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High frequency of TDR in newly diagnosed human immunodeficiency virus type 1 (HIV-1) patients from Sao Paulo/Brazil
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Autores
Pimentel,V. F.
Abecasis, A. B
Portes, L.
Pineda-Peña, Andrea C.
Matsuda, E. M.
Guimarães, P. M. S.
Hársi, C. M.
De Paula, J. L.
Vandamme, A. M.
Brígido, F. M.
Fecha
2016-05
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Oxford University Press
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Abstract
The human immunodeficiency virus type 1 (HIV-1) epidemic in Sa˜o Paulo is dominated by subtypes B, F1 and C. The aim of this study was to characterize genotypes and transmitted drug resistance (TDR) among newly diagnosed HIV-1 individuals from January 2014 to February 2015 in Sa˜o Paulo. Population sequencing (PR þ RT) was performed on plasma viral RNA for 179 patients. For subtyping, we tested different automated tools-Rega v2.0, v.3.0, Blast Los Alamos, Scueal, Comet v1.0 and jpHMM-and performed phylogenetic analysis using the Neighbor-Joining method under K2-P model with MEGA and bootscanning using SimPlot. Sequences were submitted to the Stanford HIV Database CPR tool (http://cpr.stanford.edu/cpr.cgi) to investigate TDR. Statistical analysis was performed using GraphpadPrism software. Among the 179 sequences, the more prevalent subtypes were B (74%), C (12.3%), F (5.6%) and BF1 recombinants (5.6%). BC recombinants (1%) and subtypes D and G (<1%) were also found. In total, 28 patients (15.6%) with TDR were identified. 50% of these had TDR to NNRTIs, 40% to NRTIs and 14.2% to PIs. The frequency of TDR was significantly different between subtypes B, C and F1: 16% [Cl: 20.4–36.9], 0%[0-14.9] and 50% [23.7–76.3%], respectively (p< 0.0016). The HIV-1 epidemic in Sao Paulo is driven by subtype B, however – compared to previous studies - there is an increased prevalence of subtype C. The prevalence of TDR shows important differences between subtypes, with low prevalence of TDR in subtype C compared to significantly higher prevalence in subtypes B and F1
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Microbiology , Biological Sciences , Evolutionary Biology
