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Despite high rates of HIV testing and enrolment of HIV-positive pregnant women on antiretroviral therapy in Botswana, coverage for HIV-exposed infant (HEI) testing remains suboptimal. Many factors can contribute to suboptimal HEI testing rates, but they have seldom been thoroughly investigated in Botswana. Therefore, the aim of this study was to explore the experiences and perspectives of HIV-positive mothers on the barriers and facilitators of HEI testing to inform interventions to promote HEI testing in Botswana. We conducted focus group discussions (FGDs) with HIV-positive mothers who gave birth in 2016 at the three largest public hospitals in Botswana. FGDs were held in Maun, Francistown, and Gaborone from September 2019 to March 2020. The maximum variation sampling method was used to select the participants using information that was abstracted from birth registers and other medical records at the study sites. Mothers were asked to describe their HEI testing experiences, what made it easy or difficult for them to return the HEI for testing, and what needs to be done to improve HEI testing in Botswana. A thematic approach was used to analyse the data. Fifteen FGDs with 142 mothers (aged 21-52 years) were held. Participants identified several facilitators to HEI testing, including a mother with adequate knowledge of PMTCT, intensive tracking of HEI by healthcare workers (HCWs), positive attitudes of HCWs toward clients, and social support from significant others. Staff shortages at health care facilities, frequent stock-outs of HIV test kits, fear of stigma, fear of positive test results for the child, and transportation challenges were identified as key barriers to HEI testing. Increasing staffing at healthcare facilities, having adequate supplies of HIV test kits, enhanced HEI tracking, easing access to HEI testing services in rural areas, and providing quality PMTCT education were among the proposed interventions to promote HEI testing. Optimizing HEI testing in Botswana will require multi-level interventions at the policy, health system, community, interpersonal, and individual levels.

Human immunodeficiency virus (HIV) infection remains a significant public health burden globally. The role of viral co-infection in the rate of progression of HIV infection has been suggested but not empirically tested, particularly among children. We extracted and classified 42 viral species from whole-exome sequencing (WES) data of 813 HIV-infected children in Botswana and Uganda categorised as either long-term non-progressors (LTNPs) or rapid progressors (RPs). The Ugandan participants had a higher viral community diversity index compared to Batswana (p = 4.6 × 10−13), and viral sequences were more frequently detected among LTNPs than RPs (24% vs 16%; p = 0.008; OR, 1.9; 95% CI, 1.6–2.3), with Anelloviridae showing strong association with LTNP status (p = 3 × 10−4; q = 0.004, OR, 3.99; 95% CI, 1.74–10.25). This trend was still evident when stratified by country, sex, and sequencing platform, and after a logistic regression analysis adjusting for age, sex, country, and the sequencing platform (p = 0.02; q = 0.03; OR, 7.3; 95% CI, 1.6–40.5). Torque teno virus (TTV), which made up 95% of the Anelloviridae reads, has been associated with reduced immune activation. We identify an association between viral co-infection and prolonged AIDs-free survival status that may have utility as a biomarker of LTNP and could provide mechanistic insights to HIV progression in children, demonstrating the added value of interrogating off-target WES reads in cohort studies.