Characterization of HIV Risk Behaviors and Clusters Using HIV-Transmission Cluster Engine Among a Cohort of Persons Living with HIV in Washington, DC

Abstract

Molecular epidemiology (ME) is one tool used to end the HIV epidemic in the United States. We combined clinical and behavioral data with HIV sequence data to identify any overlap in clusters generated from different sequence datasets; to characterize HIV transmission clusters; and to identify correlates of clustering among people living with HIV (PLWH) in Washington, District of Columbia (DC). First, Sanger sequences from DC Cohort participants, a longitudinal HIV study, were combined with next-generation sequences (NGS) from participants in a ME substudy to identify clusters. Next, demographic and self-reported behavioral data from ME substudy participants were used to identify risks of secondary transmission. Finally, we combined NGS from ME substudy participants with Sanger sequences in the DC Molecular HIV Surveillance database to identify clusters. Cluster analyses used HIV-Transmission Cluster Engine to identify linked pairs of sequences (defined as distance ≤1.5%). Twenty-eight clusters of ≥3 sequences (size range: 3-12) representing 108 (3%) participants were identified. None of the five largest clusters (size range: 5-12) included newly diagnosed PLWH. Thirty-four percent of ME substudy participants (n = 213) reported condomless sex during their last sexual encounter and 14% reported a Syphilis diagnosis in the past year. Seven transmission clusters (size range: 2-19) were identified in the final analysis, each containing at least one ME substudy participant. Substudy participants in clusters from the third analysis were present in clusters from the first analysis. Combining HIV sequence, clinical and behavioral data provided insights into HIV transmission that may not be identified using traditional epidemiological methods alone. Specifically, the sexual risk behaviors and STI diagnoses reported in the substudy survey may not have been disclosed during Partner Services activities and the survey data complemented clinical data to fully characterize transmission clusters. These findings can be used to enhance local efforts to interrupt transmission and avert new infections.

Keywords: District of Columbia; HIV; HIV clusters; HIV-TRACE; molecular epidemiology.

FIG. 1.

Flow of participants, samples, and sequences. ARV, antiretroviral; ME, molecular epidemiology; NGS, next-generation sequences.

FIG. 2.

Retrospective and prospective clusters of three or more participants in the DC Cohort ME substudy (n = 28 clusters from 108 participants). Edges denote genetic distance ≤0.015 substitutions/site. Light shading denotes Sanger-generated sequences. Dark shading denotes NGS-generated sequences. Color denotes HIV transmission risk. Shape denotes sex assigned at birth. DC, District of Columbia. Color images are available online.

FIG. 3.

ME substudy and DC Health molecular surveillance clusters (n = 7 clusters). Edges denote genetic distance ≤0.015 substitutions/site. Color denotes transmission risk. Shape denotes sex assigned at birth. Circles denote ME sub-study participants. IDU, injection drug user; MSM, men who have sex with men. Color images are available online.