All ETDs from UAB

Advisory Committee Chair

George M Shaw

Advisory Committee Members

Paul A Goepfert

Beatrice H Hahn

Xu Feng

Zdenek Hel

John C Kappes

Document Type


Date of Award


Degree Name by School

Doctor of Philosophy (PhD) Heersink School of Medicine


A precise molecular identification of transmitted/founder (T/F) HIV-1 genomes responsible for productive infection in humans can be an enabling strategy for elucidating mechanisms of virus transmission, immunopathogenesis and prevention. Previously, we reported a single genome sequencing approach, which when combined with a mathematical model of early random virus diversification, allowed for an unambiguous identification of T/F HIV-1 subtype B and C envelope (env) genes. Here, we apply this method to the identification and molecular cloning of full-length HIV-1 genomes and env genes of the less well-studied, but nonetheless important, HIV-1 subtypes A and D. Twelve subtype A (n=5), D (n=5) or A/D recombinant (n=2) T/F genomes contained intact canonical open reading frames and all were replication competent in primary human T-cells, with subtype D viruses replicating more efficiently (p<0.05). All 12 viruses utilized CCR5 but not CXCR4 as a co-receptor for entry and exhibited a neutralization profile typical of tier 2 primary virus strains, with significant differences observed between subtype A and D viruses with respect to sensitivity to monoclonal antibodies VRC01, PG9 and PG16 and polyclonal subtype C anti-HIV IgG (p<0.05 for each). Surprisingly, we found that T/F HIV-1 subtype B and C viruses replicated poorly in primary human macrophages. Because clinical studies have reported an association between neuropathogenesis and HIV-1 clade D infection, we characterized and contrasted the phenotypic properties of T/F clade D and A viruses, which co-circulate in East Africa, with respect to macrophage tropism and Env-mediated entry properties. Compared to clade A T/F viruses, clade D T/F viruses replicated more efficiently in primary human macrophages (p<0.05). Macrophage tropism mapped to Env and was significantly associated with virus replication rate, sensitivity to sCD4, efficient utilization of low CD4 on target cells and virus-cell fusogenicity (p<0.05 for all comparisons). These findings suggest that the enhanced neurovirulence associated with clade D infection is linked to phenotypic properties of HIV-1 clade D strains that enhance macrophage tropism from early in infection. Our work doubles the number of full-length T/F HIV-1 clones available for pathogenesis and vaccine research and extends their representation to include subtypes A, B, C and D.



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