Many countries and US states have mandatory statues that require reporting of HIV clinical data including genetic sequencing results to the public health departments. Because genetic sequencing is a part of routine care for HIV infected persons; health departments have extensive sequence collections spanning years and even decades of the HIV epidemic. How should these data be used (or not) in public health practice? This is a complex; multi-faceted question that weighs personal risks against public health benefit. The answer is neither straightforward nor universal. However; to make that judgement—of how genetic sequence data should be used in describing and combating the HIV epidemic—we need a clear image of what a phylogenetically enhanced HIV surveillance system can do and what benefit it might provide. In this paper, we present a positive case for how up-to-date analysis of HIV sequence databases managed by health departments can provide unique and actionable information of how HIV is spreading in local communities. We discuss this question broadly, with examples from the US, as it is globally relevant for all health authorities that collect HIV genetic data.

中文翻译：

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卫生部门应如何处理HIV序列数据？

许多国家和美国的州都有强制性规定，要求向公共卫生部门报告HIV临床数据，包括基因测序结果。因为基因测序是艾滋病毒感染者日常护理的一部分；卫生部门拥有广泛的序列收集资料，涵盖了艾滋病病毒流行的数十年甚至数十年。在公共卫生实践中应如何使用（或不使用）这些数据？这很复杂；权衡个人风险与公共卫生利益的多方面问题。答案既不简单也不通用。然而; 为了做出判断（如何使用基因序列数据来描述和抵抗HIV流行）作出判断，我们需要清晰地了解系统发育增强的HIV监测系统可以做什么，以及它可以提供什么好处。在本文中，对于卫生部门管理的HIV序列数据库的最新分析如何能够提供有关HIV在当地社区中如何传播的独特且可操作的信息，我们提供了一个积极的案例。我们以美国为例，对这个问题进行了广泛的讨论，因为该问题与所有收集HIV遗传数据的卫生部门在全球都相关。