ArticlePLoS neglected tropical diseases2017
Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics.
Article in PLoS neglected tropical diseases, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 38 citations in OpenAlex.
- VisPan: real-time visualisation of multiplex amplicon-based sequencing panels for rapid syndromic surveillance and pathogen detection.Bioinformatics (Oxford, England) · 2026Article
- Identification and full genome sequencing of previously unknown sandfly-borne phleboviruses using a newly established capture-based next-generation sequencing approach.Journal of clinical microbiology · 2026Article
- Rift Valley fever: An emerging zoonotic threat to global health and agriculture.World journal of virology · 2026Review
- Enrichment techniques for clinical metagenomics.Frontiers in cellular and infection microbiology · 2026Review
- Molecular Diagnosis of Phlebovirus riftense Infection Using an L-Segment-Based Real-Time RT-PCR Method.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories.Viruses · 2024Review
- Recent Advances in Crimean-Congo Hemorrhagic Fever Virus Detection, Treatment, and Vaccination: Overview of Current Status and Challenges.Biological procedures online · 2024Review
- Update on Potentially Zoonotic Viruses of European Bats.Vaccines · 2021Review
- Nanotechnology, equity and global health.Nature nanotechnology · 2021Article
- Rift Valley Fever - a Growing Threat To Humans and Animals.Journal of veterinary research · 2021Article
- Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2.Microbiome · 2021Article
- Article
- Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses.Journal of virological methods · 2020Article
- Diagnostic Testing for Crimean-Congo Hemorrhagic Fever.Journal of clinical microbiology · 2020Review
- Portable sequencer in the fight against infectious disease.Journal of human genetics · 2020Review
- Review
- Development and validation of a pen side test for Rift Valley fever.PLoS neglected tropical diseases · 2019Article
- Real-Time Selective Sequencing with RUBRIC: Read Until with Basecall and Reference-Informed Criteria.Scientific reports · 2019Article
- Clinical metagenomics.Nature reviews. Genetics · 2019Review
- A cross-sectional screening by next-generation sequencing reveals Rickettsia, Coxiella, Francisella, Borrelia, Babesia, Theileria and Hemolivia species in ticks from Anatolia.Parasites & vectors · 2019Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWe describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. METHODOLOGY: An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. PRINCIPAL
findingsThe multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours.
conclusionsVirus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.
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