Human immunodeficiency virus type 1 (HIV-1) transmitted drug resistance (TDR) is an important public health issue. In Brazil, low to intermediate resistance levels have been described. We assessed 225 HIV-1 infected, antiretroviral na？ve individuals, from HIV Reference Centers at two major metropolitan areas of Sao Paulo (Sao Paulo and Campinas), the state that concentrates most of the Brazilian Aids cases. TDR was analyzed by Stanford Calibrated Population Resistance criteria (CPR), and mutations were observed in 17 individuals (7.6%, 95% CI: 4.5%–11.9%). Seventy-six percent of genomes (13/17) with TDR carried a nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation, mostly K103N/S (9/13, 69%), potentially compromising the preferential first-line therapy suggested by the Brazilian HIV Treatment Guideline that recommends efavirenz-based combinations. Moreover, 6/17 (35%) had multiple mutations associated with resistance to one or more classes. HIV-1 B was the prevalent subtype (80%); other subtypes include HIV-1 F and C, mosaics BC, BF, and single cases of subtype A1 and CRF02_AG. The HIV Reference Center of Campinas presented more cases with TDR, with a significant association of TDR with clade B infection ( ). 1. Introduction Access to free antiretroviral therapy (ART) is part of the Brazilian response to the Aids epidemic and transmitted drug resistance (TDR); it has been a concern since the introduction of highly active antiretroviral therapy (HAART) in the late 1990s [1]. TDR surveillance is an important strategy to monitor the emergence of genetic resistance as it may impact ART efficacy [2]. This issue was especially sensible in Brazil that deployed a free ARV program in the late 90s amidst a suboptimal health care system. This initiative could boost the emergence of transmitted drug resistance variants and jeopardize Human immunodeficiency virus (HIV-1) treatment [3]. However, most studies in Brazil have shown TDR prevalence similar to that observed among developed countries. Two recent Brazilian national surveys had accessed this issue [4, 5] but included a small representation of S？o Paulo metropolitan areas. We and others have analyzed mutations in treatment-naive individuals [6–12]; but to trace trends for TDR prevalence, continual monitoring is necessary. We analyzed ARV na？ve individuals living with HIV/Aids, recruited at HIV Reference Centers from the two major metropolitan areas of Sao Paulo state to investigate the TDR prevalence. These metropolitan areas concentrate 44% of notified Aids cases of Sao Paulo state and
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