RESEARCH ARTICLE HIV-1 Diversity, Transmission Dynamics and Primary Drug Resistance in Angola

Objectives: To assess HIV-1 diversity, transmission dynamics and prevalence of transmitted drug resistance (TDR) in Angola, five years after ART scale-up. Methods: Population sequencing of the pol gene was performed on 139 plasma samples collected in 2009 from drug-naive HIV-1 infected individuals living in Luanda. HIV-1 subtypes were determined using phylogenetic analysis. Drug resistance mutations were identified using the Calibrated Population Resistance Tool (CPR). Transmission networks were determined using phylogenetic analysis of all Angolan sequences present in the databases. Evolutionary trends were determined by comparison with a similar survey performed in 2001. Results: 47.1 % of the viruses were pure subtypes (all except B), 47.1 % were recombinants and 5.8 % were untypable. The prevalence of subtype A decreased significantly from 2001 to 2009 (40.0 % to 10.8%, P50.0019) while the prevalence of unique recombinant forms (URFs) increased.2-fold (40.0 % to 83.1%, P,0.0001). The most frequent URFs comprised untypable sequences wit