Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/27611
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dc.contributor.authorHansen, Sörenen_UK
dc.contributor.authorFaye, Oumaren_UK
dc.contributor.authorSanabani, Sabri Sen_UK
dc.contributor.authorFaye, Martinen_UK
dc.contributor.authorBöhlken-Fascher, Susanneen_UK
dc.contributor.authorFaye, Ousmaneen_UK
dc.contributor.authorSall, Amadou Aen_UK
dc.contributor.authorBekaert, Michaëlen_UK
dc.contributor.authorWeidmann, Manfreden_UK
dc.contributor.authorCzerny, Claus-Peteren_UK
dc.contributor.authorAbd El Wahed, Ahmeden_UK
dc.date.accessioned2018-08-14T00:01:41Z-
dc.date.available2018-08-14T00:01:41Z-
dc.date.issued2018-09-01en_UK
dc.identifier.urihttp://hdl.handle.net/1893/27611-
dc.description.abstractBackground Outbreaks of fever of unknown origin start with nonspecific symptoms and case definition is only slowly developed and adapted, therefore, identifying the causative agent is crucial to ensure suitable treatment and control measures. As an alternative method for Polymerase Chain Reaction in molecular diagnostics diagnostic, metagenomics can be applied to identify the pathogen responsible for the outbreak through sequencing all nucleic acids present in a sample extract. Sequencing data obtained can identify new or variants of known agents. Objectives To develop a rapid and field applicable protocol to allow the identification of the causative agent of an outbreak. Study design We explored a sequencing protocol relying on multiple displacement isothermal amplification and nanopore sequencing in order to allow the identification of the causative agent in a sample. To develop the procedure, a mock sample consisting of supernatant from Zika virus tissue culture was used. Results The procedure took under seven hours including sample preparation and data analysis using an offline BLAST search. In total, 63,678 sequence files covering around 10,000 bases were extracted. BLAST search revealed the presence of Zika virus. Conclusion In conclusion, the protocol has potential for point of need sequencing to identify RNA viruses. The whole procedure was operated in a suitcase laboratory. However, the procedure is cooling chain dependent and the cost per sequencing run is still high.en_UK
dc.language.isoenen_UK
dc.publisherElsevieren_UK
dc.relationHansen S, Faye O, Sanabani SS, Faye M, Böhlken-Fascher S, Faye O, Sall AA, Bekaert M, Weidmann M, Czerny C & Abd El Wahed A (2018) Combination Random Isothermal Amplification and Nanopore Sequencing For Rapid Identification of the Causative Agent of an Outbreak. Journal of Clinical Virology, 106, pp. 23-27. https://doi.org/10.1016/j.jcv.2018.07.001en_UK
dc.rightsThis item has been embargoed for a period. During the embargo please use the Request a Copy feature at the foot of the Repository record to request a copy directly from the author. You can only request a copy if you wish to use this work for your own research or private study. Accepted refereed manuscript of: Hansen S, Faye O, Sanabani SS, Faye M, Böhlken-Fascher S, Faye O, Sall AA, Bekaert M, Weidmann M, Czerny C & Abd El Wahed A (2018) Combination Random Isothermal Amplification and Nanopore Sequencing For Rapid Identification of the Causative Agent of an Outbreak, Journal of Clinical Virology, 106, pp. 23-27. DOI: 10.1016/j.jcv.2018.07.001 © 2018, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/en_UK
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en_UK
dc.subjectNanopore sequencingen_UK
dc.subjectRandom isothermal amplificationen_UK
dc.subjectPoint of need diagnosticsen_UK
dc.subjectZika virusen_UK
dc.titleCombination Random Isothermal Amplification and Nanopore Sequencing For Rapid Identification of the Causative Agent of an Outbreaken_UK
dc.typeJournal Articleen_UK
dc.rights.embargodate2019-07-07en_UK
dc.rights.embargoreason[2017_06_11-ZIKV sequencing_Semifinal 3.pdf] Publisher requires embargo of 12 months after formal publication.en_UK
dc.identifier.doi10.1016/j.jcv.2018.07.001en_UK
dc.identifier.pmid30015285en_UK
dc.citation.jtitleJournal of Clinical Virologyen_UK
dc.citation.issn1386-6532en_UK
dc.citation.volume106en_UK
dc.citation.spage23en_UK
dc.citation.epage27en_UK
dc.citation.publicationstatusPublisheden_UK
dc.citation.peerreviewedRefereeden_UK
dc.type.statusAM - Accepted Manuscripten_UK
dc.author.emailmanfred.weidmann@stir.ac.uken_UK
dc.citation.date06/07/2018en_UK
dc.contributor.affiliationGeorg-August University Gottingenen_UK
dc.contributor.affiliationInstitut Pasteur de Dakaren_UK
dc.contributor.affiliationUniversity of Sao Pauloen_UK
dc.contributor.affiliationInstitut Pasteur de Dakaren_UK
dc.contributor.affiliationGeorg-August University Gottingenen_UK
dc.contributor.affiliationInstitut Pasteur de Dakaren_UK
dc.contributor.affiliationInstitut Pasteur de Dakaren_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationGeorg-August University Gottingenen_UK
dc.contributor.affiliationGeorg-August University Gottingenen_UK
dc.identifier.isiWOS:000442361000006en_UK
dc.identifier.scopusid2-s2.0-85049749753en_UK
dc.identifier.wtid942731en_UK
dc.contributor.orcid0000-0002-1206-7654en_UK
dc.contributor.orcid0000-0002-7063-7491en_UK
dc.date.accepted2018-07-02en_UK
dc.date.filedepositdate2018-07-23en_UK
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