A genomic surveillance system that can be packed into a suitcase and transported to the field to provide on-site Ebola virus genome sequencing, generating results within 24 hours of collecting samples, is reported in a study published in Nature. The paper describes the successful use of the system to conduct real-time surveillance of the recent West African epidemic in Guinea.
It is estimated that the Makona strain of the Ebola virus – responsible for the recent West African outbreak, which led to over 11,000 deaths – contains 16-27 mutations in each copy of its genome. Genome sequencing can be used to track this evolution and is increasingly sought after for outbreak surveillance as it can be used to inform decisions on virus control measures, so long as the results are generated quickly enough. However, genome surveillance during the West Africa epidemic has been sporadic owing to a lack of local sequencing capacity and difficulties with transporting samples to remote sequencing facilities.
Nicholas Loman and colleagues created a genomic surveillance system that uses a DNA sequencing instrument that weighs less than 100 grams, can be transported in standard airline luggage and plugs into the USB port of a laptop. The authors used the system to sequence and analyse 142 Ebola virus samples collected from March to October 2015. They find they can generate results in less than 24 hours, with the sequencing process taking less than an hour. The authors conclude that this shows real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.