Project Summary Botswana has been one of the countries most affected by HIV-1 and has always been in the top 3 countries by HIV-1 prevalence for the past 20 years. The country has responded gallantly by providing free antiretroviral therapy (ART) to persons living with HIV-1 (PLWH) in 2002 and an aggressive combination of prevention strategies. This has resulted in reduced HIV-1 incidence and associated mortality and the country was the third globally to reach the UNAIDS 95-95-95 targets of HIV-1 diagnosis, treatment, and viral suppression. Since its inception in 1996, the Botswana Harvard AIDS Institute Partnership (BHP) has conducted investigator-initiated clinical trials, observational and epidemiologic studies, laboratory-based studies, and implementation science research. BHP laboratory also carries out molecular virology research on HIV and this research has been instrumental in molecular characterizing HIV-1 subtype C, which predominates in Botswana and Southern Africa. We draw upon the depth and breadth of the experience gained over more than 2 decades of investigator-initiated research, training, and capacity building to increase access to HIV-1 genomics training. Since 2017, we have invested in implementing pathogen agnostic next- generation sequencing which was critical in the first sequencing of the SARS-CoV-2 Omicron variant of concern in Botswana. Working with our collaborators we have also established cohorts of very early treated infants and adolescents for understanding HIV-1 reservoirs. We, therefore, aim through this application to strengthen BHP in HIV-1 genomics and molecular virology capacity in Botswana and increase access to pathogen genomics in the sub-Saharan Africa region as a center of excellence. The capacity developed here will be crosscutting for virologic studies and will thus be instrumental in BHP lab’s continued diversification into research on other emerging pathogens of global public health interest. To achieve this, we aim to 1) develop and advance BHP as an HIV-1 genomics regional center of excellence. We will leverage the expertise in pathogen genomics developed over the past 20 years to facilitate capacity building by hosting courses in HIV-1 sequencing, bioinformatic analysis, and sequence data interpretation. Building on our collaboration with the University of Botswana, Harvard T.H. Chan School of Public Health (HSPH), and the Ragon Institute of MGH, MIT & Harvard, we will target students and faculty from local and regional Institutions for the training. We will facilitate the development of HIV genomics, make them accessible to local universities and other countries in the region, and 2) To establish HIV-1 Reservoir assays in support of the ongoing and planned HIV-1 cure studies at BHP. We plan to set up assays for the assessment of HIV-1 reservoirs in PLWH in Botswana. Laboratory scientists will be trained on a number of these assays at the collaborator’s laboratory in Boston (Ragon Institute of MGH, MIT & Harvard). We will also train and establish capacity for the bioinformatic analysis for HIV-1 reservoir characterization. 1

Narrative The project aims to develop specialized HIV-1 genomics laboratory training modules at BHP to build capacity for laboratory professionals and university students on HIV-1 genomics, and HIV-1 cure-related research in Botswana and the region. The proposed project will increase the human capacity for conducting advanced HIV-1 genomics research and establishing local capacity for HIV-1 Reservoirs studies to contribute toward HIV cure-related research in southern Africa. Successful implementation of this project will also result in the establishment of a core facility and center of excellence for pathogen genomics, and support future NIH- funded HIV-1 cure projects. 1