Molecular epidemiological analysis of community circulating respiratory syncytial virus in rural South Africa: Comparison of viruses and genotypes responsible for different disease manifestations

Human respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infection in children in both the industrialized and developing world. Most molecular epidemiological studies have, until now, focused on isolates from hospitalized infants in industrialized countries. Limited data have been available with regard to community circulating RSV, especially from Africa. The present study compares RSV isolates from infants attending rural community clinics in the Northern province of South Africa, with isolates from hospitalized infants in Soweto, near Johannesburg, South Africa, during the same period. A multiplex nested polymerase chain reaction was developed for analyzing the clinical specimens, a technique that permits subtyping and nucleotide sequence analysis of the second variable region of the G-protein gene. Community- and hospital-based isolates from young children in South Africa, as well as isolates from Mozambique were compared phylogenetically. One subgroup B community isolate was identified that had a G-protein truncated by approximately 35 amino acids, however, the other community isolates were not significantly different from hospital isolates. Evidence was found that the same RSV genotypes and viruses could cause mild upper respiratory tract infections or lower respiratory tract infections or severe RSV in young infants.