Author(s):
Pimentel, Victor ; Pineda-Peña, Andrea ; Sebastião, Cruz S. ; de Paula, João L. ; Ahagon, Cintia M. ; Pingarilho, Marta ; Martins, M. Rosário O. ; Coelho, Luana P. O. ; Matsuda, Elaine M. ; Alves, Daniela ; Abecasis, Ana B. ; Brígido, Luís F. M.
Date: 2024
Persistent ID: http://hdl.handle.net/10362/172722
Origin: Repositório Institucional da UNL
Subject(s): Brazil; genetic diversity; HIV-1; São Paulo; transmission clusters; Public Health, Environmental and Occupational Health; SDG 3 - Good Health and Well-being
Description
Funding Information: The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This research was funded by FAPESP (2013/19441\u20137 and 2018/14.384\u20139) and FCT MARVEL (PTDC/SAU-PUB/4018/2021) and by funds from FCT to GHTM-UID/04413/2020 and LA-REAL-LA/P/0117/2020, Calouste Gulbenkian Foundation (FCG), under the ENVOLVE Ci\u00EAncia PALOP program that funded the HITOLA project. The funding body had no role in the design of the study, collection, analysis, interpretation of data, or in writing the manuscript. Publisher Copyright: Copyright © 2024 Pimentel, Pineda-Peña, Sebastião, de Paula, Ahagon, Pingarilho, Martins, Coelho, Matsuda, Alves, Abecasis and Brígido.
Background: Molecular epidemiology techniques allow us to track the HIV-1 transmission dynamics. Herein, we combined genetic, clinical and epidemiological data collected during routine clinical treatment to evaluate the dynamics and characteristics of transmission clusters of the most prevalent HIV-1 subtypes in the state of São Paulo, Brazil. Methods: This was a cross-sectional study conducted with 2,518 persons living with HIV (PLWH) from 53 cities in São Paulo state between Jan 2004 to Feb 2015. The phylogenetic tree of protease/reverse transcriptase (PR/RT) regions was reconstructed by PhyML and ClusterPicker used to infer the transmission clusters based on Shimodaira–Hasegawa (SH) greater than 90% (phylogenetic support) and genetic distance less than 6%. Results: Of a total of 2,518 sequences, 2,260 were pure subtypes at the PR/RT region, being B (88%), F1 (8.1%), and C (4%). About 21.2% were naïve with a transmitted drug resistance (TDR) rate of 11.8%. A total of 414 (18.3%) of the sequences clustered. These clusters were less evident in subtype B (17.7%) and F1 (15.1%) than in subtype C (40.2%). Clustered sequences were from PLWH at least 5 years younger than non-clustered among subtypes B (p < 0.001) and C (p = 0.037). Men who have sex with men (MSM) predominated the cluster in subtype B (51%), C (85.7%), and F1 (63.6%; p < 0.05). The TDR rate in clustered patients was 15.4, 13.6, and 3.1% for subtypes B, F1, and C, respectively. Most of the infections in subtypes B (80%), C (64%), and F1 (59%) occurred within the state of São Paulo. The metropolitan area of São Paulo presented a high level of endogenous clustering for subtypes B and C. The São Paulo city had 46% endogenous clusters of subtype C. Conclusion: Our findings showed that MSM, antiretroviral therapy in Treatment-Naive (ART-naïve) patients, and HIV1-C, played an important role in the HIV epidemic in the São Paulo state. Further studies in transmission clusters are needed to guide the prevention intervention.
