Subacute sclerosing panencephalitis (SSPE) is a slow infection caused by measles virus in which several years separate recovery from typical acute measles and the development of a slowly progressive neurological disease. We have investigated replication of measles virus in brain tissue obtained after the onset of neurological disease and in the terminal phase. With a hybridization tomographic technique that combines in situ hybridization with macroradioautographic screening of large areas of tissue, we analyzed the spatial and temporal distribution of virus genes in vivo, using region-and strand-specific probes for the nucleocapsid and matrix genes. We show that early in the course of SSPE there is a global repression in the synthesis and expression of the genome. In the final stage of SSPE most infected cells still have depressed levels of plus-and minus-strand viral RNA and contain nucleocapsid protein but lack matrix protein. These findings provide further evidence for a unified view of slow infections of the nervous system, where the general constraints on virus gene expression provide an explanation for persistence of virus in the face of the host's immune response, and the slow evolution of pathological change. In the final phases of SSPE the more specific block in virus replication accounts for the cell-associated state of the virus and the difficulty in virus isolation.In slow infections caused by conventional viruses, periods often of years separate acquisition of virus and overt symptoms, and, during the long incubation period, virus persists in the face of the host's immune response. Subacute sclerosing panencephalitis (SSPE), for example, is a rare complication of measles infections in which the afflicted child ostensibly recovers from measles, develops normally for several years, and then slowly succumbs to a neurological disorder. The neurological disease reflects destruction of cells in the brain harboring measles virus despite high levels of virusspecific antibody in serum and cerebrospinal fluid (1-3).We have attributed the slow evolution of SSPE and the persistence of measles virus in this disease to restricted synthesis and expression of virus genes in the nervous system (4). These global constraints result in decreased levels of viral antigens in the cell and, pari passu, diminished effectiveness of immune surveillance in eradication of infected cells.Restricted gene expression also mitigates cellular injury accompanying virus replication, and tissue damage therefore accumulates slowly.This interpretation of the pathogenesis of SSPE emerged from investigations of tissues obtained for diagnosis relatively early in the disease (4). In the terminal state a more specific block in virus replication has been identified (5-9). The viral matrix (M) protein required for maturation of measles virus is markedly decreased in brain and in cell cultures derived from a patient with SSPE. In the latter case, mRNA for the M protein is present but is not translated effectively in vitro (9).In this arti...