All ETDs from UAB

Advisory Committee Chair

George M Shaw

Advisory Committee Members

Louis B Justement

John C Kappes

Brandon F Keele

Casey D Morrow

Jamil S Saad

Document Type


Date of Award


Degree Name by School

Doctor of Philosophy (PhD) Heersink School of Medicine


Vitally important to HIV-1 vaccine and prevention studies is a well-characterized animal model that recapitulates the salient features of HIV infection in humans. SIVmac and SIVsmm infection of rhesus macaques share key virological and pathological parallels with HIV-1 infection of humans including target cell entry via CD4 and CCR5 (Edinger et al., 1997), progressive T cell loss (Swanstrom & Coffin, 2012), generalized immune activation and preferential loss of mucosal Th17 cells (Brenchley et al., 2008; Klatt & Brenchley, 2010), and a vigorous but ultimately ineffective adaptive immune response. Though commonly used as a vaccine challenge strain in the macaque model, the neutralization properties of the SIVsmE660 isolate are unclear. We used single genome amplification and direct sequencing to clone envelopes (envs) from the isolate and from viruses transmitted to macaques following mucosal infection with SIVsmE660. We found that both the isolate and a majority (~70%) of these Envs were highly sensitive to neutralization by SIV-infected macaque plasmas (IC50<10-5) and monoclonal antibodies targeting V3 (IC50<0.01 ug/ml), CD4-induced (IC50<0.1 ug/ml), CD4 binding site (IC50~1 ug/ml) and V4 (IC50~5 ug/ml) epitopes. In comparison, SIVmac251 and SIVmac239 were highly resistant to neutralization by these same antibodies. Relatively few infectious molecular clones (IMCs) of the SIVsmE660 and SIVmac251 isolates exist. Genetically defined clones of acutely transmitted SIV could facilitate prevention research and inform on correlates of immune control. We identified and cloned transmitted/founder (T/F) viruses from 8 macaques mucosally infected with SIVsmE660 or SIVmac251. The clones were representative of the known diversity in the SIVmac251 and SIVsmE660 swarms and exhibited a range of sensitivities to neutralizing antibodies. All T/F viruses replicated significantly better in vitro than the common clone SIVmac239. Four T/F IMCs were inoculated into naïve rhesus macaques resulting in progressive infection and signs of simian AIDS including chronic diarrhea, cachexia, low peripheral CD4+ T cell level, and neoplasms. Such T/F viruses are useful, as they are the ones that we are most interested in analyzing and understanding from a transmission, immunopathogenesis, and vaccine protection standpoint. Phylogenetic inference of T/F viruses by SGS has been hypothesized to allow for the precise and unambiguous identification of those HIV-1 and SIV genomes responsible for productive clinical infection. By challenging Indian rhesus macaques with molecular clones of full-length T/F SIVmac251 and SIVsmmE660 genomes, we affirmed this hypothesis and thus fulfilled Koch's postulates as they apply to the T/F virus concept. Furthermore, we demonstrated the practical significance of these findings by applying the T/F strategy to the analysis of a challenge stock of SIVsmmE660, showing for the first time wide variation in the neutralization sensitivity of viruses comprising the stock and in the those T/F viruses acquired by animals infected by the stock. Altogether, these findings have important implications for the design and interpretation of preclinical and clinical HIV/AIDS vaccine trials.