Research Groups
HIV-1 Fitness
HIV-1 Recombination
HIV-1 Inhibitors
Hepatits C

Awet Abraha, Korey Demers, Fred Kyeyune, Ryan Troyer, Immaculate Nankya, Kevin Ariën.
Collaborators: Sarah Ball, Miguel Quiñones-Mateu, Guido Vanham

1. Comparing ex vivo HIV-1 fitness to disease progression
Miguel has developed an HIV-1 dual infection/competition assay to measure ex vivo fitness. We now have strong evidence that ex vivo HIV-1 fitness is strong correlate and possibly a predictor of disease progression. To expand these studies, Guido Vanham has sent us at least four consecutive HIV-1 isolates spanning a period of two to five years of approximately 20 HIV-infected patients. We will measure the ex vivo fitness of each isolate to compare with various clinical correlates of disease progression.

In a parallel study, Korey is collecting samples from newly HIV-1 infected Ugandan and Zimbabwean women participating in the HC-HIV study. Virus will be propagated from these acute/early infections as well as during the course of disease progression (2-5 years). Subtypes A, C, and D predominate in Uganda whereas subtype C is exclusively found in Zimbabwe. Thus, we can use these virus isolates to compare inter- and intrasubtype fitness as well as the impact of subtype fitness on disease progression. Studies performed by Sarah suggest that subtype C isolates may be significantly less fit than subtype B isolates. This has lead to one of the most exciting hypothesis in my career. Individuals infected with subtype C may have a slower progression to AIDS than those infected with other subtypes. This possibility coupled with enhanced subtype C transmission would explain the increased prevalence of this subtype in the worldwide epidemic.

2. Examining a possible relationship between HIV-1 fitness and quasispecies heterogeneity
The Red Queen Hypothesis states that a species must continue to evolve into multiple quasispecies to retain or gain fitness advantage. Based on this hypothesis, the continual increase HIV-1 quasispecies and genetic diversity during the course of disease may be related to increased HIV-1 fitness. Kalonji will examine this relationship using the Belgium cohort.

3. Comparing the fitness of different HIV types (-1 and –2), HIV-1 groups (M, N, and O), and SIV isolates
This project will involve collaborations with the Vanham, Quinones, and Arts laboratories. Kevin, a graduate student in Guido’s lab will perform a pairwise competition experiment with the isolates of the various primate lentiviruses, HIV types, and HIV-1 groups.

4. Mapping HIV-1 fitness to the env gene and using the env pseudotyping to measure ex vivo fitness
Sarah clearly showed that efficiency of host cell entry was controlling the dual virus competition. Thus, it appears that the HIV-1 env gene is main determinant of fitness. Based on these findings, we are comparing the fitness on env-pseudotyped HIV-1 isolates with propagated HIV-1 isolates derived from the same patient samples.

Future projects:
Possible attenuation of HIV-1 during the epidemic (top)


Heather Baird, Yong Gao.

1. Impact of fitness on the selection of intersubtype HIV-1 recombinants
In parallel to studies investigating subtype fitness, we also screened and characterized intersubtype HIV-1 env recombinants. A low frequency of recombination and possible hot sites for cross-overs suggest a limited selection of intersubtype env recombinants similar to that observed in vivo. This study will sub-clone the intersubtype env recombinants from each dual infection into a HIV-1 molecular clone via the yeast cloning method. These recombined clones will also be used in RANTES analog project and in the subsequent design of a heterogeneous vaccine. HIV-1 clones pseudotyped with these recombined env genes will be passaged in various cell lines and primary cells to select for the most fit intersubtype recombinants. We will then compare the fitness of these selected recombinants with the fitness of the parental strains.

2. Generate and test a construct containing intersubtype HIV-1 env recombinant as possible HIV-1 vaccine
This study will require extensive collaborations for small animal testing and immunological assays. Adam will generate the constructs as described. Mice will be vaccinated and boosted with the heterogeneous env DNA vaccine. We will examine both humoral and CTL responses to various HIV-1 specific epitopes of various subtypes.

3. To examine the mechanisms of intersubtype HIV-1 recombination in vitro through the use of reconstituted HIV-1 reverse transcription assays
Heather will clone several HIV-1 env DNA fragments into RNA expression vectors. HIV-1 env RNA templates from different subtypes will then be combined in reverse transcription assays. Sites of cross-overs during reverse transcription and between RNA templates will be mapped and compared to the recombination observed in dual infections. (top)


Andre Marozsan, Erika Fraundorf, Dawn Moore, Fred Kyeyune.

1. Determine the mechanism of HIV-1 inhibition by RANTES analogs
Based on results from Vince Torre, we suspect that RANTES analogs block HIV-1 entry into a host cell by competitively binding to the CCR5 co-receptor. Since different primary R5 HIV-1 isolates show variable susceptibility to AOP-RANTES inhibition, it is unlikely that CCR5 receptor down-regulation following AOP-RANTES binding could be the sole mechanism for HIV-1 inhibition.

Andre has cloned CCR5 with a mutation in cytoplasmic C-terminal that prevents receptor internalization. U87 cells were stably transfected with this mutant CCR5 construct. He is now accessing cell-surface receptor expression, receptor-ligand interactions, and receptor internalization/recycling by performing I125-RANTES binding assays and FACS analysis.

In future, we will compare RANTES analog inhibition of various primary R5 HIV-1 isolates in the wt and mutant CCR5 cell lines. Erika has also pseudotyped an HIV-1 laboratory clone with the env gene of several primary HIV-1 isolates using the yeast cloning method. These viruses will propagated from transfected cell lines and then used in drug susceptibility assays

2. Mapping the sites conferring RANTES resistance in the envelope gene of R5 HIV-1 isolates
These studies will involve two approaches. In a previous study, Vince identified a single amino acid residue (319) in the env V3 loop associated with increased or decreased sensitivity to RANTES analog inhibition. In addition, studies by Don Mosier’s group have identified an adjacent amino acid residue (318) that was mutated in NNY-RANTES-resistant HIV-1 isolates. Korey has used a site-directed PCR mutagenesis technique to introduce these mutations in the env genes of two primary HIV-1 isolates. An HIV-1 clone was then pseudotyped with these mutated env genes using the yeast cloning method.

In future, these mutated viruses will then be propagated from transfected cell lines and then used in drug susceptibility assays. We suspect that these mutations will be associated with variable sensitivity to RANTES analog inhibition.

The second approach to identify sites in the env gene associated with resistance involves the intersubtype HIV-1 recombinants generated in vitro. We have recombined an AOP-resistant and –sensitive R5 HIV-1 isolate by the dual infection technique. Recombined env genes were selected by PCR as described. Similar to Adam’s project, the recombined env genes are now being used to pseudotype the HIV-1 clone through the yeast cloning method. Using multiple recombined HIV-1 strains in drug susceptibility assays, we should be able to map the sites conferring resistance to RANTES analogs.

Future Projects:
1. Role of Vpr in AOP-RANTES stimulation of HIV-1 replication
Andre has previously demonstrated that high concentrations of AOP-RANTES can stimulate replication of primary X4 HIV-1 isolates. This stimulation appears to be mediated through a CCR5-mediated signaling cascade, ERK1,2 phosphorylation/activation, and increased HIV-1 integration. However, it is unclear why AOP-RANTES stimulates only primary and not laboratory X4 HIV-1 isolates. This discrepancy may be related to the dependence on Vpr activity for the translocation of the HIV pre-integration complex into the nucleus. In collaboration with Lou Mansky at Ohio State University, we are now sequencing the Vpr gene to identify possible polymorphism that may be related to this phenotype. In future, we may mutate the Vpr gene in the HIV laboratory clones to determine if AOP-RANTES can now stimulate virus production.

2. Introducing the natural polymorphisms into the CCR5 ORF

3. Comparing sensitivity to AOP-RANTES inhibition with HIV-1 fitness (top)


Heather Baird.
Collaborators: Kathy Howard, Karl Venezia, Dr. Mary Barkley

This project is in its infancy but is based on years of research into the mechanisms involved in the initiation of HIV-1 reverse transcription. HCV like many other (+) stand RNA viruses forms a complex RNA secondary structure at the 3’ end of RNA genome. This region may be synonymous in function with the tRNA-viral RNA interaction involved in retroviral initiation of (-) strand synthesis. Heather has cloned the HCV cDNA genome into an RNA expression vector to transcribe various fragments of the 3’end of the (+) strand HCV RNA. These RNA fragments are end-labelled and probed with chemical or nucleases to determine RNA secondary structure. In parallel, Karl and Kathy have cloned, expressed, and purified the NS5b polymerase of HCV. They will be accessing the polymerase activity of NS5b on the HCV RNA template. In addition, NS5b structure in the presence or absence of HCV RNA will be probed using a protein footprinting technique and mass spec. Heather will then footprint the RNA bound to NS5b using the 3’ end of the (+) HCV RNA. Efficient initiation of (-) strand RNA in this reconstituted assay may require the inclusion of other viral proteins, e.g. NS4 or NS3 (protease/helicase). (top)