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.
The objective is to characterize the circulating RSV strains collected from infants in South Africa during 2015-2017.
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.
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.
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.

© 2020 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.