The clinical arm of the HIV Drug Resistance Program is under the direction of Frank Maldarelli, M.D., Ph.D. Its primary research focus is to understand the population genetics, evolution, and dynamics of HIV infection in patients, particularly as related to the development of resistance and possible ways to overcome it. In collaboration with the NIAID/CCMD AIDS clinic and the NCI HIV-AIDS Malignancy Branch, Dr. Maldarelli develops and secures IRB approval for clinical trials, and implements them using the support of these groups. At present, there are three active protocols, corresponding to the three ongoing projects:

HIV expression in patients with viral loads suppressed on HAART (Protocol 02-I-0232). The goal of this study is to determine the level and nature of viremia in HIV-1-infected patients. Using the single copy assay, we are following patients on therapy whose virus load is undetectable by standard assays. We have found that about two-thirds of such patients have detectable, stable viremia in the range of 1-40 copies of RNA/ml. The level of this viremia appears to be related to regimen potency, suggesting that it is maintained by ongoing replication. We will test this relationship further by applying this analysis to stored samples from large-scale trials of regimens with different expected potencies. In another randomized, prospective, trial, we will test the effect of intensification of therapy on level of viremia. The latter study should directly test whether ongoing replication is responsible for maintaining the low, but steady, load in suppressed patients.

Analysis of HIV genetic variation in patients prior to initiation of highly active antiretroviral therapy (Protocol 00-I-0110). The goal of this study is a focused attack on the population genetics of HIV-1 in infected individuals. In the principal study, therapy-naïve individuals with long-term chronic HIV-1 infection are enrolled and sampled intensively for a short time and then continuously for an indefinite period. Those electing to start therapy are again sampled intensively immediately preceding and following the start of treatment. We are also following a few patients started on the protocol within a few months of infection. All samples are subjected to the limiting dilution sequencing analysis, and a minimum of 20 sequences are obtained for each. We are also beginning to use the allele-specific assay to study the appearance and frequency of rare alleles (such as K103N) in the samples. To date, we have found that the virus population early in infection is strikingly monomorphic; by contrast, virus in chronically infected patients exhibits a great deal of diversity in pro and pol. The pattern of diversity, however, is remarkably stable, suggestive of a large population evolving under strong purifying selection. There is also evidence for a high level of recombination in the population, such that closely spaced bases are usually unlinked. The same preservation of diversity was also found after initiation of therapy: even after a 2-log decline in virus load, the virus population was phylogenetically identical to the pretherapy population. We intend to use data from these analyses to estimate important population parameters, such as its effective size, genetic structure, recombination rates, selective forces, etc.

An assessment of the relationship between antiretroviral drug genotype/phenotype (IC50) and antiretroviral activity in HIV-infected, drug-experienced patients with suboptimal suppression of plasma viral load (Protocol 01-I-0004). This study analyzes the correlation between phenotype/genotype to selected antiretroviral agents and short-term change in viral load upon discontinuation of a single antiretroviral agent from a failing regimen. One drug in a failing multidrug regimen is withdrawn for a limited period of time, and then restored. By monitoring changes in both viremia and genotype (by the limiting dilution assay), we can discern whether the drug was contributing to partial suppression of virus, and also determine which mutations are associated with resistance to that drug, and their affect on both fitness of the virus and resistance to the drug.

For further information about these clinical trials, please contact Dr. Maldarelli (e-mail fmalli@mail.nih.gov).