HIV Reactivation from Latency after Treatment Interruption Occurs on Average Every 5-8 Days--Implications for HIV Remission

Abstract

HIV infection can be effectively controlled by anti-retroviral therapy (ART) in most patients. However therapy must be continued for life, because interruption of ART leads to rapid recrudescence of infection from long-lived latently infected cells. A number of approaches are currently being developed to 'purge' the reservoir of latently infected cells in order to either eliminate infection completely, or significantly delay the time to viral recrudescence after therapy interruption. A fundamental question in HIV research is how frequently the virus reactivates from latency, and thus how much the reservoir might need to be reduced to produce a prolonged antiretroviral-free HIV remission. Here we provide the first direct estimates of the frequency of viral recrudescence after ART interruption, combining data from four independent cohorts of patients undergoing treatment interruption, comprising 100 patients in total. We estimate that viral replication is initiated on average once every ≈6 days (range 5.1- 7.6 days). This rate is around 24 times lower than previous thought, and is very similar across the cohorts. In addition, we analyse data on the ratios of different 'reactivation founder' viruses in a separate cohort of patients undergoing ART-interruption, and estimate the frequency of successful reactivation to be once every 3.6 days. This suggests that a reduction in the reservoir size of around 50-70-fold would be required to increase the average time-to-recrudescence to about one year, and thus achieve at least a short period of anti-retroviral free HIV remission. Our analyses suggests that time-to-recrudescence studies will need to be large in order to detect modest changes in the reservoir, and that macaque models of SIV latency may have much higher frequencies of viral recrudescence after ART interruption than seen in human HIV infection. Understanding the mean frequency of recrudescence from latency is an important first step in approaches to prolong antiretroviral-free viral remission in HIV.

Fig 1. Schematic of viral recrudescence after ART-interruption.

(A) After ART-interruption, there is an initial delay when virus cannot grow, due to ‘washout’ of ART. Once viral replication is possible, there is a variable time until successful viral replication is initiated from the latent reservoir. The low initial level of replicating virus then increases until it reaches the detection threshold. Time to initiation refers to time until replicative infection commences, which is followed by a delay due to viral growth, and then by detection of plasma virus. (B) time-to-detection plotted as a ‘survival curve’. The initial shoulder occurs due to ART washout and viral growth, and is followed by an exponential decay in the proportion of patients with no detectable virus.

Fig 2. Dynamics on recrudescence in nine patients enrolled in Panobinostat trial (reference [8]).

(A) The trajectory of viral load of individual patients after ART-interruption. Dashed line indicates threshold of detection (20 copies ml^-1) (B) the ‘survival curve’ of patients without detectable virus. The frequency of recrudescence is equivalent to one initiation of viral replication occurring every 7.6 days. (C) growth rate of virus after detection is not significantly correlated with time to recrudescence (p = 0.9).

Fig 3. Dynamics of recrudescence in 59 patients enrolled in the Pulse study (reference [15]).

(A) Trajectory of viral load in individual patients. Dashed line indicates threshold of detection (50 copies ml^-1) (B) survival curve of time to detection (frequency of initiation of viral replication is once every 6.3 days). (C) Growth rate estimated from first two weeks of detectable virus. (D) Average viral load at detection for patients detected at different weeks. Dashed line indicates threshold of detection (50 copies ml^-1)

Fig 4. Time-to-detection of virus in cohorts 3 and 4.

(A) time-to-detection in cohort 3, of 18 patients undergoing interruption (reference [16]). The best-fit frequency of reactivation is once every 5.1 days. (B) time-to-detection in cohort 4, of 14 patients undergoing five interruptions, and monitored at days 4, 8, and 14 (reference [17]). The best-fit frequency over all interruptions is once every 7.2 days. (C) Time to recrudescence is not correlated with growth rate in cohort 3. (D) Higher reactivation rates in SIV than HIV. The estimated frequency of initiation of viral replication in SIV infected macaques treated with ART between 7 and 14 days post-infection (from reference [26]) is shown as solid line, and was found to be once every 1.7 days. The best-fit frequency of reactivation across the four HIV cohorts (a reactivation event every 6 days) is shown as a dashed line.

Fig 5. Modelling of kinetics of time-to-detection:

A: Using the ratio of the number of copies of reactivation founder viruses to estimate rate of initiation of viral growth. The cumulative proportion of founders with different ratios (to the size of next largest founder) is shown. Solid line is ratios from the experimental data, dashed line is the theoretical distribution with the best fit frequency of rebound of once every 3.6 (CI 1.98–6.62) days. Ratios marked with an asterisk are where we could only estimate a minimum ratio (ie: there was no detected next founder virus). (B) Estimating the reduction in frequency of recrudescence (and reservoir size) from observed delay to detection of virus. For a ‘normal’ reservoir size, we find an average frequency of reactivation of once every 6 days (which also equates to an average delay to reactivation of 6 days). For patients with longer time-to-detection we can estimate the relative size of the reservoir compared to our cohort populations. Solid line shows the fold reduction in reservoir size that would be estimated simply comparing the observed time to detection with the estimated average of 6 days. Since reactivation does not always occur at the average time, the range expected for 95% of subjects is shown (shaded area). T₁ and T₂ are the delays for two patients that underwent allogeneic stem cell transplantation (reference [30]). T₃ is the delay observed in the ‘Mississippi baby’ (reference [29]). (C) Difficulties using treatment interruption studies to measure changes in the reservoir. The number of patients required (y-axis) to have a 50% (dashed line), an 80% (solid line) or a 95% (dot-dash line) power to detect a given reduction in reservoir (x-axis) is shown, based on Log-rank test. This assumes a 100-day follow up after ART-interruption.