Abstract
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.
Highlights
An HIV infected person in care in most developed countries will typically have part of the polymerase gene of their HIV population sequenced at least once, and often multiple times, to help guide clinical/therapeutic decisions
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 address the question, what should public health departments do with HIV
Summary
An HIV infected person in care in most developed countries will typically have part of the polymerase gene of their HIV population sequenced at least once, and often multiple times, to help guide clinical/therapeutic decisions. Many United States (US) state health departments collect HIV sequence data from healthcare providers and laboratories as a matter of state law and communicate those sequences to the Centers for Disease Control and Prevention (CDC), as part of an integrated HIV prevention and surveillance program [1,2] In some states, such as Michigan, these collections go back for more than 15 years, containing >10,000 sequences [3]. The state and county-level sequence collections likely match or possibly outnumber the number of entries in the public HIV sequence database (859,952 as of July 2020) that contains most published HIV sequences These databases likely represent the single largest, most well sampled, document on the historical and statistical properties of the HIV epidemic as it plays out in locations ranging from dispersed rural communities to large urban centers in the US and worldwide. We discuss this sensitive question primarily in the context of the US HIV epidemic, but the issues, benefits, and risks associated with these analyses are broadly applicable to many other countries that mandate collection of HIV genetic data from laboratories and clinics
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