Nanotrap particle viral enrichment technology for enabling portal, next-generation sequencing-based surveillance

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PROJECT SUMMARY RNA viruses, such as influenza and the Ebola virus, have been classified as the greatest threat for causing a global pandemic given their high mutation rates and abilities to jump between host species. National and global agencies have called for research and development efforts to improve RNA virus surveillance capabilities. While the tools for surveilling DNA viruses have advanced dramatically over the last two decades, the unique properties of RNA viruses have thwarted attempts to develop similar surveillance tools for them. Current state-of-the-art screening methods, like RT-qPCR and genome sequencing, require heavy equipment and wet-lab facilities, which has hindered progress of field-deployable surveillance and monitoring practices by federal agencies, such as the Centers for Disease Control’s Influenza Genomics Team (IGT). Furthermore, pathogen loads from biological samples decay rapidly over an infection’s course, decreasing below detectable levels only days after symptoms appear. Thus, there is a need to define new protocols and devices for RNA virus sample enrichment that combine speed, cost-effectiveness, ease of use, and the capacity for field operation. This need is underscored by early field work by the IGT, which utilized a potential new field-deployable viral surveillance sequencing protocol but demonstrated that the sensitivity and specificity of this protocol is lacking. Collaborations between the IGT and the applicant, Ceres Nanosciences, has led to the current SBIR Phase I initiative, aimed at testing the feasibility of leveraging Ceres’ innovative nanoparticle technology, termed Nanotrap (NT), as a companion virus enrichment device that is inexpensive, easy-to-use, and rapid enough to integrate prior to the use of RNA and DNA viral sequencing tools recently developed by the CDC and other organizations. The major technical objective now is to transition this work into a portable device that can be used to enrich viruses from samples collected in the field, so that it can be used in coordination with field-deployable viral sequencing tools. This work will be accomplished through the following specific aims over a nine-month project period: Aim 1 will demonstrate the feasibility of using NT particles to capture and concentrate influenza pathogens from low-titer (<30 ct), contrived viral transport media (VTM) samples and improve MinION sensitivity; Aim 2 will test the performance characteristics of using the NT-enabled pre-enrichment step prior to genomic sequencing to detect the presence of respiratory pathogens. The importance of this work would be the generation of a technology to significantly improve the rapid identification and characterization of known and novel strains of RNA or DNA viruses circulating in samples collected from the field. The long-term commercial product resulting from this work would be an optimized, validated, field-deployable virus enrichment device that would be marketed for use by the CDC, USDA, DHS, DoD, and any other laboratories that monitor RNA- or DNA-based infectious diseases.