Characteristics of HCV-HIV Coinfected Liver Transplant Recipients.

<p>^a Most recent pre-transplant value, within 16 weeks of transplant.</p><p>LT—liver transplantation;</p><p>Characteristics of HCV-HIV Coinfected Liver Transplant Recipients.</p

Univariate and Multivariate Proportional Hazards Regression Models for Treated Acute Rejection.

<p>Abbreviation: HR, Hazard Ratio</p><p>^a Baseline predictor (log-scale)</p><p>^b Incorporated known predictors of treated acute rejection and biomarkers found in the univariate analysis.</p><p>^c Post-transplant (time-varying covariate)</p><p>Univariate and Multivariate Proportional Hazards Regression Models for Treated Acute Rejection.</p

sCD14 pre-LT and Graft Loss.

<p>Proportional hazards regression models for graft loss were developed. Univariate analyses were performed with each biomarker singly (upper panel); multivariate models were developed that incorporated known predictors of graft loss and biomarkers found in the univariate analysis.</p

HIV RNA Levels Pre-LT and Immune Activation.

<p>Full immunologic profile was performed using the MSD platform, while IP-10 levels were measured by ELISA. Persons with detectable HIV RNA pre-LT had higher levels of IL-2 (p = 0.01), IL-5 (p = 0.02), IL-10 (p = 0.01), and IP-10 (p = 0.01), by Wilcoxon rank-sum test.</p

Univariate and Multivariate Proportional Hazards Regression Models for Graft Loss.

<p>Abbreviation: HR, Hazard Ratio</p><p>^a Baseline predictor (log-scale)</p><p>^b Incorporated known predictors of graft loss and biomarkers found in the univariate analysis.</p><p>Univariate and Multivariate Proportional Hazards Regression Models for Graft Loss.</p

sCD14 Levels Pre-LT.

<p>sCD14 levels were measured by ELISA in 69 HIV-HCV co-infected persons pre-LT; graft loss post-LT occurred in 35/69 (51%) persons. In a univariate Cox regression model, higher sCD14 levels pre-LT were marginally associated with lower risk of graft loss post-LT (p = 0.08).</p

Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes

<div><p>Chronic liver infection by hepatitis C virus (HCV) is a major public health concern. Despite partly successful treatment options, several aspects of intrahepatic HCV infection dynamics are still poorly understood, including the preferred mode of viral propagation, as well as the proportion of infected hepatocytes. Answers to these questions have important implications for the development of therapeutic interventions. In this study, we present methods to analyze the spatial distribution of infected hepatocytes obtained by single cell laser capture microdissection from liver biopsy samples of patients chronically infected with HCV. By characterizing the internal structure of clusters of infected cells, we are able to evaluate hypotheses about intrahepatic infection dynamics. We found that individual clusters on biopsy samples range in size from infected cells. In addition, the HCV RNA content in a cluster declines from the cell that presumably founded the cluster to cells at the maximal cluster extension. These observations support the idea that HCV infection in the liver is seeded randomly (e.g. from the blood) and then spreads locally. Assuming that the amount of intracellular HCV RNA is a proxy for how long a cell has been infected, we estimate based on models of intracellular HCV RNA replication and accumulation that cells in clusters have been infected on average for less than a week. Further, we do not find a relationship between the cluster size and the estimated cluster expansion time. Our method represents a novel approach to make inferences about infection dynamics in solid tissues from static spatial data.</p></div

Cluster structure and age of infection.

<p>(<b>A</b>) Factors influencing the observed viral landscape in a cluster including (i) viral transmission, (ii) the viral eclipse phase, and (iii) intracellular viral replication. (<b>B, C</b>) Relationship between the maximal cluster extension and the age of the assumed founder cell of the cluster (<b>B</b>) and the time until this cluster extension was possibly reached, (<b>C</b>), i.e., the difference between the age of the assumed founder cell and cells that were more recently added to the cluster. Estimates were obtained using the model on intracellular HCV replication discussed in the text. The mean and the 2.5% and 97.5% percentiles of 10,000 bootstrap replicates for each individual cluster are shown. (<b>D</b>) Comparison of the average fractional decrease in intracellular HCV RNA, , between the founder cell and the surrounding cells of a cluster comprising 9 cells. Expansion of individual foci was simulated in a 2D-grid with different assumptions for the average duration of the eclipse phase , and the probability for viral transmission, . We simulated 1000 individual foci and selected all foci showing clusters comprising 9 cells with radial spread. The average fractional decrease is calculated relative to the amount of viral RNA within the founder cell of the cluster. The mean and 95%-percentiles are shown. For a detailed description of the simulation environment see <i>Supporting Information</i> (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003934#pcbi.1003934.s007" target="_blank">Text S3</a>).</p

Decline of viroscape profile.

<p>Decline of viroscape profile.</p

Subject characteristics.

<p>Subject characteristics.</p