Few reports have described the molecular characteristics of the AIDS epidemic within the interior regions of Brazil, a country of continental dimensions. To help fill this gap, the prevalence of transmitted antiretroviral drug resistance and human immunodeficiency virus type 1 (HIV-1) diversity in Mato Grosso State, central western Brazil are reported. Drug-naïve patients (n = 105) were recruited at a reference center in Cuiabá/Mato Grosso State located across the border with Bolivia and considered a southern gate to the Amazon forest. For 92 HIV-1 isolates, the protease and partial reverse transcriptase fragments were amplified by nested-PCR and sequenced. Drug resistance was analyzed by the Calibrated Population Resistance tool and the International AIDS Society-USA database. HIV-1 subtypes were determined by REGA and phylogenetic analyses. Recombinant viruses were analyzed by SIMPLOT. Drug resistance mutations were observed in 5.4%: nucleoside reverse transcriptase inhibitor mutations M41L (n = 1), D67N (n = 1), and K219E (n = 1), the non-nucleoside reverse transcriptase inhibitor mutation K103N (n = 1) and the protease inhibitor mutation L90M (n = 1). Around 20% of the isolates were recombinants: different patterns of B/F1 mosaics (n = 11), four B/C, one F1/C/B, one F1/C, and one D/F1. Subtype B(PR) B(RT) represented 71.7%, 5.4% were of subtype C(PR) C(RT) and 3.3% were of subtype F1(PR) F1(RT) . A moderate prevalence of transmitted resistance and the co-circulation of subtypes B, F1, C, different recombinants, including the first report of subtype D, were found in Mato Grosso State, far from the epicenter of the epidemic. These results highlight the importance of monitoring transmitted drug resistance and HIV-1 genetic diversity in the interior regions of Brazil.
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