Tree Lab: Portable genomics for early detection of plant viruses and pests in Sub-Saharan Africa
Authors: Boykin Laura M. , Sseruwagi Peter , Alicai Titus , Ateka Elijah , Mohammed Ibrahim Umar , Stanton Jo-Ann L. , Kayuki Charles , Mark Deogratius , Fute Tarcisius , Erasto Joel , Bachwenkizi Hilda , Muga Brenda , Mumo Naomi , Mwangi Jenniffer , Abidrabo Phillip , Okao-Okuja Geoffrey , Omuut Geresemu , Akol Jacinta , Apio Hellen B. , Osingada Francis , Kehoe Monica A. , Eccles David , Savill Anders , Lamb Stephen , Kinene Tonny , Rawle Christopher B. , Muralidhar Abishek , Mayall Kirsty , Tairo Fred , Ndunguru Joseph 
Published: July 2019

In this case study we successfully teamed the PDQeX DNA purification technology developed by MicroGEM, New Zealand, with the MinION and MinIT mobile sequencing devices developed by Oxford Nanopore Technologies to produce an effective point-of-need field diagnostic system. The PDQeX extracts DNA using a cocktail of thermophilic proteinases and cell wall degrading enzymes, thermo-responsive extractor cartridges and a temperature control unit. This single-step closed system delivers purified DNA with no cross contamination. The MinIT is a newly released data processing unit that converts MinION raw signal output into base called data locally in real time, removing the need for high specification computers and large file transfers from the field. All three devices are battery powered with an exceptionally small footprint that facilitates transport and set up.

To evaluate and validate capability of the system for unbiased pathogen identification by realtime sequencing in a farmer’s field setting, we analysed samples collected from cassava plants grown by subsistence farmers in three sub-Sahara African countries (Tanzania, Uganda and Kenya). A range of viral pathogens, all with similar symptoms, greatly reduce yield or completely destroy cassava crops. 800 million people worldwide depend on cassava for food and yearly income, and viral diseases are a significant constraint on its production (https://cassavavirusactionproject.com). Early pathogen detection at a molecular level has great potential to rescue crops within a single growing season by providing results that inform decisions on disease management, use of appropriate virus resistant or replacement planting.

This case study presented conditions of working in-field with limited or no access to mains power, laboratory infrastructure, internet connectivity and highly variable ambient temperature. An additional challenge is that, generally, plant material contains inhibitors of downstream molecular processes making effective DNA purification critical. We successfully undertook real-time on-farm genome sequencing of samples collected from cassava plants on three farms, one in each country. Cassava mosaic begomoviruses were detected by sequencing leaf, stem, tuber and insect samples. The entire process, from arrival on farm to diagnosis including sample collection, processing and provisional sequencing results was complete in under 4 hours. The need for accurate, rapid and on-site diagnosis grows as globalized human activity accelerates. This technical breakthrough has applications that are relevant to human and animal health, environmental management and conservation.