There has been a lot of discussion and interest in using portable nanopore sequencing technology to undertake real-time genomic epidemiology in the response to Ebola virus outbreaks. This has obviously become more relevant in recent weeks because of the developing situation in the DRC. We have been developing and testing protocols and software for this goal as part of this project working with colleagues at Public Health England. We have drawn on our experiences of undertaking portable sequencing in Guinea in 2015 and methods developed for sequencing Zika in Brazil in 2016.
It is clear there is interest among fixed and mobile laboratory groups in terms of defining kit and reagent lists, laboratory standard operating protocols and bioinformatics pipeline to undertake this work. Therefore we have formalised our existing resources in order to create a package of documents, data, and software that we hope will be useful to everyone interested in Ebola virus sequencing for genomic epidemiology.
The package is hosted here: http://artic.network/ebov/
- a costed tick-list of equipment, reagents and consumables for a portable Nanopore sequencing lab,
- a primer scheme generated using the known diversity of Ebola virus (aliquots available on request),
- a step by step protocol that covers primers, amplicon preparation and clean-up, a single-tube protocol to barcode and adaptor ligate the library, and running MinION,
- a suggested software setup for installation prior to off-line work,
- a bioinformatics protocol for base-calling, mapping, polishing and consensus generation of MinION data,
- a preliminary phylogenetic analysis protocol.
We hope that by making these resources available we can foster a collaborative network of teams in which to exchange knowledge and experience. We are hosting these resources on the GitHub open source repository so they can be readily installed, copied, and modified as required.