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

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.