Detection of the 5' region of the rubella virus genome in clinical samples by polymerase chain reaction

Background: Maternal rubella infection in early pregnancy has a high probability of causing congenital rubella infection. In some cases it may be difficult to establish the risk of congenital infection and polymerase chain reaction (PCR) based techniques are therefore being applied to prenatal diagnosis. Objectives: To investigate whether the non-structural region of the rubella virus (RV) genome can be detected in clinical samples using PCR, thereby providing a prenatal assay independent of those currently used to detect the structural protein coding region. Study Design: Oligonucleotide primers coding for RV nucleotides 1-17 and 541-558 from the non-structural protein coding region of the RV genome were used in a reverse transcription polymerase chain reaction (NS RT-PCR) to amplify 558 nucleotides of RV cDNA. Amplification of RV specific sequences was confirmed by Southern hybridization. Results: The specificity of the assay was confirmed by the detection of RV RNA from both wild-type and vaccine strains of RV, pharyngeal swabs from two adult males with acute rubella and products of conception from three women with serologically confirmed primary rubella in pregnancy. RV RNA was not detected in uninfected HEL and Vero cells or peripheral blood mononuclear cells. The results were concordant with those of an RT-PCR directed to the E1 protein coding region and with virus isolation. Conclusions: Detection of the non-structural coding region of the RV genome in clinical samples suggests that NS RT-PCR could be used as a confirmatory assay for prenatal diagnosis of congenital rubella, and that it will be of value for the identification of nucleotide changes in the 5' region of the RV genome.