Phylodynamics for Human Immunodeficiency Virus Prevention: A Miami-Dade County Case Study

Area of Science:

• Epidemiology
• Virology
• Public Health

Background:

• Traditional HIV molecular epidemiology focuses on cluster detection, raising privacy and ethical concerns.
• An alternative approach using phylodynamics can offer public health benefits without compromising privacy.

Purpose of the Study:

• To demonstrate an alternative approach to HIV molecular epidemiology using phylodynamics.
• To identify geographic regions and populations that may benefit from targeted HIV prevention interventions.

Main Methods:

• Phylodynamic and genetic linkage analyses were performed on 7274 HIV sequences from Miami-Dade County (2015-2021).
• Data were curated and annotated by neighborhood health district (NBHD) and genetic distance (≤0.5%).
• Viral transmissions into and between NBHDs were inferred.

Main Results:

• The proportion of HIV sequences in local clusters increased over time.
• North Miami NBHDs showed higher local introductions, suggesting earlier diagnosis but potential gaps in pre-exposure prophylaxis.
• South Dade/Homestead NBHD had a low ratio of local introductions, indicating later diagnosis and less durable viral suppression.

Conclusions:

• Phylodynamic and genetic linkage analyses effectively highlight areas for targeted HIV prevention.
• Further evaluation is needed to assess the impact of scaling up interventions informed by these analyses.