AB005. Genomics on site of detection of malaria

Abstract

Nanopore sequencer, MinION, has enabled sequencing analysis without pre-installation of expensive conventional sequencers or pre-requisite of specific skills in biological experiments. Even electric supply is not always necessary, by connecting MinION to a laptop PC. These features of MinION have opened the opportunity to enable precise genotyping of pathogens on site. In this study, we conducted genotyping of presumed drug resistance-causing SNVs in malaria parasites, Plasmodium falciparum. We subjected ten PCR amplicon-mixes covering these SNVs to the MinION sequencing. In spite that the sequence alignments generated by a Smith-Waterman-based program, SSEACH showed that the average sequence identity was 75%, we found that the mutations at a particular position could be called by the accuracy of 90%, when all the reads covering the corresponding positions were collectively evaluated. We provide the first simple experimental and analytical MinION sequencing procedure, which can be easily followed on site to effectively genotype pathogens of other tropical diseases.