Background To date, HIV molecular epidemiology (HIV ME) has been primarily used to identify clusters of related infections (cluster detection and response [CDR]) and then address interventions to these clusters. Community groups have raised concern regarding CDR regarding privacy and ethical concerns. Here we demonstrate how an alternative approach to HIV ME can provide public health benefit. Methods A limited dataset for Miami-Dade County provided by the Florida Department of Public Health was curated and annotated by neighborhood health district (NBHD) and genetic linkage (using a genetic distance threshold of ≤ 0.5%) and phylodynamic analyses were performed. Phylodynamic analyses were used to infer viral transmissions into Miami-Dade County, and between NBHDs within the county. Results 7274 HIV sequences from unique persons collected between 1/1/2015 and 12/31/2021 were analyzed, including 50% of the 7894 new diagnoses during this period. The proportion of sequences in local clusters increased over time. Higher ratios of local introductions, compared to viral egress (i.e., source of local clusters in other NBHDs) were observed in three NBHDs in North Miami [range 1.9-2.5], suggesting earlier diagnosis, but high numbers of susceptible persons not on pre-exposure prophylaxis. South Dade/Homestead had a low ratio (0.3) of local introductions compared to egress, suggesting later diagnosis and less durable suppression. Conclusions Phylodynamic and genetic linkage analyses can highlight populations and geographic regions that might benefit more from particular types of HIV prevention interventions. These findings will need to be explored by evaluating the impact of scaling up interventions informed by these analyses.

中文翻译：

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预防 HIV 的系统动力学：迈阿密戴德案例研究


背景 迄今为止，HIV 分子流行病学 （HIV ME） 主要用于识别相关感染集群（集群检测和反应 [CDR]），然后解决对这些集群的干预措施。社区团体对 CDR 提出了隐私和道德问题的关注。在这里，我们展示了 HIV ME 的替代方法如何提供公共卫生益处。方法 佛罗里达州公共卫生部提供的迈阿密-戴德县有限数据集由邻里卫生区 （NBHD） 和遗传连锁 （使用 ≤ 0.5% 的遗传距离阈值）进行整理和注释，并进行了系统动力学分析。系统动力学分析用于推断病毒传播到迈阿密-戴德县以及县内 NBHD 之间的传播。结果 分析了 2015 年 1 月 1 日至 2021 年 12 月 31 日期间收集的 7274 个独特个体的 HIV 序列，包括在此期间 7894 例新诊断中的 50%。序列在局部簇中的比例随着时间的推移而增加。在北迈阿密的三个 NBHD 中观察到较高的本地引入比率（即其他 NBHD 中局部聚集的来源）[范围 1.9-2.5]，表明诊断较早，但大量易感者未接受暴露前预防。与出口相比，South Dade/Homestead 的本地引入比率较低 （0.3），表明诊断较晚且抑制持续时间较差。结论 系统动力学和遗传连锁分析可以突出可能从特定类型的 HIV 预防干预措施中受益更多的人群和地理区域。需要通过评估这些分析所告知的扩大干预措施的影响来探索这些发现。