Brunker et al, 2020
Brunker K, Jaswant G, Thumbi SM et al. Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes (version 2; peer review: 3 approved). Wellcome Open Res 2020, 5:3 (https://doi.org/10.12688/wellcomeopenres.15518.2 )
New refinements are expected to reduce costs further from a current estimate of **~£60 to £35 per sample**, according to projections with flowcell re-use or the smaller low cost Flongle flowcell.
Brunker et al (2020) likewise used the Oxford Nanopore MinION, in their case, for RABV, in Kenya, Tanzania and the Philippines. They observe that "genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries." The reason for this is "limited laboratory infrastructure, cost, supply chains and other logistical challenges." However, low-cost and portable sequencing genomics technologies like the Oxford Nanopore MinION changes the game. With their paper, the authors aimed to "show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories." The most useful parts of the paper for the proposed project are its detailed explanation of their library preparation protocol, including the need for Biosafety Level 2 or 3 for handling of samples; cost estimates; and challenges and risks. In the area of technology transfer, they demonstrated that local laboratory technicians could be trained in library preparation, nanopore sequencing and basic bioinformatics.