GRAID's Portable DNA sequencer project helps identify infectious diseases in developing countries

An international consortium of medical scientists has launched the Global Research Alliance in Infectious Diseases, GRAID, to help train local researchers to quickly sequence potential pathogens in developing countries. 

Rapid onsite sequencing of DNA in the field using a portable sequencer can help diagnose viruses, bacteria, fungi and other pathogens in real time, enabling a fast response to disease outbreaks in humans and animals. GRAID is working to provide hands-on experience in developing countries with MinION, a small sequencer that can process 1 Mb (megabit) of nucleotide with no interruption.

GRAID's ongoing work in introducing MinION and using its data is described in an article in BMC Research Notes, Feb. 12. The authors report specifically on the results of a training course in Indonesia which looked at an organism that infects cattle, Theileria orientalis. 

T. orientalis is a tickborne parasite that causes infectious anemia in cows and can result in animal death leading to economic losses. It is not easily detected, because the animals may not show symptoms.

The lead author, Lucky Runtuwene, is in the Department of Computational Biology and Medical Science, The University of Tokyo.

The consortium has held six training courses in four countries in Asia, Europe, and Africa. It has also published research papers on the malaria parasite and dengue and developed software to analyze and interpret MinION-generated data.

A useful field tool 

The authors describe the advantages of MinION, as "low overhead cost, simplicity of library preparation, real-time sequencing and a small sequencer size as compared to the other sequencing techniques." It's also easily transportable, they note, and provides good quality data, although, as they mention, it has a higher error rate than more advanced sequencers. 

MinION, they report, was used in Africa to identify the Ebola virus in patients, and to determine that the Lassa virus was not transmissible to humans. 

In Indonesia GRAID's 2019 training course taught participants how "to identify the pathogens in blood samples using a metagenomic sequencing approach." The participants were directly involved "in all aspects of the sample preparation and sequencing, starting from DNA extraction, DNA concentration measurement, library preparation and sequencing." They used two web services, BLAST and One Codex, to identify pathogens.

The authors report that one of the sample sequences in this training course was "not optimal," but they determined the probable cause as an error in the length of time of one part of the DNA cleaning process. This will be stressed in future courses, they note.

The participants were able to construct the genome of T. orientalis from their results.

The authors conclude, "We believe, with our activities that focus on portable sequencer MinION, we will be able to broaden this technology to countries where sequencing is still not a routine research technology. This will eventually open new exciting studies, such as identifying disease-causing agents in an outbreak where shipping samples to another center or country is not possible."