Publication Date


Document Type

Doctoral Dissertation

Academic Program

Immunology and Microbiology


Program in Molecular Medicine

First Thesis Advisor

Paul Clapham, Ph.D.


HIV-1, HIV Infections, Human Immunodeficiency Virus env Gene Products, High-Throughput Nucleotide Sequencing


Dissertations, UMMS; HIV-1; HIV Infections; env Gene Products, Human Immunodeficiency Virus; High-Throughput Nucleotide Sequencing


Despite the development of effective antiretroviral treatments, there is still no cure for HIV-1. Major barriers to HIV-1 eradication include the diversity of intrapatient viral quasispecies and the establishment of reservoirs in tissue sanctuary sites. A better understanding of these populations is required for targeted treatments. While previous studies have examined the relationship between brain and blood or immune tissues, few have looked at and compared the properties of viruses from other tissue compartments. In this study, 75 full length HIV-1 envelopes were isolated from the frontal lobe, occipital lobe, parietal lobe, colon, lung, and lymph node of an HIV-1 infected subject. No envelopes could be amplified from the plasma or serum. Envelopes were subjected to genotypic and phenotypic characterization. Of the 75 envelopes, 53 were able to infect HeLa TZM-bl cells. The greatest proportion of non-functional envelopes was from the lung, a result of APOBEC-induced hypermutation. Lower frequencies of hypermutation were also observed in the occipital lobe and colon. Envelopes from regions of the brain were almost all macrophage tropic, while those from the body were predominantly non-macrophage tropic. All envelopes used CCR5 as a coreceptor. Phylogenetic analyses showed that sequences were compartmentalized inside the brain. These findings were also observed using PacBio next generation sequencing to examine 32,152 full length sequences. Envelopes from tissues of the body displayed greater variation in sequence length, charge, and number of potential N-linked glycosylation sites in comparison to envelopes from tissues of the brain. Increased variation was also observed in IC50s for inhibition and neutralization assays using sCD4, maraviroc, b12, PG16, 17b, and 447-52D. The increased variation observed in envelopes from tissues outside the brain suggests that different pressures may be influencing the evolution of these viruses and emphasizes the importance of further studies in these tissue sites.



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