Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisbon, Portugal.
Centro de Investigação em Saúde de Angola (CISA), Caxito, Angola.
Front Public Health. 2024 Jun 5;12:1384512. doi: 10.3389/fpubh.2024.1384512. eCollection 2024.
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.
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%.
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 ( < 0.001) and C ( = 0.037). Men who have sex with men (MSM) predominated the cluster in subtype B (51%), C (85.7%), and F1 (63.6%; < 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.
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.
分子流行病学技术使我们能够追踪 HIV-1 的传播动态。在此，我们结合了在常规临床治疗过程中收集的遗传、临床和流行病学数据，以评估巴西圣保罗州最流行的 HIV-1 亚型的传播集群的动态和特征。
这是一项横断面研究，涉及 2004 年 1 月至 2015 年 2 月期间来自圣保罗州 53 个城市的 2518 名 HIV 感染者 (PLWH)。通过 PhyML 重建蛋白酶/逆转录酶 (PR/RT) 区的系统发育树，使用 ClusterPicker 根据 Shimodaira-Hasegawa (SH) 大于 90%（系统发育支持）和遗传距离小于 6%推断传播集群。
在总共 2518 个序列中，2260 个是 PR/RT 区域的纯亚型，分别为 B (88%)、F1 (8.1%)和 C (4%)。约 21.2%的患者是初治患者，其传播耐药率 (TDR) 为 11.8%。共有 414 个序列 (18.3%)聚类。在 B 亚型 (17.7%)和 F1 亚型 (15.1%)中，这些集群的比例明显低于 C 亚型 (40.2%)。与非聚类的 B 型 ( < 0.001) 和 C 型 ( = 0.037) 相比，聚类序列的 PLWH 至少年轻 5 岁。在 B 型 (51%)、C 型 (85.7%)和 F1 型 (63.6%； < 0.05)中，男男性行为者 (MSM) 为主导集群。聚类患者的 TDR 率分别为 B、F1 和 C 亚型的 15.4%、13.6%和 3.1%。B 型 (80%)、C 型 (64%)和 F1 型 (59%)的大多数感染均发生在圣保罗州内。圣保罗大都市区 B 型和 C 型的内源性聚类水平较高。圣保罗市 C 型内源性聚类占 46%。
我们的研究结果表明，MSM、初治抗逆转录病毒治疗 (ART-naïve) 患者和 HIV1-C 在圣保罗州的 HIV 流行中发挥了重要作用。需要进一步研究传播集群，以指导预防干预。
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