Phylogenetic Analysis of HIV-1 Migration into and out of Houston, Texas

Chloe Ng-Wing-Sheung, The University of Texas School of Public Health


More than 30 years after the first confirmed cases of Human Immunodeficiency Virus (HIV) within the United States, about 15% of the 1.1 million Americans infected with HIV remain unaware of their diagnosis. The Center for Disease Control and Prevention (CDC) estimated that new HIV infections declined by 18% between 2008 and 2014, but the decline was not consistent among certain populations. Despite efforts to understand the factors contributing to the prevalence among groups with higher risks of infection throughout the US, patterns of viral introduction and spread among discrete populations have not been characterized. Previous literature has shown that the HIV epidemic has largely been defined by sexual orientation and race/ethnicity. However, few studies have explored the effects of human migration on the continued transmission of HIV in the US, particularly in Houston, Texas. In this study, we conducted a phylogenetic reconstruction of HIV surveillance data from Houston alongside publicly available data from the United States using two computational approaches (maximum likelihood phylogenetic analysis and HIV-TRACE) in order to characterize the evolutionary relationship of HIV in Houston and identify possible migration events of the virus into and out of Houston from the greater US. Transmission clusters were first identified from our maximum likelihood tree as sequences that shared a most recent common ancestor with an equal or greater than 70% bootstrap support, then again using an equal or greater than 95% bootstrap support. HIV TRAnsmission Cluster Engine (HIV-TRACE) was then used for the genetic network reconstruction of clusters. The results of our study provide support of compartmentalization of Houston and the greater US along with transmission links between the two distinct geographic locations. These viral transmission links suggest that migration and travel can introduce viral variants into communities and further the transmission of HIV. Such links can connect susceptible, homogenous populations and impact the movement of the epidemic by bridging geographically disparate populations. By using HIV genomic data in conjunction with clinical data, time, and geography, future studies may reveal more insight into transmission dynamics influenced by the movement of people and identify susceptible groups in order to more effectively decrease HIV incidence, reduce transmission of HIV, and increase rates of treatment for affected individuals.

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Recommended Citation

Ng-Wing-Sheung, Chloe, "Phylogenetic Analysis of HIV-1 Migration into and out of Houston, Texas" (2018). Texas Medical Center Dissertations (via ProQuest). AAI10789252.