Open Peer Review Discuss this article (0) Comments RESEARCH NOTE Real time portable genome sequencing for global food security [version 1; referees: 1 approved, 1 approved with reservations] Laura Boykin , Ammar Ghalab , Bruno Rossitto De Marchi , Anders Savill , James M. Wainaina , Tonny Kinene , Stephen Lamb , Myriam Rodrigues , Monica Kehoe , Joseph Ndunguru , Fred Tairo , Peter Sseruwagi , Charles Kayuki , Deogratius Mark , Joel Erasto , Hilda Bachwenkizi , Titus Alicai , Geoffrey Okao-Okuja , Phillip Abridrabo , Emmanuel Ogwok , John Francis Osingada , Jimmy Akono , Elijah Ateka , Brenda Muga , Samuel Kiarie 6 School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009, Australia School of Agriculture, Dept. of Plant Protection, São Paulo State University (UNESP), Botucatu (SP), CEP 18610-307, Brazil Crop Protection Branch, Department of Agriculture and Food Western Australia, South Perth, Western Australia, 6151, Australia Mikocheni Agricultural Research Institute (MARI), Dar es Salaam, Tanzania National Crops Resources Research Institute (NaCRRI), Kampala, Uganda Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya Abstract Crop losses due to viral diseases and pests are major constraints on food security and income for millions of households in sub-Saharan Africa (SSA). Such losses can be reduced if plant diseases and pests are correctly diagnosed and identified early. Currently, accurate diagnosis for definitive identification of plant viruses and their vectors in SSA mostly relies on standard PCR and next generation sequencing technologies (NGS). However, it can take up to 6 months before results generated using these approaches are available. The long time taken to detect or identify viruses impedes quick, within-season decision-making necessary for early action, crop protection advice and disease control measures by farmers. This ultimately compounds the magnitude of crop losses and food shortages suffered by farmers. The MinION portable pocket DNA sequencer was used, to our knowledge globally for the first time, to sequence whole plant virus genomes. We used this technology to identify the begomoviruses causing the devastating cassava mosaic virus, which is ravaging smallholder farmers’ crops in sub-Saharan Africa. Keywords cassava, uganda, kenya, tanzania, nanopore, minion, SDG2 1 1 1,2 1 1 1 1 1 3 4 4 4 4 4 4 4 5 5 5 5 5 5 6 6 6 1 2 3 4 5 6 Referee Status: Invited Referees version 1 published 18 Jul 2018 1 2 report report , U.S. Food and Drug Ruth E. Timme Administration, USA 1 , Institute of Alfonso Benítez-Páez Agrochemistry and Food Technology-Spanish National Research Council (IATA-CSIC), Spain 2 18 Jul 2018, :1101 ( First published: 7 ) https://doi.org/10.12688/f1000research.15507.1 18 Jul 2018, :1101 ( Latest published: 7 ) https://doi.org/10.12688/f1000research.15507.1 v1 Page 1 of 11 F1000Research 2018, 7:1101 Last updated: 13 NOV 2018