Combination random isothermal amplification and nanopore sequencing for rapid identification of the causative agent of an outbreak

•The causative agent of an outbreak can be identified by nanopore sequencing in 7 h.•The whole procedure was conducted in a mobile suitcase laboratory, which allows the use under field condition.•An offline sequence data analysis protocol was applied. Outbreaks of fever of unknown origin start with...

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Published in:Journal of clinical virology Vol. 106; pp. 23 - 27
Main Authors: 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
Format: Journal Article
Language:English
Published: Netherlands Elsevier B.V 01-09-2018
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Summary:•The causative agent of an outbreak can be identified by nanopore sequencing in 7 h.•The whole procedure was conducted in a mobile suitcase laboratory, which allows the use under field condition.•An offline sequence data analysis protocol was applied. 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. To develop a rapid and field applicable protocol to allow the identification of the causative agent of an outbreak. 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. 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. 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.
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ISSN:1386-6532
1873-5967
DOI:10.1016/j.jcv.2018.07.001