AUTHOR=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. TITLE=Dynamics and features of transmission clusters of HIV-1 subtypes in the state of São Paulo, Brazil JOURNAL=Frontiers in Public Health VOLUME=12 YEAR=2024 URL=https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2024.1384512 DOI=10.3389/fpubh.2024.1384512 ISSN=2296-2565 ABSTRACT=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.