Lab in a suitcase, and other adventures with Nanopore sequencing

Josh Quick
European Mobile Laboratory Project and the
University of Birmingham

recorded 19th June 2015, Wellcome Centre for Human Genetics, the University of Oxford

Genome surveillance of viral outbreaks is an increasingly important tool in outbreak epidemiology. However surveillance of the on-going Ebolavirus outbreak in West Africa has been hampered by logistical difficulties transporting samples to laboratories equipped with conventional sequencing instruments. Sequencing genomes at or near the point of diagnosis has potential benefits including maintaining sample quality, reduced time to results, difficulty in exporting material and the absence of shipping costs. We established the first genome surveillance system that can be transported in travel luggage on a passenger aircraft and deployed the system within European Mobile Labs infrastructure in Guinea.
Deployed in April 2015, we have established proof-of-principle for real-time genomic surveillance by generating over 40 genome sequences in as little as 48 hours from obtaining a patient sample and feeding the information back to the Ebola central coordination team. We showed that the sequence data could be transferred over a portable 3G mobile connection and that technological improvements in sequencing means it is now feasible to set up genomic surveillance rapidly even in resource-limited settings.