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Serotyping Dengue virus using an isothermal amplification and a portable sequencer

Identifiers: SRA: DRP003849
BioProject: PRJDB4297
UT-MGS: DRP003849
Study Type: 
Other
Abstract: A novel method for detecting and genotyping of pathogens of a tropical disease, using Dengue fever as a model case. This method consists of an isothermal amplification of pathogen DNA followed by the amplicon sequencing using a portable sequencer. Starting from a serum sample, the entire procedure can be finished in a single day, requiring no laboratory instruments or even electric supplies, thus, could be performed in field of a developing country. After evaluating its sufficient accuracy and sensitivity using laboratory materials, we applied this method for serotyping Dengue viruses in clinical samples. For the blood samples collected from a total of 147 Indonesian patients, we demonstrate this method enables clinical identification and serotyping of the infecting Dengue viruses with high accuracy and sensitivity. In addition to the precise serotyping, nucleotide polymorphisms of the viral genomes could be also detected. By strikingly reducing the technical difficulties in conducting sequencing analysis in field circumstances, this method should accelerate the genotyping of infecting pathogens, which should explain the varying clinical symptoms.
Description: A novel method for detecting and genotyping of pathogens of a tropical disease, using Dengue fever as a model case. This method consists of an isothermal amplification of pathogen DNA followed by the amplicon sequencing using a portable sequencer. Starting from a serum sample, the entire procedure can be finished in a single day, requiring no laboratory instruments or even electric supplies, thus, could be performed in field of a developing country. After evaluating its sufficient accuracy and sensitivity using laboratory materials, we applied this method for serotyping Dengue viruses in clinical samples. For the blood samples collected from a total of 147 Indonesian patients, we demonstrate this method enables clinical identification and serotyping of the infecting Dengue viruses with high accuracy and sensitivity. In addition to the precise serotyping, nucleotide polymorphisms of the viral genomes could be also detected. By strikingly reducing the technical difficulties in conducting sequencing analysis in field circumstances, this method should accelerate the genotyping of infecting pathogens, which should explain the varying clinical symptoms.

Related SRA data

Experiments:
6 ( 6 samples )
Runs:
6 (75.7Mbp; 47.2Mb)