Introduction: The poor fidelity of the HIV reverse transcriptase enzyme leads to a significant sequence diversity across infected individuals. Although this complicates antiretroviral therapy, this diversity allows researchers to characterize relationships between sampled viruses using phylogenetic tools. Once the phylogenetic relationships of HIV sampled from infected individuals are characterized, socio-demographic data from the sampled individuals may be overlaid onto these phylogenetic relationships leading to inferred reconstruction of social networks that may create a better understanding of socio-demographic patterns and drivers of the sampled epidemic. Previous work has characterized some of the risk factors for HIV infection in both San Diego, CA and Tijuana, Mexico. We propose to utilize objective sequence data along with clinical and socio-demographic data to improve the understanding of the relationship of the HIV-1 sub-epidemics along the San Diego-Tijuana border. Methods: In this proposal, sequence, clinical, and socio-demographic data gathered from HIV positive individuals enrolled in seven different collaborating cohorts along the San Diego- Tijuana border will be combined for analysis. HIV pol sequence data will be collected from the collaborating cohorts or generated from blood samples provided by them. Socio-demographic and clinical data will be abstracted from the databases of the cohorts in a de-identified manner, except for location of residence. Maximum likelihood based methods will then be used to determine the phylogenetic structure (i.e. clustering) of the sampled sequences, and then associations between the clustering and socio-demographic variables will be assessed including: location of residence, HIV risk factors, drug resistance, duration of infection, cross- border movement, and others. We will next determine the spatial and temporal dynamics of the HIV epidemics across the border region using geographic information systems, and coalescent theory based Bayesian phylogeographic analyses. These analyses can incorporate temporal and geographic data into the prior estimations of phylogenetic structure so that the final results may identify temporal and spatial transmission 'hot spots'. In order to address privacy issues, all geographic data will be smoothed at the time of presentation so that identification of individuals will not be possible. We will also work closely with our bioinformatics colleagues to understand the limitations of our convenience data, and develop statistical techniques to make our findings generalizable. Conclusions: We anticipate that our findings will improve understanding of HIV transmission dynamics in this region so that prevention strategies can be designed and targeted more effectively. This research project has two major aims: 1) to identify risk factors related to HIV transmission, and 2) identify temporal and spatial 'hot spots of transmission in the San Diego-Tijuana border region. These results will assist public health agencies in Mexico and the US to more efficiently develop appropriate and targeted intervention strategies to curb ongoing HIV transmission.
This research project has two major aims: 1) to identify risk factors related to HIV transmission, and 2) identify temporal and spatial 'hot spots of transmission in the San Diego-Tijuana border region. These results will assist public health agencies in Mexico and the US to more efficiently develop appropriate and targeted intervention strategies to curb ongoing HIV transmission.
|Chaillon, Antoine; Essat, Asma; Frange, Pierre et al. (2017) Spatiotemporal dynamics of HIV-1 transmission in France (1999-2014) and impact of targeted prevention strategies. Retrovirology 14:15|
|Pérez-Santiago, Josué; De Oliveira, Michelli F; Var, Susanna R et al. (2017) Increased cell-free mitochondrial DNA is a marker of ongoing inflammation and better neurocognitive function in virologically suppressed HIV-infected individuals. J Neurovirol 23:283-289|
|Vitomirov, Andrej; Ramirez-Gaona, Miguel; Mehta, Sanjay R et al. (2017) Random shearing as an alternative to digestion for mitochondrial DNA processing in droplet digital PCR. Mitochondrion 32:16-18|
|Chaillon, Antoine; Avila-Ríos, Santiago; Wertheim, Joel O et al. (2017) Identification of major routes of HIV transmission throughout Mesoamerica. Infect Genet Evol 54:98-107|
|Mehta, Sanjay R; Pérez-Santiago, Josué; Hulgan, Todd et al. (2017) Cerebrospinal fluid cell-free mitochondrial DNA is associated with HIV replication, iron transport, and mild HIV-associated neurocognitive impairment. J Neuroinflammation 14:72|
|Chaillon, Antoine; Smith, Davey M; Vanpouille, Christophe et al. (2017) HIV Trafficking Between Blood and Semen During Early Untreated HIV Infection. J Acquir Immune Defic Syndr 74:95-102|
|Carter, Christoph C; Fierer, Joshua; Chiu, Wei Wei et al. (2016) A Novel Shiga Toxin 1a-Converting Bacteriophage of Shigella sonnei With Close Relationship to Shiga Toxin 2-Converting Pages of Escherichia coli. Open Forum Infect Dis 3:ofw079|
|Chin, Bum Sik; Chaillon, Antoine; Mehta, Sanjay R et al. (2016) Molecular epidemiology identifies HIV transmission networks associated with younger age and heterosexual exposure among Korean individuals. J Med Virol 88:1832-5|
|Pérez-Santiago, Josué; Schrier, Rachel D; de Oliveira, Michelli F et al. (2016) Cell-free mitochondrial DNA in CSF is associated with early viral rebound, inflammation, and severity of neurocognitive deficits in HIV infection. J Neurovirol 22:191-200|
|Chaillon, Antoine; Hoenigl, Martin; Mehta, Sanjay R et al. (2016) A practical online tool to estimate antiretroviral coverage for HIV infected and susceptible populations needed to reduce local HIV epidemics. Sci Rep 6:28707|
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