Genomic_drivers_of_syphilis_diversity_in_South_Africa

Syphilis, caused by the spirochaete Treponema pallidum (TP) is one of the oldest known sexually transmitted diseases. The incidence of syphilis has increased substantially over the last decade in many high-income countries (HICs), and syphilis remains one of the most important global health challenges today. Genomic surveillance of TP is valuable, both for understanding the epidemiology and transmission dynamics of the disease and for informing new initiatives towards vaccine design and development (where a globally representative view of strain diversity is essential). Our recent studies have enabled a comprehensive view of the genomic diversity and population structure of TP circulating in HICs, but similar information is largely lacking from lower-and-middle-income-countries (LMICs), and almost completely absent from Africa. Prospective studies are currently underway to sample TP diversity in at least four African countries, but these will only provide data from a two-year period. Longitudinally collected samples will enable a more nuanced understanding of lineage flux and transmission. In this study, we will perform direct TP sequencing on a collection of approximately 250 syphilis samples collected from across South Africa over a 12-year time-period. Analysis of these data will provide further insight into lineage flux and diversity, and will be compared to previous analyses of lineage flux in the UK and Canada, as well as providing a historical perspective of genomic diversity over that offered by African prospective collection studies.