February 26, 2019 – MicroGEM today announced that the Proceedings of the National Academy of Sciences (PNAS) published an article describing the ability to screen Cassava crops for Cassava Mosaic Virus (CMV) using MicroGEM’s PDQeX for rapid DNA extraction. The PDQeX was used as the enabling technology to complement DNA sequencing being conducted in the field in real-time.
The Cassava Virus Action Project (CVAP) is a network of researchers and farmers collaborating to use genomic technologies to improve the management of Cassava viruses. CVAP researchers undertook the study to positively diagnose CMV through molecular testing at the point-of-need. CVAP member, Jo Stanton, PhD, Senior Research Fellow, Department of Anatomy, University of Otago, along with MicroGEM researchers and CVAP members, David Saul, PhD, and Abishek Muralidhar, PhD, provided rapid DNA extraction expertise.
The collaboration between East African, Australian and New Zealand scientists diagnosed CMV using whole genome sequencing in the field at remote African farms. This achievement opens the way to rapid and accurate pathogen identification permitting immediate corrective action to prevent crop failure. For the subsistence farmers of East Africa, this is the difference between having food and an income or going hungry.
Two technologies made on-farm whole genome sequencing possible. MicroGEM’s PDQeX enabled on-site DNA extraction. Oxford Nanopore’s MinIT base-calling mini-supercomputer and MinION, a portable DNA sequencer, made it possible to select either leaf, stem or insect samples on-farm, prepare the DNA for sequencing and convert raw data output to base-calls for data interpretation, all in real time. The whole process took less than 4 hours from sampling to diagnostic result and all devices were run on battery working outdoors at isolated African cassava farms.
The team worked with cassava growers in three countries: Tanzania, Uganda and Kenya. Cassava is under attack from viral pathogens that reduce or destroy the crop. Farmers affected by the growing viral threat depend on cassava for their main food source and yearly income. Crop failure means a loss of food security and no income for school fees, supplies, farm improvements or maintenance. 800 million people worldwide depend on cassava as their main source of calories and virus spread is a significant global threat.
On a broader level, this breakthrough has applications in areas of human and animal health, environmental management and conservation. The need for accurate, rapid and on-site diagnosis is growing as globalization of human activity accelerates.
Download the article (pdf).
Shaffer, L. (2019). Inner Workings: Portable DNA sequencer helps farmers stymie devastating viruses. Proceedings of the National Academy of Sciences,116(9), 3351-3353. doi:10.1073/pnas.1901806116