The objectives of this program are to establish reagents and methods for rapid, simultaneous molecular detection of a wide range of viruses. Oligonucleotide primer sets useful for detection of some viral sequences by consensus PCR (cPCR) are established; however, at present there are neither comprehensive databases wherein investigators can obtain core sequences conserved within viral families, nor algorithms suitable for extracting such core sequences. We will create algorithms for extraction of core sequences; build virtual libraries of core sequences; synthesize primers suitable for detection of core sequences; and clone core sequences from representative viral families. These tools will be used to develop three complementary technologies for pathogen identification: cDNA microarrays, Domain-Specific Differential Display (DSDD), and multiplexed bead-based flow cytometric (MB-BFC) assays. Assays will be optimized using synthetic viral nucleic acid targets, validated using materials from experimentally infected cultured cells, and applied in programs focused on pathogen discovery and the epidemiology of chronic diseases. Our initial focus will be two chronic diseases where specific viral taxa are associated and potentially implicated in pathogenesis: bronchioalveolar cell carcinoma and amyotrophic lateral sclerosis.
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