Viral Infection Detection Understanding viral pathogenesis is critical for prevention of outbreaks, development of antiviral drugs, and biodefense. We have developed a novel molecular beacon based approach to directly detect the viral genome and characterize the formation of inclusion bodies in living cells. Using a clinical isolate of bovine respiratory syncytial virus (bRSV) as a model system, we designed molecular beacons to target the viral genome, therefore having a positive identification of infected cells. For example, by imaging the fluorescence signal of molecular beacons in live, primary bovine turbinate cells, the spreading of bRSV was monitored for 7 days with a high signal-to-noise ratio (Fig. 3, for days 1, 3, 5 and 7 post-infection). We found that molecular beacon signal could be detected in single living cells infected, even when the initial viral titer (2x103.6 TCID50/ml) was diluted a thousand-fold, demonstrating high detection sensitivity. Low background in uninfected cells, and simultaneous staining of fixed cells with molecular beacons and antibodies showed high detection specificity. Using confocal microscopy to image the viral genome in live, infected cells, we were able to observe a connected, highly three-dimensional, amorphous inclusion-body structure not seen in fixed cells. Taken together, the use of molecular beacons for active virus imaging provides a powerful tool for rapid viral infection detection, the characterization of RNA viruses, and the design of new antiviral drugs.