The utility of in situ--based methodologies including in situ polymerase chain reaction for the diagnosis and study of viral infections.

Molecular in situ-based assays are a useful adjunct to the diagnosis of viral infections by the surgical and cytopathologist. In some cases, the viral nucleic acids and/or proteins are abundant and easily detected by in situ hybridization or immunohistochemistry. In other cases, such as the one integrated provirus typical of latent retroviral localization, in situ polymerase chain reaction amplification is required to localize the virus in the intact cell. Direct correlation of viral localization and the histologic changes will demonstrate in many cases that routine histopathology often does not provide sufficient information to determine what specific cells are infected and/or the number of infected cells in a given biopsy. By combining this information with, for example, cytokine localization, one can elucidate much about the pathophysiology of the viral infection that cannot be afforded by polymerase chain reaction-based methods alone.