Zika Virus Amplification Using Strand Displacement Isothermal Method and Sequencing Using Nanopore Technology

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 (2020) Zika Virus Amplification Using Strand Displacement Isothermal Method and Sequencing Using Nanopore Technology. In: Kobinger G & Racin T (eds.) Zika Virus: Methods and Protocols. Methods in Molecular Biology, 2142. New York: Springer, pp. 123-136. https://doi.org/10.1007/978-1-0716-0581-3_11

Abstract
Development of novel point of care diagnostic methods in order to help in implementing disease control program and identifying the causative agent of an outbreak is crucial. Classical diagnostic techniques, e.g., real-time polymerase chain reaction (PCR), rely on the presence of the nucleic acid sequence of the target in GenBank. In the case of an emerging new strain of a known or novel pathogen, false-negative results will be recorded by PCR. On the other hand, next-generation sequencing technologies allow rapid whole genome sequencing without previous knowledge of the target. One of these methods is the Oxford Nanopore sequencing technique, which utilizes a portable device named MinION and has a short run time. In this protocol, we describe the development of a novel nanopore sequencing protocol by combining random isothermal amplification technology and nanopore sequencing. The established protocol is rapid (

Keywords
Zika virus; Sequencing; Isothermal amplification; BLAST search; Outbreak