Online Program

Phylogenetic Analyses of HIV-1 Sequences can be used to Target Prevention Programs in Chicago

Wednesday, November 4, 2015

Ethan Morgan, PhD, Department of Public Health Sciences, University of Chicago, Chicago, IL
Donna Peace, City of Chicago, Chicago, IL
Stephanie Townsell, MPH, Surveillance, Epidemiology & Research Section, Chicago Department of Public Health, Chicago, IL
Nanette Benbow, MAS, HIV/STI Services Division, Chicago Department of Public Health, Chicago, IL
John Schneider, MD, MPH, Departments of Public Health Sciences & Medicine, University of Chicago, Chicago, IL
Phylogenetic analysis of HIV sequences can be used to determine the size/number of transmission clusters. An increase in either the number of clusters or wider geographic clustering can indicate continued transmission or a more mobile transmission network, respectively. Identifying the sections of a city that harbor the largest clusters can aid public health departments in targeting prevention programs.

HIV-1 sequences (N=855) were obtained in Chicago from 2006-2010 through the Variant Atypical and Resistant HIV Surveillance program. These were aligned to HXB2 reference sequence, pairwise comparison was performed, and an HIV transmission network built. Clusters were defined as having at least two connected individuals with K2P distanace ≤ 1.5% and were stratified by year.

249 (29.1%) of strains originated on the North side, 525 (61.4%) originated on the South side, and 81 (9.5%) originiated on the West side. Overall, there were few direct transmissions. In 2006, only 2 clusters existed whereas by 2010, there were 8 clusters with the largest located on the South side. There was a relatively constant rate (~40%) of cross-city transmission. Finally, when combining data across all years, the data were too divergent to complete cluster analyses.

We found a modest increase in the number of clusters in the city over the period of the study. The divergence of the sequences suggests a surprising variety of HIV-1 strains in Chicago, much greater than expected. This study shows that phylogenetic cluster analysis can be used to understand citywide transmission networks and target resources to specific geographic areas. 

Learning Areas:

Public health or related research

Learning Objectives:
Demonstrate the use of phylogenetic analyses to build complex HIV transmission networks. Identify the specific geographic areas most in need of targeted intervention.

Keyword(s): HIV/AIDS, Epidemiology

Presenting author's disclosure statement:

Qualified on the content I am responsible for because: I have focused the majority of my PhD studies on the analysis of HIV/AIDS data in Chicago (with several publications in progress), as well as learning the methods required to complete phylogenetic analyses. This work, as well as subsequent analyses, will form the foundation for my dissertation research and has been informed by leading researchers in the field.
Any relevant financial relationships? No

I agree to comply with the American Public Health Association Conflict of Interest and Commercial Support Guidelines, and to disclose to the participants any off-label or experimental uses of a commercial product or service discussed in my presentation.