Background: This study aimed to determine the extent of viral resistance over time among non-clade B HIV type-1-infected patients in Uganda who were maintained on first-line highly active antiretroviral therapy (HAART) following virological failure.

Methods: Genotyping was performed on 16 patients with virological failure who were enrolled in an open-label randomized clinical trial of short-cycle treatment interruption.

Results: All patients receiving efavirenz-containing HAART had > or =1 efavirenz resistance mutation develop during follow-up. The majority (13/15, 86%) developed lamivudine resistance during follow-up, but no thymidine analogue mutations (TAMs) developed during a median duration of virological failure of 325.5 days.

Conclusions: Genotype resistance to both efavirenz and lamivudine developed early during the course of treatment after virological failure. TAMs did not emerge early despite moderate exposure time to thymidine analogues during virological failure.