Phylodynamics for HIV Prevention: A Miami-Dade Case Study

Abstract

Background: To date, HIV molecular epidemiology (HIV ME) has been primarily used to identify clusters of related infections (cluster detection and response [CDR]) and then address interventions to these clusters. Community groups have raised concern regarding CDR regarding privacy and ethical concerns. Here we demonstrate how an alternative approach to HIV ME can provide public health benefit.

Methods: A limited dataset for Miami-Dade County provided by the Florida Department of Public Health was curated and annotated by neighborhood health district (NBHD) and genetic linkage (using a genetic distance threshold of ≤ 0.5%) and phylodynamic analyses were performed. Phylodynamic analyses were used to infer viral transmissions into Miami-Dade County, and between NBHDs within the county.

Results: 7274 HIV sequences from unique persons collected between 1/1/2015 and 12/31/2021 were analyzed, including 50% of the 7894 new diagnoses during this period. The proportion of sequences in local clusters increased over time. Higher ratios of local introductions, compared to viral egress (i.e., source of local clusters in other NBHDs) were observed in three NBHDs in North Miami [range 1.9-2.5], suggesting earlier diagnosis, but high numbers of susceptible persons not on pre-exposure prophylaxis. South Dade/Homestead had a low ratio (0.3) of local introductions compared to egress, suggesting later diagnosis and less durable suppression.

Conclusions: Phylodynamic and genetic linkage analyses can highlight populations and geographic regions that might benefit more from particular types of HIV prevention interventions. These findings will need to be explored by evaluating the impact of scaling up interventions informed by these analyses.

Keywords: HIV prevention; clustering; molecular epidemiology; phylodynamics; resource allocation; sequencing.