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Determinants of HIV Phylogenetic Clustering in Chicago Among Young Black Men Who Have Sex With Men From the uConnect Cohort

Morgan, Ethan PhD*; Nyaku, Amesika N. MD; D'Aquila, Richard T. MD; Schneider, John A. MD, MPH*,‡

JAIDS Journal of Acquired Immune Deficiency Syndromes: July 1st, 2017 - Volume 75 - Issue 3 - p 265–270
doi: 10.1097/QAI.0000000000001379

Introduction: Phylogenetic analysis determines similarities among HIV genetic sequences from persons infected with HIV, identifying clusters of transmission. We determined characteristics associated with both membership in an HIV transmission cluster and the number of clustered sequences among a cohort of young black men who have sex with men (YBMSM) in Chicago.

Methods: Pairwise genetic distances of HIV-1 pol sequences were collected during 2013–2016. Potential transmission ties were identified among HIV-infected persons whose sequences were ≤1.5% genetically distant. Putative transmission pairs were defined as ≥1 tie to another sequence. We then determined demographic and risk attributes associated with both membership in an HIV transmission cluster and the number of ties to the sequences from other persons in the cluster.

Results: Of 86 available sequences, 31 (36.0%) were tied to ≥1 other sequence. Through multivariable analyses, we determined that those who reported symptoms of depression and those who had a higher number of confidants in their network had significantly decreased odds of membership in transmission clusters. We found that those who had unstable housing and who reported heavy marijuana use had significantly more ties to other individuals within transmission clusters, whereas those identifying as bisexual, those participating in group sex, and those with higher numbers of sexual partners had significantly fewer ties.

Conclusions: This study demonstrates the potential for combining phylogenetic and individual and network attributes to target HIV control efforts to persons with potentially higher transmission risk, as well as suggesting some unappreciated specific predictors of transmission risk among YBMSM in Chicago for future study.

*Department of Public Health Sciences, University of Chicago, Chicago, IL;

Department of Medicine, Northwestern University, Chicago, IL; and

Department of Medicine, University of Chicago, Chicago, IL.

Correspondence to: Ethan Morgan, Department of Public Health Sciences, University of Chicago, 5841 S. Maryland Avenue, MC 5065 Chicago, IL 60637 (e-mail:

The sample development, analyses, and phylogenetic work were supported by the University of Chicago Office of Diversity & Inclusion and NIH grants R21MH098768, R01DA033875, R01DA039934, and P30AI 117943. The dried blood spot assay development and validation was supported by NIH grants P30AI-027757 and UM1-AI-68636 and -06701.

The authors have no conflicts of interest to disclose.

Received January 27, 2017

Accepted March 13, 2017

Copyright © 2017 Wolters Kluwer Health, Inc. All rights reserved.