The goal of this project is to integrate subject data from local research, clinical and public health entities that are screening for and treating HIV infected individual. Data from these sources will be obtained in a de?identified manner, parsed and then organized into a HIPAA compliant database containing socio?demographic, geographic and phylogenetic information for each subject. The database will be set up to update itself in real?time as new HIV infections are identified in our catchment area. In addition, we will use the viral sequence data to map out the phylogenetic network structure of our local epidemic. We will utilize a background of nationwide sequences obtained HIV sequence repositories to improve the signal in our phylogenetic structures, and use Bayesian maximum likelihood analysis to build these networks in a robust manner, leveraging the bioinformatics expertise at our institution, the University of California, San Diego. We will also update this network structure in a real?time fashion as new infections are identified. Finally we will use this constructed surveillance system to map the socio?demographic, geographic and phylogenetic locations of newly identified acute and early HIV infections, and use this information to direct community specific prevention resources (i.e. needle exchange, education resources etc) with the ultimate goal of preventing HIV transmission clusters from developing or expanding.

Public Health Relevance

This project will build a real-time database with socio-demographic, geographic and phylogenetic data of HIV infected individuals in the San Diego region. This database will be then used to target HIV prevention resources in a efficient manner to hopefully reduce new transmission of HIV.

National Institute of Health (NIH)
NIH Director’s Pioneer Award (NDPA) (DP1)
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Study Section
Special Emphasis Panel (ZDA1)
Program Officer
Lambert, Elizabeth
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University of California San Diego
Internal Medicine/Medicine
Schools of Medicine
La Jolla
United States
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Heaton, Robert K; Franklin Jr, Donald R; Deutsch, Reena et al. (2015) Neurocognitive change in the era of HIV combination antiretroviral therapy: the longitudinal CHARTER study. Clin Infect Dis 60:473-80
Okulicz, Jason F; Le, Tuan D; Agan, Brian K et al. (2015) Influence of the timing of antiretroviral therapy on the potential for normalization of immune status in human immunodeficiency virus 1-infected individuals. JAMA Intern Med 175:88-99
Little, Susan J; Kosakovsky Pond, Sergei L; Anderson, Christy M et al. (2014) Using HIV networks to inform real time prevention interventions. PLoS One 9:e98443
Chaillon, Antoine; Gianella, Sara; Vazquez, Homero et al. (2014) Novel codon insert in HIV type 1 clade B reverse transcriptase associated with low-level viremia during antiretroviral therapy. AIDS Res Hum Retroviruses 30:165-9
Hepler, N Lance; Scheffler, Konrad; Weaver, Steven et al. (2014) IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform. PLoS Comput Biol 10:e1003842
Murrell, Ben; Murrell, Daniel; Murrell, Hugh (2014) R2-equitability is satisfiable. Proc Natl Acad Sci U S A 111:E2160
Jeong, Su Jin; Kim, Min Hyung; Song, Je Eun et al. (2014) Short communication: prospective comparison of qualitative versus quantitative polymerase chain reaction for monitoring virologic treatment failure in HIV-infected patients. AIDS Res Hum Retroviruses 30:827-9
Scheffler, Konrad; Murrell, Ben; Kosakovsky Pond, Sergei L (2014) On the validity of evolutionary models with site-specific parameters. PLoS One 9:e94534
Tilghman, M W; PĂ©rez-Santiago, J; Osorio, G et al. (2014) Community HIV-1 drug resistance is associated with transmitted drug resistance. HIV Med 15:339-46
Wagner, Gabriel A; Pacold, Mary E; Kosakovsky Pond, Sergei L et al. (2014) Incidence and prevalence of intrasubtype HIV-1 dual infection in at-risk men in the United States. J Infect Dis 209:1032-8

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