Mehta Sanjay R, Wells Alan B, Cohen Colby, Campbell Angela, Truong Michelle, Little Susan J, Chaillon Antoine
Division of Infectious Diseases & Global Public Health, University of California San Diego, La Jolla California, USA.
Department of Medicine, San Diego Veterans Affairs Medical Center, San Diego, California, USA.
J Infect Dis. 2025 Mar 17;231(3):643-652. doi: 10.1093/infdis/jiae605.
To date, human immunodeficiency virus (HIV) molecular epidemiology has been primarily used to identify clusters of related infections (cluster detection and response) and then address interventions to these clusters. Community groups have raised concern regarding cluster detection and response related to privacy and ethical concerns. Here we demonstrate how an alternative approach to HIV molecular epidemiology can provide public health benefit.
A limited data set for Miami-Dade County provided by the Florida Department of 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.
A total of 7274 HIV sequences from unique persons collected between 1 January 2015 and 31 December 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 (ie, source of local clusters in other NBHDs) were observed in 3 NBHDs in North Miami (range, 1.9-2.5), suggesting earlier diagnosis, but high numbers of susceptible persons not receiving preexposure prophylaxis. South Dade/Homestead had a low ratio (0.3) of local introductions compared with egress, suggesting later diagnosis and less durable suppression.
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.
迄今为止，人类免疫缺陷病毒（HIV）分子流行病学主要用于识别相关感染集群（集群检测与应对），然后针对这些集群采取干预措施。社区团体对与隐私和伦理问题相关的集群检测与应对表示担忧。在此，我们展示了HIV分子流行病学的另一种方法如何能带来公共卫生益处。
对佛罗里达州卫生部提供的迈阿密-戴德县的有限数据集进行整理，并按邻里健康区（NBHD）进行注释，进行遗传连锁分析（使用≤0.5%的遗传距离阈值）和系统动力学分析。系统动力学分析用于推断病毒传入迈阿密-戴德县以及该县内各NBHD之间的传播情况。
对2015年1月1日至2021年12月31日期间收集的来自独特个体的7274条HIV序列进行了分析，占该期间7894例新诊断病例的50%。本地集群中的序列比例随时间增加。在北迈阿密的3个NBHD中，观察到本地引入比例高于病毒流出比例（即其他NBHD中本地集群的来源）（范围为1.9 - 2.5），这表明诊断较早，但有大量易感人群未接受暴露前预防。与流出相比，南戴德/霍姆斯特德的本地引入比例较低（0.3），这表明诊断较晚且抑制效果不持久。
系统动力学和遗传连锁分析可以突出那些可能从特定类型的HIV预防干预措施中获益更多的人群和地理区域。这些发现需要通过评估扩大基于这些分析的干预措施的影响来进一步探索。
