The goal of this project is to integrate data from local research, clinical and public health entities that are screening for and treating HIV infected persons. These data will be obtained in a de- identified manner, parsed and then organized into a HIPAA compliant database containing socio- demographic, geographic, reported risk behaviors and viral sequence information. The database will update itself in real-time as new HIV infections are identified, and viral sequence data will be used to map out the phylogenetic network of our local epidemic, focusing on drug using risk groups. We will utilize a background of nationwide HIV sequences obtained from publically available repositories to improve the signal in our phylogenetic structures and use Bayesian maximum likelihood analysis to build these networks in a robust manner. Finally, we will use this system to map the socio-demographic, geographic, risk behavior and phylogenetic data to locations of newly identified acute and early HIV infections. In real-time, these results will be used to identify micro-communities and sub-networks with HIV transmission associated with injection drugs or methamphetamine use, and we will use this information to direct community specific prevention resources (i.e. needle exchange, HIV testing, education, etc.) with the ultimate goal of preventing HIV transmission clusters from developing or expanding, particularly among substance using communities.
Specific Aims

National Institute of Health (NIH)
National Institute on Drug Abuse (NIDA)
NIH Director’s Pioneer Award (NDPA) (DP1)
Project #
Application #
Study Section
Special Emphasis Panel (ZDA1-NXR-B (06))
Program Officer
Lambert, Elizabeth
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Budget Start
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Fiscal Year
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University of California San Diego
Internal Medicine/Medicine
Schools of Medicine
La Jolla
United States
Zip Code
Dubé, Karine; Gianella, Sara; Concha-Garcia, Susan et al. (2018) Ethical considerations for HIV cure-related research at the end of life. BMC Med Ethics 19:83
Chaillon, Antoine; Gianella, Sara; Lada, Steven M et al. (2018) Size, Composition, and Evolution of HIV DNA Populations during Early Antiretroviral Therapy and Intensification with Maraviroc. J Virol 92:
Oliveira, Michelli F; Chaillon, Antoine; Nakazawa, Masato et al. (2017) Early Antiretroviral Therapy Is Associated with Lower HIV DNA Molecular Diversity and Lower Inflammation in Cerebrospinal Fluid but Does Not Prevent the Establishment of Compartmentalized HIV DNA Populations. PLoS Pathog 13:e1006112
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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
Gianella, Sara; Chaillon, Antoine; Mutlu, Ece A et al. (2017) Effect of cytomegalovirus and Epstein-Barr virus replication on intestinal mucosal gene expression and microbiome composition of HIV-infected and uninfected individuals. AIDS 31:2059-2067
Gianella, Sara; Taylor, Jeff; Brown, Timothy R et al. (2017) Can research at the end of life be a useful tool to advance HIV cure? AIDS 31:1-4
Chen, Xin; Ye, Mei; Duo, Lin et al. (2017) First description of two new HIV-1 recombinant forms CRF82_cpx and CRF83_cpx among drug users in Northern Myanmar. Virulence 8:497-503
Chaillon, Antoine; Nakazawa, Masato; Wertheim, Joel O et al. (2017) No Substantial Evidence for Sexual Transmission of Minority HIV Drug Resistance Mutations in Men Who Have Sex with Men. J Virol 91:
Ahn, Mi Young; Wertheim, Joel O; Kim, Woo Joo et al. (2017) Short Communication: HIV-1 Transmission Networks Across South Korea. AIDS Res Hum Retroviruses 33:827-831

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