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2017-11-20Zeitschriftenartikel DOI: 10.1371/journal.pntd.0006075
Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics
dc.contributor.authorBrinkmann, Annika
dc.contributor.authorErgünay, Koray
dc.contributor.authorRadonić, Aleksandar
dc.contributor.authorTufan, Zeliha Kocak
dc.contributor.authorDomingo, Cristina
dc.contributor.authorNitsche, Andreas
dc.date.accessioned2018-05-07T21:00:39Z
dc.date.available2018-05-07T21:00:39Z
dc.date.created2018-01-30
dc.date.issued2017-11-20none
dc.identifier.otherhttp://edoc.rki.de/oa/articles/re6A0dgOkH1/PDF/26gxY86rcJaTg.pdf
dc.identifier.urihttp://edoc.rki.de/176904/2959
dc.description.abstractBackground: We 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 findings: The 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. Conclusions: Virus 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.eng
dc.language.isoeng
dc.publisherRobert Koch-Institut, Biologische Sicherheit
dc.subject.ddc610 Medizin
dc.titleDevelopment and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics
dc.typeperiodicalPart
dc.identifier.urnurn:nbn:de:0257-10057163
dc.identifier.doi10.1371/journal.pntd.0006075
dc.identifier.doihttp://dx.doi.org/10.25646/2884
local.edoc.container-titlePLoS Neglected Tropical Diseases
local.edoc.fp-subtypeArtikel
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttp://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0006075
local.edoc.container-publisher-namePublic Library of Science
local.edoc.container-volume11
local.edoc.container-issue11
local.edoc.container-year2017

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