Serotyping dengue virus with isothermal amplification and a portable sequencer

Area of Science:

• Molecular Biology
• Infectious Diseases
• Genomics

Background:

• Portable nanopore DNA sequencers offer field-based sample analysis capabilities.
• Traditional pathogen detection methods can be time-consuming and require specialized laboratory equipment.

Purpose of the Study:

• To develop a novel, field-deployable method for detecting and genotyping tropical disease pathogens.
• To utilize dengue fever as a model to validate the new sequencing approach.

Main Methods:

• Integration of a portable nanopore sequencer with isothermal amplification.
• Direct sequencing of viral genomes from serum samples.
• Clinical analysis of patient blood samples from Indonesia, Vietnam, and Thailand.

Main Results:

• Successful detection and serotyping of dengue virus with high sensitivity and specificity.
• Achieved an overall successful detection rate of 79% and identified 58 single nucleotide variants (SNVs).
• Demonstrated the method's effectiveness across diverse geographical patient cohorts.

Conclusions:

• The developed method enables rapid, single-day pathogen detection and genotyping directly in the field.
• Provides crucial genetic information for analyzing pathogen diversification and epidemiological studies.
• Highlights the potential of portable sequencing for real-time infectious disease surveillance.