Nanopore sequencing for metagenomic diagnosis of infectious diseases

Unbiased diagnosis of all pathogens in a single test by metagenomic next-generation sequencing is now feasible, but has been limited to date by concerns regarding sensitivity and sample-to-answer turnaround times. Here we will describe the development, validation, and implementation of a rapid, field-ready assay for differential diagnosis of acute febrile illness on an Oxford Nanopore MinION sequencer that can be performed in under 6 hours. Nanopore sequencing data will be analyzed in real-time on a laptop computer using SURPIrt, a portable version of the SURPI computational pipeline that is currently being implemented for precision medicine diagnosis in hospitals. The eventual goal of these studies is clinical performance validation and deployment at field sites for use in clinical diagnosis and public health surveillance in patients with any unknown febrile illness — including but not limited to infections by Zika virus, Ebola virus, Lassa virus, chikungunya virus, dengue virus, and the malarial parasite Plasmodium falciparum.