The SA Pathology Microbiology and Infectious Diseases Laboratories, Molecular diagnostics laboratory (RAH) performs real-time in-house PCR assays for the diagnosis of viral infections. The detection of viruses in clinical samples by in-house molecular methods is not new, however as the volume of samples being tested and the complexity of assays continues to grow new challenges emerge. This presentation describes the Molecular diagnostics laboratory’s responses to these challenges and presents the epidemiological results derived from these assays.