Infectious metagenome of human clinical samples

Acute febrile illness is one of the most common presenting symptoms in clinical medicine, with a broad differential that includes a variety of infectious etiologies. Conventional laboratory testing can take days to a result, and most rapid detection technologies such as PCR are limited to the detection of a single or narrow range of targets. Unbiased diagnosis of all pathogens in a single test by metagenomic next-generation sequencing has proven feasible, although still requires >24 hours due to long sequencing times, lack of portable instrumentation, and/or the complexity of bioinformatics analysis. Here we propose to use the nanopore sequencer, a pocket sized, portable sequencing instrument, to develop a diagnostic assay to rapidly diagnose patients with acute febrile illness by screening for all potential pathogens in under 3 hours. We will all perform traditional Illumina sequencing for purposes of comparison and develop techniques to enrich for pathogen targets in clinical samples. We will test positive and negative control clinical samples from patients with acute febrile illness. We will also use it to investigate clinical samples from patients with febrile respiratory and systemic illnesses and infected by a variety of pathogens, including influenza virus, Ebola virus, Lassa virus, Chikungunya virus, enterovirus D68, and Plasmodium falciparum (malaria). We will also test the platform at point-of-care field sites in California (California Department of Public Health), Central America (American Red Cross), countries in South America and Africa. Ultimately, the goal of this project is implementation of a field-ready, real-time sequencing assay for unbiased pathogen diagnosis of acute febrile illness by metagenomic sequencing.