BackgroundThe objective is to estimate HIV incidence and characterize subtypes among recently diagnosed individuals from different at-risk populations (men who have sex with men (MSM); female and male drug users (FDUs and MDUs); female, male and transvestite sex workers (FSWs, MSWs and TSWs)) and pregnant women (PW) from Argentina in the context of a Global Fund Project (Sub-project N°112).MethodsFrom October 2006 to September 2008, HIV prevalence surveys were conducted among MSM, FDUs, MDUs, FSWs, MSWs, TSWs and PW. Volunteers older than 18years old without previous HIV positive diagnosis were interviewed and tested for HIV. HIV positive samples were analyzed by the Serological Testing Algorithms for Recent HIV Seroconversion (STARHS) to estimate incidence. By partial RT-PCR and sequencing of HIV pol gene HIV sub-type was determined.ResultsA total of 12,200 volunteers were recruited in the cross-sectional HIV prevalence surveys. HIV prevalence between self-reported HIV negative or unknown status was 10.4% (161/1549), 5.1% (24/473), 2.9% (7/241), 10.8% (12/111), 33.9% (38/112), 1.9% (21/1112) and 0.12% (10/8570) for MSM, MDUs, FDUs, MSWs, TSWs, FSWs and PW, respectively. HIV incidence estimates by STARHS were 6.36, 1.62, 2.73, 6.08, 11.31, 0.62 and 0.05 per 100 person-years for MSM, MDUs, FDUs, MSWs, TSWs, FSWs and PW, respectively. Phylogenetic analysis showed that 122 (61.6%) samples were subtype B, 74 (37.4%) were inter-subtype BF recombinants and 2 (1.0%) were sub-type C. In all groups, men had higher prevalence of sub-type B.ConclusionGiven the high HIV prevalence and incidence found in this study, it is imperative to have a well documentedmolecular profile of the epidemics in these groups. The high incidences observed in most of them make them suitable for considering them as potential volunteers in vaccine trials