An HIV Epidemic Model Based on Viral Load Dynamics: Value in Assessing Empirical Trends in HIV Virulence and Community Viral Load

<div><p>Trends in HIV virulence have been monitored since the start of the AIDS pandemic, as studying HIV virulence informs our understanding of HIV epidemiology and pathogenesis. Here, we model changes in HIV virulence as a strictly evolutionary process, using <i>set point viral load</i> (SPVL) as a proxy, to make inferences about empirical SPVL trends from longitudinal HIV cohorts. We develop an agent-based epidemic model based on HIV viral load dynamics. The model contains functions for viral load and transmission, SPVL and disease progression, viral load trajectories in multiple stages of infection, and the heritability of SPVL across transmissions. We find that HIV virulence evolves to an intermediate level that balances infectiousness with longer infected lifespans, resulting in an optimal SPVL∼4.75 log₁₀ viral RNA copies/mL. Adaptive viral evolution may explain observed HIV virulence trends: our model produces SPVL trends with magnitudes that are broadly similar to empirical trends. With regard to variation among studies in empirical SPVL trends, results from our model suggest that variation may be explained by the specific epidemic context, <i>e.g.</i> the mean SPVL of the founding lineage or the age of the epidemic; or improvements in HIV screening and diagnosis that results in sampling biases. We also use our model to examine trends in community viral load, a population-level measure of HIV viral load that is thought to reflect a population's overall transmission potential. We find that community viral load evolves in association with SPVL, in the absence of prevention programs such as antiretroviral therapy, and that the mean community viral load is not necessarily a strong predictor of HIV incidence.</p></div

A. Empirical SPVL trends overlaid onto distributions of simulated 20-year trends.

<p>Distributions of linear SPVL trends (log₁₀ HIV RNA copies/mL/year) were estimated from 100 randomly sampled 20-year time periods for 10 replicate simulations for each initial mean SPVL = 3.5, 4.5 or 5.5 log₁₀ HIV RNA copies/mL (creating 1000 total 20-year trends for each initial mean SPVL). Empirical (published) annual linear SPVL trends are overlaid (arrows and references). References with asterisks are seroprevalent cohorts; all others are seroconverter cohorts. <b>B. </b><b>Selection of an appropriate null changes the distribution of simulated SPVL trends.</b> Separate null distributions, each spanning a different subset of the complete 100-year simulated epidemics: all 100 years of the model output; years 10–100 of the model output, as European and North American subtype B epidemics began ∼1970, and studies of empirical SPVL trends began sampling at the earliest in 1984, leaving a ∼10-year window of the HIV epidemic not sampled by the cohorts; years 0–40 of the model output, as the empirical studies of SPVL trends include years up to ∼2010, so this represents the first 40 years of the subtype B epidemic (∼1970 to 2010); and years 10–40, reflecting the empirical sampling years ∼1980 to 2010.</p

Parameters of the model and standard initial values.

<p>Parameters of the model and standard initial values.</p

Mean community viral load is not linearly or consistently associated with annual incidence.

<p><b>A.</b> Plot of yearly estimates of mean community viral load versus annual incidence, for 100 years of a simulated epidemic. <b>B.</b> Distributions of <i>P</i>-values for Spearman correlations between mean community viral load and incidence, by year, for 10-year periods from the same 100 year epidemic, from a sliding window of 10 with one year increments. Shown are a plot of CVL and incidence for a 100-year simulated epidemic, Spearman correlation coefficients between CVL and incidence for each overlapping 10-year period, and <i>P</i>-value for each Spearman correlation test. Significant associations between CVL and incidence can be positive or negative, depending on epidemic context.</p

A. Distributions of SPVL trends change as simulated epidemics progress.

<p>More extreme SPVL trends occur very early in simulated epidemics (the first 20 years). Boxplots of linear SPVL trends estimated from 100 randomly sampled 20-year time periods; thick line = median; box edges = quartiles; whiskers = minimum and maximum trends. <b>B. </b><b>Trends in mean community viral load and mean set point viral load are related.</b> Mean community viral load can evolve over time in the absence of HIV prevention programs. Community viral loads are estimated for each day using viral load measurements from each infected and alive individual, except for those individuals who have been infected less than 45 days (acute infection lasts for 3 months days in these simulations).</p

Variation across replicate simulated epidemics.

<p><b>A.</b> Epidemic size over time. Epidemic runs with each initial SPVL were repeated 10 times, each run with a different random number seed. <b>B.</b> Population mean set point viral load (SPVL; log₁₀ HIV RNA copies/mL at the end of acute infection) over time, using a locally weighted polynomial regression curve (Lowess fit = 0.1). Mean SPVL evolves toward 4.75 log₁₀ copies/mL.</p

The effect of sampling biases on the estimation of model-based SPVL trends.

<p><b>A.</b> Comparison of distribution of 20-year linear SPVL trends estimated from unbiased (black lines, initial mean SPVL = 3.5; grey lines, initial mean SPVL = 4.5) and biased (dotted lines, multiple colors representing multiple sub-sampling levels) data sets. The underlying distributions are produced from years 0 to 100 from simulated epidemics. Removing subsets (%) of all individuals (a schematic representation of the biased sampling process is shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003673#pcbi.1003673.s001" target="_blank">Figure S1A</a>) results in a distribution of linear trends with a median SPVL trend of greater magnitude than the unbiased trends. <b>B.</b> Comparison of distribution of 20-year linear SPVL trends estimated from unbiased and biased data sets, but with the underlying distributions produced from years 10 to 40 from simulated epidemics.</p

Silibinin Inhibits HIV-1 Infection by Reducing Cellular Activation and Proliferation

<div><p>Purified silymarin-derived natural products from the milk thistle plant (<em>Silybum marianum</em>) block hepatitis C virus (HCV) infection and inhibit T cell proliferation in vitro. An intravenous formulation of silibinin (SIL), a major component of silymarin, displays anti-HCV effects in humans and also inhibits T-cell proliferation in vitro. We show that SIL inhibited replication of HIV-1 in TZM-bl cells, PBMCs, and CEM cells in vitro. SIL suppression of HIV-1 coincided with dose-dependent reductions in actively proliferating CD19+, CD4+, and CD8+ cells, resulting in fewer CD4+ T cells expressing the HIV-1 co-receptors CXCR4 and CCR5. SIL inhibition of T-cell growth was not due to cytotoxicity measured by cell cycle arrest, apoptosis, or necrosis. SIL also blocked induction of the activation markers CD38, HLA-DR, Ki67, and CCR5 on CD4+ T cells. The data suggest that SIL attenuated cellular functions involved in T-cell activation, proliferation, and HIV-1 infection. Silymarin-derived compounds provide cytoprotection by suppressing virus infection, immune activation, and inflammation, and as such may be relevant for both HIV mono-infected and HIV/HCV co-infected subjects.</p> </div

SIL inhibits HIV-1 infection in primary cells and a T cell line.

<p><b>A</b>, SIL inhibits LAI and BAL infection of PBMCs derived from 5 different donors. PBMC were activated with PHA and 3 days later, cells were washed to remove PHA and resuspended in media containing IL-2. The cells were plated in 96 well plates in the presence or absence of 243 µM SIL. Cells were then infected with 3-fold serial dilutions of LAI and BAL virus stocks until the end point dilution was reached. Cultures were incubated 24 hours, input virus removed, and cultures were fed with media containing IL-2 and SIL. Supernatants were harvested 6 days later and assayed for p24 levels using HIV p24 Antigen Capture ELISA. <b>B</b>, Dose response of LAI inhibition by SIL. The five PBMC cultures were treated as described above and infected with LAI in the presence of the indicated concentrations of SIL. p24 ELISA was performed at 7 days post-infection. <b>C</b>, SIL inhibits HIV-1 infection of PBMCs and CEM cells. PBMCs were treated as described above. CEM cells were infected with LAI (MOI = 0.001) in the presence of the indicated amounts of SIL and p24 antigen was measured in culture supernatants at 4–7 days post-infection. The data represent pooled data from individual experiments of PBMCs infected with LAI (N = 10) or BAL (N = 6) and CEM infected with LAI (N = 8). <b>D</b>, SIL's anti-HIV effects are durable. PBMCs were activated and infected with LAI in the presence of 243 µM of SIL and p24 antigen was measured at the indicated times (days post-infection). Cells were fed every 3–4 days with medium containing fresh SIL. Virus control refers to cells that only received virus and no SIL.</p

SIL suppresses HIV-1 Infection of TZM-bl cells.

<p><b>A</b>, Cytotoxicity profile of SIL in TZM-bl cells. Cells were infected with LAI, a CXCR4-using virus, or BAL, a CCR5-using virus, at an MOI of 0.05 in the presence of the indicated concentrations of SIL and ATP was measured using the ATPlite kit 48 hours later. The data are representative of 2 (BAL) and 3 (LAI) independent technical repeats. <b>B</b>, Antiviral profile of SIL in TZM-bl cells. Serial dilutions of SIL were tested for inhibition of infection in TZM cells. Following addition of compounds and virus, cells were incubated for 48 hours before luciferase activity was measured. Percent inhibition refers to percent reduction in luciferase activity of SIL versus untreated cultures. Error bars represent standard deviation of 3 independent technical repeats. <b>C</b>, SIL inhibits pseudovirus replication in TZM-bl cells. TZM-bl cells were infected with the indicated viruses in the presence of the indicated concentrations of SIL and luciferase activity was measured 48 hours post-infection. The D013M12 psuedovirus contains a subtype D envelope sequence, while the D769 psuedovirus contains a subtype A envelope sequence. Error bars represent standard deviations of triplicate wells per condition.</p