS one2015
Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 29 citations in OpenAlex.
- Integrating metagenomics and metatranscriptomics intoThe Journal of general virology · 2026Review
- Characterizing the parvovirome of Swazi bats: novel species, highly divergent lineages, endogenous viral elements, and taxonomic challenges.Virus evolution · 2026Article
- Target Enrichment Metagenomics Reveals Human Pegivirus-1 in Pediatric Hematopoietic Stem Cell Transplantation Recipients.Viruses · 2022Article
- Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini.EcoHealth · 2021Article
- Emergence of a Novel Pathogenic Poxvirus Infection in the Endangered Green Sea Turtle (Viruses · 2021Article
- Review
- High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.The Journal of infectious diseases · 2019Article
- A novel method for the capture-based purification of whole viral native RNA genomes.AMB Express · 2019Article
- Metagenomic analysis of viruses in toilet waste from long distance flights-A new procedure for global infectious disease surveillance.PloS one · 2019Article
- Limited Correlation of Shotgun Metagenomics Following Host Depletion and Routine Diagnostics for Viruses and Bacteria in Low Concentrated Surrogate and Clinical Samples.Frontiers in cellular and infection microbiology · 2018Article
- Molecular and microscopic characterization of a novel Eastern grey kangaroopox virus genome directly from a clinical sample.Scientific reports · 2017Article
- The Human Virome: Implications for Clinical Practice in Transplantation Medicine.Journal of clinical microbiology · 2017Review
- Genomic characterization of two novel pathogenic avipoxviruses isolated from pacific shearwaters (Ardenna spp.).BMC genomics · 2017Article
- Clinical and biological insights from viral genome sequencing.Nature reviews. Microbiology · 2017Review
- Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus.BMC genomics · 2016Article
- Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing.Journal of clinical microbiology · 2016Article
- Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers.Viruses · 2016Article
- Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing.Scientific reports · 2015Article
- A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection.mSphereArticle
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing.
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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.