Residual HIV-1 Replication in Patients Receiving Combination Antiretroviral Therapy and with Undetectable HIV-RNA

H. Mens*, A. G. Pedersen**, T. L. Katzenstein* and J. Gerstoft*

*Department of Infectious Diseases, Rigshospitalet, Copenhagen (Denmark).

** Center for Biological Sequence Analysis, Technical University of Denmark (Denmark).

Background: In patients infected with HIV-1, combination antiretroviral therapy can result in sustained suppression of plasma levels of the virus. It is still unknown which mechanisms maintain this viral reservoir. Objective: To determine whether there is an ongoing replication of HIV-1 in patients receiving HAART, with HIV-RNA below the limit of detection (20 cop/mL). Design: We followed a group of 55 HIV infected individuals, receiving HAART, for 24 months. The criterion for entering the study was HIV-RNA below the limit of detection. Proviral DNA was amplified and bulk sequenced every six months. In seven patients we also cloned and sequenced the PCR product. The patients were subdivided into three groups depending on the level of HIV-RNA during the study time. Group 1 displayed HIV-RNA levels that were constantly below 20 cop/mL, group 2 had HIV-RNA levels between 20 and 200 cop/mL and group 3 had HIV-RNA above 200 cop/mL at one or more time points. Preliminary Results: Seventeen of the patients belonged to group 1, 28 to group 2, and 10 to group 3. The average number of nucleotide changes per site per month was 0.034 +/- 0.034 for group 1, 0.039 +/- 0.025 for group 2, and 0.031 +/- 0.018 for group 3. None of these differences are statistically significant. Only two patients belonging to group 1 and one patient belonging to group 2 displayed no changes over all 5 time points. In 7 patients, two belonging to group 3, one to group 2 and four to group 1, we performed a maximum likelihood analysis on cloned material for the five consecutive time points. Here we found a positive selection pressure on V3 part of the envelope gene in all the patients. We also performed tip-date analysis to measure the mutation rate on the branches of the tree and calculated the viral divergence, these results are in progress. Conclusions: We observe changes in the population of proviral DNA in all three groups of patients. We also find a positive selection pressure on the V3 gene in all the three groups of patients. This could suggest an ongoing viral replication in patients receiving HAART and with HIV-RNA below the limit of detection. Alternatively this could reflect a non-random loss of lymphocytes over time.