Background Shenzhen, a city with a substantial mobile population, was identified as the first discovered region of human immunodeficiency virus-1 (HIV-1) CRF55_01B and epicenter of its severe epidemic. During the implementation of venue-based behavioral interventions and the “treat-all” policy, identifying the patterns of spread and transmission hotspots of CRF55_01B is imperative. Methods In this study, 1450 partial pol sequences, with demographic information, were collected from all newly diagnosed CRF55_01B infections in Shenzhen from 2008 to 2020. Molecular networks were constructed using the maximum likelihood and time-resolve phylogenies. Transmission rates, effective reproduction numbers (Re) of clusters, and viral dispersal were evaluated using Bayesian inference. Results In total, 526 sequences formed 114 clusters, including 7 large clusters. The status and size of clusters were strongly correlated with age, ethnicity, occupation, and CD4+ T-cell counts. The transmission rates of clusters were significantly higher than the national epidemic estimate. Four large clusters had Re exceeding 1 at the end of the sampling period. Immigrants from Guangdong and Hunan, along with local residents, were identified as the transmission hubs, with heterosexual men being the main source and MSM being the main destination. The virus exhibited a high movement frequency from individuals aged 30–49 years toward diverse age groups. Conclusions This study demonstrated that the hidden CRF55_01B transmissions continued despite current combined interventions in Shenzhen, and at-risk individuals susceptible to infection or transmission were identified, potentially serving as targets for more effective prevention and control of the local epidemic, thereby mitigating cross-regional spread nationwide due to population migration.

中文翻译：

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HIV-1 CRF55_01B在其起源地的持续传播：动态和热点


背景 深圳是一个流动人口较多的城市，被确定为人类免疫缺陷病毒 1 （HIV-1） CRF55_01B最早被发现的地区，也是其严重流行的中心。在实施基于场所的行为干预和“全能治疗”政策期间，确定CRF55_01B的传播模式和传播热点势在必行。方法 本研究收集了 2008—2020 年深圳所有新诊断CRF55_01B感染病例的 1450 个部分 pol 序列和人口学信息。使用最大似然和时间解析系统发育构建分子网络。使用贝叶斯推理评估传播率、簇的有效繁殖数 （Re） 和病毒传播。结果 共 526 个序列形成 114 个簇，其中 7 个大簇。簇的状态和大小与年龄、种族、职业和 CD4+ T 细胞计数密切相关。聚集性病例的传播率显著高于全国疫情估计值。在采样期结束时，四个大型集群的 Re 超过 1。来自广东和湖南的移民以及当地居民被确定为传播中心，异性恋男性是主要来源，MSM 是主要目的地。该病毒从 30-49 岁的个体向不同年龄组的运动频率很高。 结论 本研究显示，尽管深圳目前采取了联合干预措施，但隐性CRF55_01B传播仍在继续，并确定了易感染或传播的高危个体，可能成为更有效防控本地疫情的目标，从而缓解人口迁移导致的全国跨区域传播。