Genomic outbreak surveillance in resource-poor settings

Viral disease outbreaks are common in Africa, often starting in remote areas at the animal–human interface, with the potential to reach epidemic proportions. For example, the West African Ebola outbreak of 2014–2016 received significant international attention owing to its scale (~28,000 infected, ~11,000 dead) and international cases. Coincidentally, 2014 saw the development of an affordable, highly portable sequencing device that measures the disruption of ion charges caused by the different nucleic acid bases when a DNA strand passes through a nanopore. This palm-sized device was unlike conventional whole-genome sequencing platforms, which were large and non-portable, required a steady power supply and, if moved, needed extensive calibration. A paper by Quick et al., who were part of the swift international response to the Ebola outbreak, demonstrates how leveraging a novel sequencing technology challenged the notion that genomic surveillance could not be carried out in resource-poor field settings.

Quick et al. elegantly describe their steps to surmount all previous barriers to conducting on-site Ebola virus genome sequencing in remote settings using this new mobile nanopore sequencing technology. First, to generate enough material for sequencing from patient samples, they optimized a targeted reverse transcriptase PCR protocol using 38 primers sets to amplify the RNA genome of the Ebola virus and identified a minimal 11-amplicon set to cover 97% of the 19 kb Ebola virus genome.