Department of Zoology, University of Oxford, United Kingdom.
New College, University of Oxford, United Kingdom.
J Infect Dis. 2019 Jun 19;220(2):233-243. doi: 10.1093/infdis/jiz085.
Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies.
Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups.
We identified 5 subtype B Portuguese clades (26-79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998-2000) and 2000 (95% BCI, 1998-2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73-2.09) to 0.62 (95% BCI,.52-.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39-1.59) to 0.72 (95% BCI, .63-.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively.
The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.
估计人类免疫缺陷病毒（HIV）传播模式的时间变化可以帮助阐明预防策略和公共卫生政策的影响。
将葡萄牙 HIV-1 亚型 B 和 G 聚合酶遗传序列添加到全球参考数据集，以确定特定国家的传播谱系。贝叶斯出生-死亡模型用于估计亚型特异性有效繁殖数（Re）。离散性状分析（DTA）用于量化传播组之间的混合。
我们确定了 5 个葡萄牙亚型 B 谱系（26-79 个序列）和一个大型单系葡萄牙亚型 G 谱系（236 个序列）。我们估计，HIV-1 传播的重大转变分别发生在 1999 年左右（95%贝叶斯可信区间[BCI]，1998-2000 年）和 2000 年（95%BCI，1998-2001 年）。对于亚型 B，Re 从 1.91（95%BCI，1.73-2.09）降至 0.62（95%BCI，0.52-0.72）。对于亚型 G，Re 从 1.49（95%BCI，1.39-1.59）降至 0.72（95%BCI，0.63-0.8）。DTA 表明，静脉注射吸毒者（PWID）和异性恋者分别是大多数（>80%）病毒谱系转变的来源，分别为亚型 G 和 B。
估计的 Re 下降与高效抗逆转录病毒疗法的引入以及针对 PWID 的减少伤害措施的扩大相吻合。推断出的跨传播组的传播事件强调了为桥梁人群进行预防努力的重要性。
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