Contextualizing HIV phylogenetic research through community, programmatic, and structural lenses

Abstract

Background: Despite decades of progress in HIV prevention and treatment, HIV remains a persistent global public health challenge. Amidst growing funding gaps in the HIV response, precision public health has emerged as a strategy to optimize interventions, relying on a broad array of data, including genomics. Within this framework, HIV phylogenetics has been touted as a valuable tool for understanding transmission at a more granular level. Yet its use remains ethically contested, especially in jurisdictions where HIV transmission is criminalized. Recognizing its growing role in public health practice, this thesis explores HIV phylogenetics through community, programmatic, and structural perspectives. Methods: This research draws on bio-behavioural surveys conducted among key populations in Kenya, Pakistan, and Ukraine. Each survey included structured interviews and biological specimen collection. Sequencing of the HIV pol gene, followed by phylogenetic analyses, was used to infer transmission clusters and estimate time since infection. In parallel, the CIPHR project used a community-based participatory approach to examine the ethical and practical dimensions of HIV phylogenetics. Results: From a programmatic perspective, findings revealed unmet prevention and care needs among Kenyan men who have sex with men and adolescent girls and young women, highlighting the importance of reaching populations earlier and more consistently along their HIV risk trajectories. Viewed through a structural lens, analyses from Pakistan and Ukraine illustrated how economic decline and geopolitical instability shaped HIV transmission dynamics by altering individual behaviour. Through CIPHR, community members acknowledged ethical concerns but still identified opportunities for using HIV phylogenetics to support their peers and key population programs. Conclusions: Although HIV phylogenetics remains controversial, it is likely to remain part of public health practice for the foreseeable future. Its value, however, hinges on meaningful contextualization. This work argues that integrating molecular methods with community voices, programmatic priorities, and structural perspectives can help shape a more grounded, inclusive, and ethical vision of precision public health.