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The Human Heredity and Health in Africa (H3Africa) initiative aims to enhance genomics research in Africa while fostering a sustainable research enterprise led by African scientists for the benefit of African people and the global community. The H3Africa hosted a workshop in Nairobi, Kenya, focusing on HIV genomics. The workshop provided numerous insights within five major themes on HIV genomics research in Africa: (1) HIV across the lifespan, (2) non-communicable diseases (NCDs) among people living with HIV (PLWH), (3) HIV and coinfections, (4) HIV vaccine development and (5) ethical and social issues related to the use of genomics methods for HIV prevention.