Josh Quick | Nanopore Sequencing of Ebola Viruses Under Outbreak Conditions

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Determining the full-length genome sequences of viruses during disease outbreaks such as the ongoing Ebola virus outbreak in West Africa, which is of unprecedented scale with about 24,000 cases and 10,000 deaths as of March 2015, can provide important information about virus evolution, and ensure the continued efficacy of molecular diagnostics and sequence-based countermeasures such as siRNAs. However, transport of samples out of affected countries and be logistically and politically challenging, and establishing conventional Sanger or Next-Generation sequencing technologies, which are heavy and of larger foot-print, in outbreak areas poses significant logistical and technical hurdles. The MinION sequencing device represents an extremely attractive alternative due to its small size and robustness as compared to other platforms, and sequencing protocols have been developed allowing determination of the full-length sequences of Ebola viruses using this technology. We will share our experiences developing these protocols, as well as our experiences field-testing the device under outbreak conditions.

Related publications:
– A complete bacterial genome assembled de novo using only nanopore sequencing data, Nature Methods
https://nanoporetech.com/publications/2014/10/20/a-complete-bacterial-genome-assembled-de-novo-using-only-nanopore-sequencing-data-2
– Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella, Genome Biology
https://nanoporetech.com/publications/2015/05/14/rapid-draft-sequencing-and-real-time-nanopore-sequencing-in-a-hospital-outbreak-of-salmonella
– A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer, BioRxiv
https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-3-22

Flongle, GridION, MinION, MinIT, PromethION, and VolTRAX are currently for research use only.

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