naive, chronically HIV-infected individuals. The high rate of X4 and D/M tropism seen in this study may be explained at least partly by the fact that most of the samples in this study were derived from MSM individuals. It is noteworthy that the prevalence of X4 and D/M tropism among 7 October 2011 | Volume 6 | Issue 10 | e25869 ~ Analysis of HIV-1 Strains in Sao Paulo, Brazil our MSM group is high compared to the 3.2% reported in the study of 126 recently infected MSM from six major cities in the USA. This high prevalence should seriously be considered when decisions are made about initial regimens for therapy-naive individuals, and HIV-1 coreceptor usage should be screened before initiation of any chemokine receptor CCR5 antagonists in clinical settings. These suggestions are in agreement with the conclusions of Frange et al. that noted that X4/DM strains can heavily fuel the cellular HIV-1 reservoir leading to viral persistence over a long period complicating future therapeutic options, including CCR5 antagonists. The assessment of HIV tropism in our study was limited to sequence- based algorithms rather than using phenotypic methods. Although phenotypic assays still have an edge over genotypic methods, genotypic predictors prove to be highly concordant with phenotype data and can reliably be used to determine viral tropism with better results in PBMC than in plasma samples. In this study, we used geno2pheno because it allows for an 8 October 2011 | Volume 6 | Issue 10 | e25869 ~ Analysis of HIV-1 Strains in Sao Paulo, Brazil Sample ID Resistance mutations “23303071 PI NRTI M41L, D67N, T215Y NNRTI HIV-1 subtype Tropism Risk 04BR 1050 06BR 1123 05BR 1105 04BR 1055 03BR 1020 05BR 1077 05BR 1088 05BR 1075 05BR 1107 03BR 1042 03BR 2018 04BR 1053 04BR 1067 05BR 1111 L24I,M46I,F53L, I54V, V82S D30N, M46I D30N, M46I D30N G73S V82A B B B B B B X4 R5 ND R5 R5 R5 X4 R5 R5 ND R5 X4 R5 X4 MSM MSM MSM MSM MSM MSM HETM MSM MSM MSM HETM MSM HETM MSM V75A M184V M184I M184I M184V K103N K103N K103N K103N K103N B “ 21526763 B B B BF1 B BF1 B HET; heterosexual man, MSM; men who have sex with men. doi:10.1371/journal.pone.0025869.t003 M 9 October 2011 | Volume 6 | Issue 10 | e25869 ~ Analysis of HIV-1 Strains in Sao Paulo, Brazil adjustable cutoff, and it can determine HIV-1 co-receptor usage in all viral genotypes. This method has shown a similar performance to the Trofile phenotypic assay, the most often used tropism method. Moreover, the method has been shown to achieve higher sensitivity while retaining high level of specificity when compared with the performance of different algorithms. Our study represents the largest analysis of the NFLG of the HIV-1 genomes undertaken to date from well-characterized recently infected patients and provides recent data on the molecular characterization of HIV-1 in treatment-naive patients residing in Sao Paulo, Brazil. Overall, our results demonstrate a ~ cocirculation of 3 group M viral subtypes, 3 URFs, and 2 CRFs. However, these data need to be interpreted with some caution, as the samples recruited may not fully represent the general population of Sao Paulo because they disproportionately represent men who ~ reported having sex with men. The existence of various HIV-1 subtypes in Brazil will invariably challenge existing diagnostic tests and/or interpretation algorithms. Depending on future findings related to the transmis- CF-101 sibility, pathogenicity, and treatment implications of various subtypes, these variant subtypes may also play