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Updated: Dec 22, 2025
06:18
Multiplexed Isothermal Amplification Based Diagnostic Platform to Detect Zika, Chikungunya, and Dengue 1
Published on: March 13, 2018
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Zika Virus Amplification Using Strand Displacement Isothermal Method and Sequencing Using Nanopore Technology
Sören Hansen1, Oumar Faye2, Sabri S Sanabani3
1Division of Microbiology and Animal Hygiene, University of Goettingen, Goettingen, Germany.
Methods in Molecular Biology (Clifton, N.J.)
|May 6, 2020
Summary
This study presents a rapid nanopore sequencing protocol for pathogen identification. The method enables quick and sensitive detection of viruses like Zika, even in remote locations without internet access.
Area of Science:
- Molecular Biology
- Genomics
- Infectious Disease Diagnostics
Background:
- Classical diagnostic methods like real-time PCR may yield false negatives for novel pathogen strains.
- Next-generation sequencing offers whole genome sequencing without prior target knowledge.
- Oxford Nanopore sequencing provides rapid, portable genomic analysis.
Purpose of the Study:
- To develop a novel, rapid point-of-care diagnostic method for pathogen identification during outbreaks.
- To establish a sensitive nanopore sequencing protocol for detecting emerging viral strains.
- To enable remote diagnostics through an offline data analysis capability.
Main Methods:
- Development of a novel nanopore sequencing protocol integrating random isothermal amplification.
- Utilized Oxford Nanopore's portable MinION device for rapid sequencing.
- Implemented an offline BLAST search for data analysis, enabling remote use.
Main Results:
- The protocol is rapid, completing in under 7 hours.
- Demonstrated high sensitivity, detecting Zika virus when it constituted <4% of sequenced RNA.
- Successful implementation of an offline analysis tool for remote diagnostic applications.
Conclusions:
- The developed nanopore sequencing protocol is a rapid and sensitive diagnostic tool for pathogen identification.
- This method overcomes limitations of traditional PCR for novel or emerging strains.
- The offline analysis feature makes the protocol suitable for resource-limited and remote settings.
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