BackgroundAs Sub-Saharan Africa transitions to a new era of universal ART, up-to-date assessments of HIV RNA (viral load, VL) suppression at a population level are needed to understand demographic and geographic sources of ongoing viremia and to inform interventions to optimize ART delivery. We sought to measure population viral load (VL) metrics to assess current viral suppression levels and characterize demographic groups and geographic locations with high-level detectable viremia in East Africa.MethodsIn the SEARCH HIV test-and-treat study (NCT01864683), we conducted baseline HIV testing (89% uptake) and HIV RNA assessments in 32 rural communities in 2013–2014 in Uganda and Kenya (N=303,461). We measured VL in 8,828 HIV+ adults, and defined viral suppression as VL<500 copies/mL. To assess geographic sources of transmission risk, we determined the proportion of all adults (both HIV-positive and HIV-negative) with detectable VL (termed ‘local prevalence of viremia’). Transmission risk ‘hotspots’ were defined as geopolitical subunits within communities with >5.0% local prevalence of viremia. We also assessed sero-discordant couples, measuring the proportion in which the HIV+ partner had detectable viremia.FindingsViral suppression was 82% (3,427/4,202) among adults on ART, and 51% (4,490/8,828) among all HIV+ adults. Regional viral suppression among HIV+ adults was 48% (West Uganda), 45% (East Uganda) and 53% (Western Kenya). Transmission risk ‘hotspots’ included 1/21 W.Uganda, 0/18 E.Uganda, and 16/26 Kenya geopolitical subunits. In Uganda, sero-discordancy was 3.1% (492 discordant/16,023 total couples). In 58% of discordant couples, the HIV+ partner was viremic (14% had VL>100,000). In Kenya, sero-discordancy was 10.0% (859/8,616 total couples). In 53%, the HIV+ partner was viremic (15% with VL>100,000).InterpretationPrior to the 2013–2014 start of the SEARCH trial, 51% of East African HIV+ adults had viral suppression, reflecting ART scale-up efforts to date. However, geographic ‘hotspots’ of potential HIV transmission risk as well as detectable viremia among sero-discordant couples warrant intensified interventions.FundingUS National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health. President’s Emergency Plan for AIDS Relief (PEPFAR).