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BACKGROUND The aim of this study was to assess trends in drug resistance and associated clinical and programmatic factors at a national level during the rapid scale up of ART. METHODS Logistic regression was used to identify the factors associated with HIVDR. Variables associated with drug resistance in multivariable logistic regression were included in the Cochran-Armitage test for trend. RESULTS A total of 11,976 patients were enrolled in the study. The prevalence of HIVDR among patients who received ART for 9-24 months during 2003-2