i Characterization of HIV-1 subtype B near full- length genome sequences identified at the start of the HIV epidemic in South Africa Adetayo Emmanuel Adegbenga Obasa Thesis presented in fulfilment of the requirements for the degree of Masters of Science (Medical Virology) at the Faculty of Medicine and Health science, Stellenbosch University Supervisor Dr. Graeme Brendon Jacobs Co-supervisor Professor Susan Engelbrecht March 2017