2006 Annual Report 4d.Progress report. This report serves to document research conducted under a reimbursable agreement (No. 5805410-5-430) between ARS and the Colorado State University (Subaward No. G-4728-3). Additional details of research can be found in the report for the parent project 5410-32000-011-00D Molecular Biology and Pathogenesis of Arboviruses. The goals of this project are to develop assay methods for the clinically similar West Nile Virus (WNV) and St. Louis Encephalitis (SLE) viruses, as well as the instrumentation that allows the assays to be carried out in the field and in laboratory settings. The basis of the assay methods to be investigated is surface enhanced Raman spectroscopy (SERS). It was proposed that the extraordinarily large signal enhancement attendant upon localization of some dyes at silver or gold surfaces would provide the sensitivity necessary for detection of WNV and SLE. The two assay formats chosen for examination were a nucleic acid hybridization (NAH) assay and an immunoassay. The overall project involves a three way collaboration: organic synthesis (UW), assay development (ABADRL and UW) and Raman instrumentation development to complement the assays (DeltaNu). The ABADRL temporary staff for this project have been hired and components for the NAH assay have been synthesized. Preliminary studies have developed the unique hybridization condition necessary for this assay and are being optimized. New Raman instrumentation have been made that afford more flexibility in assay design.