Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/27611
Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Combination Random Isothermal Amplification and Nanopore Sequencing For Rapid Identification of the Causative Agent of an Outbreak
Author(s): Hansen, Sören
Faye, Oumar
Sanabani, Sabri S
Faye, Martin
Böhlken-Fascher, Susanne
Faye, Ousmane
Sall, Amadou A
Bekaert, Michaël
Weidmann, Manfred
Czerny, Claus-Peter
Abd El Wahed, Ahmed
Contact Email: manfred.weidmann@stir.ac.uk
Keywords: Nanopore sequencing
Random isothermal amplification
Point of need diagnostics
Zika virus
Issue Date: 1-Sep-2018
Citation: 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. https://doi.org/10.1016/j.jcv.2018.07.001
Abstract: Background 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.
DOI Link: 10.1016/j.jcv.2018.07.001
Rights: This 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/

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