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Little is known about prevalence of drug resistance among HIV-infected Ugandans, a setting with over 15 years of public sector access to antiretroviral therapy (ART) and where virological monitoring was only recently introduced.This study was conducted in the adults' out-patient clinic of the Infectious Diseases Institute, Kampala, Uganda.HIV genotyping was performed in ART-naive patients and in treatment-experienced patients on ART for ≥6 months with virological failure (≥1000 copies/mL).A total of 152 ART-naive and 2430 ART-experienced patients were included. Transmitted drug resistance was detected in 9 (5.9%) patients. After a median time on ART of 4.7 years [interquartile range: 2.5–8.7], 190 patients (7.8%) had virological failure with a median viral load of 4.4 log10 copies per milliliter (interquartile range: 3.9–4.9). In addition, 146 patients had a viral load between 51 and 999 copies per milliliter. Most patients with virological failure (142, 74.7%) were on first-line ART. For 163 (85.8%) ART-experienced patients, genotype results were available. Relevant drug-resistance mutations were observed in 135 (82.8%), of which 103 (63.2%) had resistance to 2 drug classes, and 11 (6.7%) had resistance to all drug classes available in Uganda.The prevalence of transmitted drug resistance was lower than recently reported by the WHO. With 92% of all patients virologically suppressed on ART, the prevalence of virological failure was low when a cutoff of 1000 copies per milliliter is applied, and is in line with the third of the 90-90-90 UNAIDS targets. However, most failing patients had developed multiclass drug resistance.