Broad Detection of Infectious Agents in Blood by Microarrays and Deep Sequencing

University Of California, San Francisco, San Francisco CA

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Abstract

DESCRIPTION (provided by applicant): Bloodborne infectious agents, including novel / emerging pathogens of concern, pose a continual threat to our blood supply and the safety of the 5 million transfusions performed annually in the United States. Here we propose to apply two state-of-the-art diagnostic technologies, a pan-viral microarray called the Virochip and massively parallel deep sequencing, to comprehensively identify infectious agents in blood. The Virochip will be expanded to cover bloodborne nonviral as well as viral pathogens, and we will rigorously assess analytical test characteristics (e.g. sensitivity, specificity, limits of detection, accuracy) for detection of pathogens associated with the most common bloodborne infections, including malaria, Chagas disease, HIV, hepatitis B/C, and dengue virus. The expanded Virochip and deep sequencing will then be used to launch a broad- spectrum surveillance program for bloodborne infectious agents. We will initially focus on analyzing serum samples from patients with nonA-E clinical hepatitis and deferred blood donors with post-donation acute illness such as fever - samples which carry a high a priori probability of harboring known / novel infectious agents. We will analyze random individual or pooled serum samples from donors matched by age, sex, and geographic location for infectious agents circulating in our blood supply. We will perform whole-genome sequencing and epidemiological screening by serology and PCR for any novel viruses identified in transfused blood. A major goal of this research is to assess the utility of Virochip and deep sequencing as comprehensive pathogen screening tools for ensuring transfusion safety. Identification of novel infectious agents in blood will also spur further detailed investigations into their epidemiology and pathogenicity.