Genetic characterization of rebounding HIV-1 after cessation of highly active antiretroviral therapy

Abstract

Despite prolonged treatment with highly active antiretroviral therapy (HAART), infectious HIV-1 continues to replicate and to reside latently in resting memory CD4(+) T lymphocytes, creating a major obstacle to HIV-1 eradication. It is therefore not surprising to observe a prompt viral rebound after discontinuation of HAART. The nature of the rebounding virus, however, remains undefined. We now report on the genetic characterization of rebounding viruses in eight patients in whom plasma viremia was undetectable throughout about 3 years of HAART. Taking advantage of the extensive length polymorphism in HIV-1 env, we found that in five patients who did not show HIV-1 replication during treatment, the rebound virus was identical to those isolated from the latent reservoir. In three other patients, two of whom had been free of plasma viremia but had showed some residual viral replication, the rebound virus was genetically different from the latent reservoir virus, corresponding instead to minor viral variants detected during the course of treatment in lymphoid tissues. We conclude that in cases with apparent complete HIV-1 suppression by HAART, viral rebound after cessation of therapy could have originated from the activation of virus from the latent reservoir. In patients with incomplete suppression by chemotherapy, however, the viral rebound is likely triggered by ongoing, low-level replication of HIV-1, perhaps occurring in lymphoid tissues.

Figure 1

Changes in plasma viral load and CD4⁺ lymphocyte count during and after HAART. Shaded areas indicate the treatment periods. The drug regimens are as indicated: AZT, zidovudine; 3TC, lamivudine; RIT, ritonavir; and IND, indinavir. The open arrows indicate the days on which boosted cultures were undertaken to isolate latent viruses from resting memory CD4⁺ T cells. The solid arrows indicate the days when tissue biopsies were collected from the lymph node, tonsil, and/or rectum.

Figure 2

Length polymorphism in the V1–V2 (in red) and V4–V5 (in blue) regions of HIV-1 env found in the plasma of eight acutely infected (left) and eight chronically infected (right) patients. The length of each V1–V2 or V4–V5 region is indicated by the scale at the top of each panel.

Figure 3

Length polymorphism of the rebounding plasma virus in comparison with those isolated from the latent reservoir during therapy and those in the plasma before therapy. Multiple samples collected after cessation of HAART are separated into three time groups: 14–42 days, 43–140 days, and 141–280 days. The V1–V2 region is shown in red; the V4–V5 region is shown in blue. The size of each peak is indicated by the scale at the top of each panel.