ArticleBMC genomics2019
Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Integrating metagenomics and metatranscriptomics intoThe Journal of general virology · 2026Review
- Enrichment techniques for clinical metagenomics.Frontiers in cellular and infection microbiology · 2026Review
- Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples.Molecular biology and evolution · 2025Article
- Quantifying viral load and characterizing virus diversity in wildlife samples with target enrichment sequencing.Microbial genomics · 2025Article
- From Panels to Pathogen Networks: The Expanding Role of Targeted Sequencing in Veterinary Medicine.Biology · 2025Review
- Genomics in plant pathogen identification and control.Frontiers in plant science · 2025Review
- A case report of rapid diagnosis ofFrontiers in medicine · 2025Article
- Enriching the future of public health microbiology with hybridization bait capture.Clinical microbiology reviews · 2024Review
- Target enrichment metaviromics enables comprehensive surveillance of coronaviruses in environmental and animal samples.Heliyon · 2024Article
- Dengue: A review of laboratory diagnostics in the vaccine age.Journal of medical microbiology · 2024Review
- Development of a Targeted NGS Assay for the Detection of Respiratory Pathogens including SARS-CoV-2 in Felines.Pathogens (Basel, Switzerland) · 2024Article
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens.Frontiers in microbiology · 2024Article
- Whole genome sequencing reveals insights into hepatitis E virus genome diversity, and virus compartmentalization in chronic hepatitis E.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2023Article
- Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases.Cells · 2023Review
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- ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa.BMC genomics · 2022Article
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- Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene.Journal of genetics and genomics = Yi chuan xue bao · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundSequencing-based detection and characterization of viruses in complex samples can suffer from lack of sensitivity due to a variety of factors including, but not limited to, low titer, small genome size, and contribution of host or environmental nucleic acids. Hybridization-based target enrichment is one potential method for increasing the sensitivity of viral detection via high-throughput sequencing.
resultsThis study expands upon two previously developed panels of virus enrichment probes (for filoviruses and for respiratory viruses) to include other viruses of biodefense and/or biosurveillance concern to the U.S. Department of Defense and various international public health agencies. The newly expanded and combined panel is tested using carefully constructed synthetic metagenomic samples that contain clinically relevant amounts of viral genetic material. Target enrichment results in a dramatic increase in sensitivity for virus detection as compared to shotgun sequencing, yielding full, deeply covered viral genomes from materials with Ct values suggesting that amplicon sequencing would be likely to fail. Increased pooling to improve cost- and time-effectiveness does not negatively affect the ability to obtain full-length viral genomes, even in the case of co-infections, although as expected, it does decrease depth of coverage.
conclusionsHybridization-based target enrichment is an effective solution to obtain full-length viral genomes for samples from which virus detection would fail via unbiased, shotgun sequencing or even via amplicon sequencing. As the development and testing of probe sets for viral target enrichment expands and continues, the application of this technique, in conjunction with deeper pooling strategies, could make high-throughput sequencing more economical for routine use in biosurveillance, biodefense and outbreak investigations.
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