SPADA Draft Documents

The SPADA In Silico Analysis Working Group 2

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Abstract/Objective: 26 Well defined and well characterized assays are needed for accurately detecting pathogens in 27 environmental and patient samples and also for evaluation of the efficacy of a medical 28 countermeasure that may be administered to patients. The polymerase chain reaction (PCR) 29 remains the gold standard for pathogen detection due to the simplicity of its instrumentation, low 30 cost of reagents, and outstanding limit of detection, sensitivity, and specificity. However, 31 creation of such PCR assays often involves iterations of design, preliminary testing, and 32 thorough validation with clinical isolates and testing in relevant matrices, which can be time 33 consuming, costly, and result in sub-optimal assays. Since formal validation (e.g. for Emergency 34 Use Authorization or Food and Drug Administration licensure) of an infectious disease assay is 35 estimated to cost at least 1 million USD and require 6-12 months, having a well-designed assay 36 upfront is a critical first step. Yet, many assays described in the literature utilized limited design 37 capabilities and many initially promising assays fail the validation process, resulting in increased 38 costs and timelines for successful product development. Here we describe approaches to improve 39 this process and reduce the time and cost, by utilizing available databases of whole genome 40 pathogen sequences combined with modern bioinformatics and physical modeling tools. While 41 the computational approaches outlined in this document by no means obviate the need for wet 42

2 Stakeholder Panel on Agent Detection Assays (SPADA) In Silico Analysis Working Group members: Jessica Appler, Linda Beck, Trevor Brown, Sharon Brunelle, Donald Cronce, Matthew Davenport, Bruce Goodwin, Scott Jackson, Jeffrey Koehler, Nancy Lin, Timothy Minogue, Victoria Olson, Richard Ozanich, Kristian Roth, John SantaLucia, Sanjiv Shah, Ricky Soong, Shanmuga Sozhamannan

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