Portable DNA sequencing in remote East African farms

Charles Kayuki (Tanzania Agricultural Research Institute – Mikocheni) opened his lightning talk by explaining that his talk would represent the Cassava Virus Action Project, an extensive team project that uses genomics to fight plant pathogens, especially in cassava. Why cassava? The crop is easy to grow, an industrial source of starch, and a staple food for millions, making it crucial to maintain, particularly as the yield is often fairly low. Cassava brown streak and mosaic viruses infect crops and can be devastating to small farmers and communities, meaning early diagnosis of these plant diseases is key.

Charles went on to describe how the use of modern sequencing and similar technologies in the developing world is currently extremely limited for a number of reasons, particularly due to the high cost of establishing and maintaining facilities, time investment and the costs of shipping samples to and from centralised locations. The solution, Charles explained, has to be portable, low cost, decentralised technology, which lead the team to use the MinION and MinIT, in field, at the affected farm. DNA extraction was performed with PDQeX, and the extract prepped and loaded on to the MinION. Real-time access to the results and detection of the virus allowed the team to immediately advise the farmer, considering the age of any affected plants, as to the best course of action to take for their crop.

Overall, Charles concluded that the MinION and other field-forward technologies are portable, affordable, and advantageous for tackling problems in developing countries.