Characterization of human respiratory syncytial virus (RSV) isolated from HIV‐exposed‐uninfected and HIV‐unexposed infants in South Africa during 2015‐2017

BACKGROUND: RSV is a leading cause of lower respiratory tract infection in infants. Monitoring RSV glycoprotein sequences is critical for understanding RSV epidemiology and viral antigenicity in the effort to develop anti‐RSV prophylactics and therapeutics. OBJECTIVES: The objective is to characterize the circulating RSV strains collected from infants in South Africa during 2015‐2017. METHODS: A subset of 150 RSV‐positive samples obtained in South Africa from HIV‐unexposed and HIV‐exposed‐uninfected infants from 2015 to 2017, were selected for high‐throughput next‐generation sequencing of the RSV F and G glycoprotein genes. The RSV G and F sequences were analyzed by a bioinformatic pipeline and compared to the USA samples from the same three‐year period. RESULTS: Both RSV A and RSV B co‐circulated in South Africa during 2015‐2017, with a shift from RSV A (58%‐61% in 2015‐2016) to RSV B (69%) in 2017. RSV A ON1 and RSV B BA9 genotypes emerged as the most prevalent genotypes in 2017. Variations at the F protein antigenic sites were observed for both RSV A and B strains, with dominant changes (L172Q/S173L) at antigenic site V observed in RSV B strains. RSV A and B F protein sequences from South Africa were very similar to the USA isolates except for a higher rate of RSV A NA1 and RSV B BA10 genotypes in South Africa. CONCLUSION: RSV G and F genes continue to evolve and exhibit both local and global circulation patterns in South Africa, supporting the need for continued national surveillance.