Comprehensive Clinical and Laboratory Analyses

All samples were analysed in the MRC/UVRI Uganda Unit’s CDLS laboratories. The Clinical chemistry analyser, COBAS Integra 400 plus (Roche Diagnostics) was used to measure fasting serum lipids and blood glucose, and renal and liver function test parameters. Full blood counts were measured using the Coulter AcT5 Diff CP Analyser (Beckman Coulter, USA). CD4 cell counts were measured using either the FACSCount or FACSCalibur machine (Becton–Dickinson, USA). Plasma HIV-1 RNA was quantified using the COBAS Ampliprep/Taqman V2.0 HIV-1 viral load assay (Roche Molecular Diagnostics [RMD], NJ, USA) with a lower detection limit of 20 copies/ml. For urine strip testing, we used the Siemens Multistix 10SG and read with Clinitek Status Analyzer (Siemens Healthcare Diagnostics). For ARV drug resistance, PCR and sequencing reactions were conducted and the sequences submitted to the Stanford University HIV Drug Resistance database. The surveillance drug resistance mutations were identified using the 2009 WHO list for surveillance of transmitted drug resistances [36 (link)], using the Stanford calibrated population resistance analysis tool version 5.0 beta [37 (link)]. Sequences with genetic mixtures of wild-type and mutant sequences at amino acid sites that code for SDRMs were considered to be drug-resistant.