In HIV research, there is a persistent and vigorous debate around the question of whether or not viral replication persists in the face of successful antiretroviral therapy. During a plenary session at the International AIDS Conference in Mexico City back in August, Bob Siliciano made a compelling argument that, in most cases, antiretroviral therapy completely shuts down virus production. Now, a new paper in PNAS provides additional support for this view. Beda Joos and colleagues evaluated a staggering 1,753 genetic sequences from the envelope region of HIV, sampled over the course of a treatment interruption trial known as SSITT (Swiss-Spanish Intermittent Treatment Trial). The study design involved a series of two-week treatment breaks followed by a prolonged interruption (therapy was subsequently reinitiated according to the CD4 and viral load thresholds used in current treatment guidelines).
The researchers used the sequence data to plot the relationships between the different viruses, using a technique called phylogenetic analyses. For each study participant analyzed, the sequences were used to define “the most recent common ancestor” (MRCA), which is an approximation of the ancestral virus sequence from which all the others derived. Viruses that appeared during treatment interruptions (TIs) were then compared to the MRCA, to see if the sequences suggested that there had been ongoing replication and evolution while the study participants were on ART. The results showed that the rebounding viruses during TI were actually more distant from the MRCA than the viruses detected when the participants first entered the study. The researchers conclude: “the striking lack of a temporal relationship between rebounding virus and pretreatment viruses strongly suggests that rebounding virus originates from reactivated, latently infected cells rather than from a cellular pool or compartment engaged in low-level replication.”
PNAS October 28, 2008 vol. 105 no. 43 16725-16730
Published online before print October 20, 2008, doi: 10.1073/pnas.0804192105
Beda Joosa,1, Marek Fischera, Herbert Kustera, Satish K. Pillaib, Joseph K. Wongb, Jürg Bönic, Bernard Hirscheld, Rainer Webera, Alexandra Trkolaa, Huldrych F. Güntharda,1, and The Swiss HIV Cohort Study2
aDepartment of Medicine, Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, CH-8091 Zurich, Switzerland;
bSan Francisco Veterans Affairs Medical Center, University of California, San Francisco, CA 94121;
cNational Center for Retroviruses, University of Zurich, CH-8028 Zurich, Switzerland; and
dDivision of Infectious Disease, University Hospital Geneva, 1211 Geneva, Switzerland
Rapid rebound of plasma viremia in patients after interruption of long-term combination antiretroviral therapy (cART) suggests persistence of low-level replicating cells or rapid reactivation of latently infected cells. To further characterize rebounding virus, we performed extensive longitudinal clonal evolutionary studies of HIV env C2-V3-C3 regions and exploited the temporal relationships of rebounding plasma viruses with regard to pretreatment sequences in 20 chronically HIV-1-infected patients having undergone multiple 2-week structured treatment interruptions (STI). Rebounding virus during the short STI was homogeneous, suggesting mono- or oligoclonal origin during reactivation. No evidence for a temporal structure of rebounding virus in regard to pretreatment sequences was found. Furthermore, expansion of distinct lineages at different STI cycles emerged. Together, these findings imply stochastic reactivation of different clones from long-lived latently infected cells rather than expansion of viral populations replicating at low levels. After treatment was stopped, diversity increased steadily, but pretreatment diversity was, on average, achieved only >2.5 years after the start of STI when marked divergence from preexisting quasispecies also emerged. In summary, our results argue against persistence of ongoing low-level replication in patients on suppressive cART. Furthermore, a prolonged delay in restoration of pretreatment viral diversity after treatment interruption demonstrates a surprisingly sustained evolutionary bottleneck induced by punctuated antiretroviral therapy.