Use of the polymerase chain reaction for the sensitive detection of St. Louis encephalitis viral RNA

Polymerase chain reaction (PCR) assays were developed for the detection of RNA from the St. Louis encephalitis (SLE) virus. Using computer-assisted analysis of the MSI-7 strain SLE virus genome, two primer pairs were selected from the capsid-coding and the membrane associated protein-coding genes, and one from the envelope-coding gene. Reverse transcription was primed with either specific oligomers or with random hexamers; these methods were compared for cDNA synthesis and subsequent PCR amplification with the oligomeric pairs. Random hexamers provided more sensitive detection of viral RNA. Each primer pair specifically amplified the expected sized fragment from the Parton SLE strain grown in Aedes albopictus cells, but did not amplify Aedes albopictus cell RNA controls. The technique also detected SLE virus RNA in 1 pg of total cellular RNA added to a background of 1 μg boiled brain tissue, and in 0.5 pg of total RNA added to homogenized mosquito abdomen. PCR-based assays may be adaptable to detect SLE virus RNA in naturally infected mosquitoes, birds, and human cerebrospinal fluid and brain.