Biology subjects

Dahari, H.

Publications and source records attributed to Dahari, H..

8 recordsLinked to original sources

bioRxiv2026

Modeling in vitro cell-to-cell spread of hepatitis C viral infection using an agent-based approach

Mechanisms that lead to viral chronicity are poorly understood, but cell-to-cell spread has been implicated in the establishment of chronic infections. We previously developed mathematical models to explore the nature of hepatitis C virus (HCV) cell-to-cell spread in vitro and quantified the effect of inhibiting individual host factors involved. However, the previous models were not designed to (i) address cell proliferation, (ii) account for differences in cell size, and (iii) did not include possible foci merging. Herein we have developed an agent-based model (ABM) to simulate HCV cell-to-cell spread in vitro by modeling individual cell behaviors. This model recapitulates the natural increase of cell confluence that occurs in vitro accompanied by a concomitant decrease in cell size by allowing for independent proliferation cycles of individual cells within a restricted space. The model fits the experimental foci expansion data well and allows assessment of foci merging while reproducing the irregular HCV foci shape observed in cell culture. Altogether, the new more inclusive model has the potential to help elucidate the dynamics of HCV cell-to-cell spread and provide accurate predictions regarding the efficacy of antiviral drugs. Author SummaryDespite remarkable progress in treatments for hepatitis C virus (HCV), HCV infection remains a global public health burden with over 50 million chronic HCV infections and about 1 million new infections occurring annually. Once infection occurs, HCV can spread in the liver multiple ways. One mechanism is cell-to-cell (CTC) spread where the virus moves directly from one infected cell to an adjacent cell without moving through the extracellular space. Previous mathematical models of HCV CTC spread were not designed to incorporate cell proliferation, cell size, or foci merging. Therefore, to better mimic cells in culture, we developed a novel agent-based model (ABM) that allows the simulated cells to proliferate resulting in an increased number of cells with concomitant decrease in cell/agent size analogous to what happens as cells become tightly packed in culture. This new ABM not only can be used to estimate efficacy values of HCV cell-to-cell spread inhibitors (e.g., when different factors involved in cell-to-cell spread are blocked), but also should enable modeling of HCV CTC spread under a wider variety of cell culture conditions and thus help elucidate the impact of different viral-host dynamics on HCV CTC spread.

microbiology↗

bioRxiv2026

Rat hepatitis E virus infection has multiphasic viral replication kinetics in vivo

Background and AimsHepatitis E virus (HEV) infections are a growing threat to global public health. To obtain an in-depth understanding of HEV infections in untreated and ribavirin-treated rats, we characterized the early HEV viral kinetics using rat HEV (rHEV) as a surrogate model and using two routes of virus inoculation: intravenous (I.V.) or oral infection. Approach and ResultsWe frequently collected feces, serum, and tissue samples up to 60 days after infection in both infection models to characterize the rHEV viral kinetics. A ~2-week delay in quantifiable RNA levels in feces was observed in the oral versus the I.V. infection model. Early rHEV viral kinetics in feces were found to be multiphasic and showed good concordance with those in the various tissue compartments studied. Comparison of the viral kinetics in these samples also revealed that the liver may serve as the initial site of rHEV replication, followed by replication in the intestine and spleen. While a dosage of 60 mg/kg/day ribavirin was found optimal to maintain rHEV RNA levels at (nearly) undetectable in feces, levels were detectable in the liver and increased both in feces and liver after treatment discontinuation. ConclusionsWe found that the two rHEV infection models share similar multiphasic viral kinetics with the liver as the main site of viral replication. Additionally, the rHEV RNA load in feces could be used as a reliable proxy for that in the liver, spleen, and intestine. We also show that ribavirin at 60 mg/kg/day was partially effective in preventing viral rebound. These findings may aid in exploring the correlation between the infection phases and antiviral efficacy, ultimately guiding therapeutic decisions.

microbiology↗

bioRxiv2025

Modeling of hepatitis B virus infection spread in primary human hepatocytes

Chronic hepatitis B virus (HBV) infection poses a significant global health threat, causing severe liver diseases including cirrhosis and hepatocellular carcinoma. We characterized HBV DNA kinetics in primary human hepatocytes (PHH) over 32 days post-inoculation (pi) and used agent-based modeling (ABM) to gain insights into HBV lifecycle and spread. Parallel PHH cultures were mock-treated or HBV entry inhibitor Myr-preS1 (6.25 g/mL) was initiated 24h pi. In untreated PHH, 3 viral DNA kinetic patterns were identified: (1) an initial decline, followed by (2) rapid amplification, and (3) slower amplification/accumulation. In the presence of Myr-preS1, viral DNA and infected cell numbers in phase 3 were effectively blocked, with minimal to no increase. This suggests that phase 2 represents viral amplification in initially infected cells, while phase 3 corresponds to viral spread to naive cells. The ABM reproduced well the HBV kinetic patterns observed and predicted that the viral eclipse phase lasts between 18 and 38 hours. After the eclipse phase, the viral production rate increases over time, starting with a slow production cycle of 1 virion per day, which gradually accelerates to 1 virion per hour after 3 days. Approximately 4 days later, virion production reaches a steady state production rate of 4 virions/hour. The estimated median efficacy of Myr-preS1 in blocking HBV spread was 91% (range: 90-92%). The HBV kinetics and the predicted estimates of the HBV eclipse phase duration and HBV production cycles in PHH are similar of those predicted in uPA/SCID mice with human livers. ImportanceWhile primary human hepatocytes (PHH) are the most physiologically relevant culture system for studying HBV infection in vitro, comprehensive understanding of HBV infection kinetics and spread in PHH is lacking. In this study, we characterize HBV viral kinetics and employ agent-based modeling (ABM) to provide quantitative insights into the HBV production cycle and viral spread in PHH. The ABM provides an estimate of HBV eclipse phase duration, HBV production cycles and Myr-preS1 efficacy in blocking HBV spread in PHH. The results resemble those predicted in uPA/SCID mice with human livers, demonstrating that estimated HBV infection kinetic parameters in PHH in vitro mirrors that observed in in vivo HBV infection chimeric mouse model.

systems biology↗

bioRxiv2023

Hepatitis delta virus RNA decline post inoculation in human NTCP transgenic mice is biphasic

Background and AimsChronic infection with hepatitis B and hepatitis delta viruses (HDV) is considered the most serious form of viral hepatitis due to more severe manifestations of and accelerated progression to liver fibrosis, cirrhosis, and hepatocellular carcinoma. There is no FDA-approved treatment for HDV and current interferon-alpha treatment is suboptimal. We characterized early HDV kinetics post inoculation and incorporated mathematical modeling to provide insights into host-HDV dynamics. MethodsWe analyzed HDV RNA serum viremia in 192 immunocompetent (C57BL/6) and immunodeficient (NRG) mice that did or did not transgenically express the HDV receptor - human sodium taurocholate co-transporting peptide (hNTCP). ResultsKinetic analysis indicates an unanticipated biphasic decline consisting of a sharp first-phase and slower second-phase decline regardless of immunocompetence. HDV decline after re-inoculation again followed a biphasic decline; however, a steeper second-phase HDV decline was observed in NRG-hNTCP mice compared to NRG mice. HDV-entry inhibitor bulevirtide administration and HDV re-inoculation indicated that viral entry and receptor saturation are not major contributors to clearance, respectively. The biphasic kinetics can be mathematically modeled by assuming the existence of a non-specific binding compartment with a constant on/off-rate and the steeper second-phase decline by a loss of bound virus that cannot be returned as free virus to circulation. The model predicts that free HDV is cleared with a half-life of 18 minutes (standard error, SE: 2.4), binds to non-specific cells with a rate of 0.06 hour-1 (SE: 0.03), and returns as free virus with a rate of 0.23 hour-1 (SE: 0.03). ConclusionsUnderstanding early HDV-host kinetics will inform pre-clinical therapeutic kinetic studies on how the efficacy of anti-HDV therapeutics can be affected by early kinetics of viral decline. LAY SUMMARYThe persistence phase of HDV infection has been studied in some animal models, however, the early kinetics of HDV in vivo is incompletely understood. In this study, we characterize an unexpectedly HDV biphasic decline post inoculation in immunocompetent and immunodeficient mouse models and use mathematical modeling to provide insights into HDV-host dynamics. Understanding the kinetics of viral clearance in the blood can aid pre-clinical development and testing models for anti-HDV therapeutics.

microbiology↗

bioRxiv2022

Multiphasic hepatitis B virus kinetic patterns in humanized chimeric mice can be explained via stochastic agent-based modeling of intracellular virion production cycles

Serum hepatitis B virus (HBV) kinetics in urokinase-type plasminogen activator/severe combined immunodeficient (uPA-SCID) mice reconstituted with humanized livers from inoculation to steady state is highly dynamic despite the absence of an adaptive immune response. We developed a stochastic agent-based model that includes virion production cycles in individual infected human hepatocytes. The model was calibrated using a genetic algorithm approach with the serum HBV kinetics observed in mice inoculated with 108 HBV genome equivalents and fit the data well when the following viral production parameters were assumed: (1) An eclipse phase lasting 5-50 hours and (2) a post-eclipse phase production rate that is based on increasing production cycles initially starting with a long production cycle of 1 virion per 20 hours that gradually reaches 1 virion per hour after approximately 3-4 days before virion production increases dramatically to reach to a steady state production rate of 4 virions per hour per cell. The model was then validated by showing it could accurately simulate the viral kinetics observed with lower HBV inoculation doses (104-107 genome equivalents) in which similar, but delayed patterns were observed. Together, modeling suggests that it is the cyclic nature of the virus lifecycle combined with an initial slow but increasing rate of HBV production from each cell that plays a role in generating the observed multiphasic HBV kinetic patterns in humanized mice.

systems biology↗

bioRxiv2021

HCV spread kinetics reveal varying contributions of transmission modes to infection dynamics

Hepatitis C virus (HCV) is capable of spreading within a host by two different transmission modes: cell-free and cell-to-cell. Although viral dissemination and diffusion of viral particles facilitates the infection of distant cells, direct cell-to-cell transmission to uninfected neighboring cells is thought to shield the virus from immune recognition. However, the contribution of each of these transmission mechanisms to HCV spread is unknown. To dissect the contribution of these different transmission modes to HCV spread, we measured HCV lifecycle kinetics and used an in vitro spread assay to monitor HCV spread kinetics after low multiplicity of infection in the absence and presence of a neutralizing antibody that blocks cell-free spread. By analyzing these data with a spatially-explicit mathematical model that describes viral spread on a single-cell level, we quantified the contribution of cell-free and cell-to-cell spread to the overall infection dynamics and show that both transmission modes act synergistically to enhance the spread of infection. Thus, the simultaneous occurrence of both transmission modes likely represents an advantage for HCV that may contribute to the efficient establishment of chronic infection. Notably, the relative contribution of each viral transmission mode appeared to vary dependent on different experimental conditions and suggests that viral spread is optimized according to the environment. Together, our analyses provide insight into the transmission dynamics of HCV and reveal how different transmission modes impact each other. ImportanceHepatitis C Virus can spread within a host by diffusing viral particles or direct cell-to-cell transfer of viral material between infected and uninfected cells. To which extend these cell-free and cell-to-cell transmission modes contribute to HCV spread, establishment of chronicity and antiviral escape is still unknown. By combining in vitro experimental HCV spread data with a multi-scale mathematical model we have disentangled the contribution and interplay of cell-free and cell-to-cell transmission modes during HCV infection. Our analysis revealed synergistic effects between the two transmission modes, with the relative contribution of each transmission mode varying dependent on the experimental conditions. This highlights the adaptability of the virus and suggests that transmission modes might be optimized dependent on the environment, which could contribute to viral persistence.

microbiology↗

bioRxiv2020

Understanding hepatitis B virus dynamics and the antiviral effect of interferon-alpha treatment in humanized chimeric mice

BackgroundWhereas the mode of action of lamivudine (LAM) against hepatitis B virus (HBV) is well established, the inhibition mechanism(s) of interferon- are less completely defined. To advance our understanding, we mathematically modelled HBV kinetics during pegylated interferon--2a (pegIFN), LAM and pegIFN+LAM treatment of chronically HBV-infected humanized uPA/SCID chimeric mice. MethodsThirty-nine uPA/SCID mice with humanized livers whose pre-treatment steady-state serum HBV reached 9.2{+/-}0.4 logIU/mL were treated with pegIFN, LAM or pegIFN+LAM for 14 days. Serum HBV DNA and intracellular HBV DNA were measured frequently. We developed a nonlinear mixed effect viral kinetic model and simultaneously fit it to the serum and intracellular HBV DNA data. ResultsUnexpectedly, even in the absence of an adaptive-immune response, a biphasic decline in serum HBV DNA and intracellular HBV DNA was observed in response to all treatments. Modeling predicts that the first phase represents pegIFN inhibiting intracellular HBV DNA synthesis with efficacy of 86%, which was similar under LAM and pegIFN+LAM. In contrast, there were distinct differences in HBV decline during the 2nd phase which was accounted for in the model by a time-dependent inhibition of intracellular HBV DNA synthesis with the steepest decline observed during pegIFN+LAM (0.46/d) and the slowest (0.052/d) during pegIFN mono-treatment. ConclusionsReminiscent of observations in patients treated with pegIFN and/or LAM, a biphasic HBV decline was observed in treated humanized mice in the absence of adaptive immune response. Interestingly, combination treatment does not increase the initial inhibition of HBV production; however, enhancement of second phase decline is observed providing insight into the dynamics of HBV treatment response and the mode of action of interferon- against HBV. Author SummaryChronic hepatitis B virus (HBV) infection remains a global health care problem as we lack sufficient curative treatment options. Elucidating the dynamic of HBV infection and treatment at the molecular level would potentially facilitate the development of novel, more effective HBV antivirals. Currently, the only well-established small animal HBV infection model available is the chimeric uPA/SCID mice with humanized livers; however, the HBV infection kinetics under interferon- (IFN) in this model system have not been determined in sufficient detail to support the in-depth studies of HBV treatment response needed to identify/confirm more effective drug targets. In this study 39 chronic HBV-infected uPA/SCID humanized mice treated with IFN and/or lamivudine were analysed using a mathematical modelling approach. We found that IFN main mode of action is blocking HBV DNA synthesis and that 73% of synthesized HBV DNA per are secreted from infected cells. Our data-driven mathematical modeling study provides novel insights into IFN anti-HBV mechanism(s) and viral-host interplay at the molecular level.

systems biology↗

bioRxiv2020

Understanding the antiviral effects of RNAi-based therapy on chronic hepatitis B infection

Reaching hepatitis B surface antigen (HBsAg) loss (called functional cure) with approved treatment with pegylated interferon- (IFN) and/or nucleos(t)ide analogues (NAs) in chronic hepatitis B virus (HBV) infected patients is suboptimal. The RNA interference (RNAi) drug ARC-520 was shown to be effective in reducing serum HBV DNA, HBsAg and hepatitis B e antigen (HBeAg) in chimpanzees and small animals. A recent clinical study (Heparc-2001) showed reduction of serum HBV DNA, HBeAg and HBsAg in HBeAg-positive patients treated with a single dose of ARC-520 and daily NA (entecavir). To provide insights into HBV dynamics under ARC-520 treatment and its efficacy in blocking HBV DNA, HBsAg, and HBeAg production we developed a a multi-compartmental pharmacokinetic-pharamacodynamic model and calibrated it with measured HBV data. We showed that the time-dependent ARC-520 efficacies in blocking HBsAg and HBeAg are more than 96% effective around day 1, and slowly wane to 50% in 1-4 months. The combined ARC-520 and entecavir effect on HBV DNA is constant over time, with efficacy of more than 99.8%. HBV DNA loss is entecavir mediated and the strong but transient HBsAg and HBeAg decays are solely ARC-520 mediated. We added complexity to the model in order to reproduce current long-term therapy outcomes with NAs by considering the tradeoff between hepatocyte loss and hepatocyte division, and used it to make in-silico long-term predictions for virus, HBsAg and HBeAg titer dynamics. These results may help assess ongoing RNAi drug development for hepatitis B virus infection. Author summaryWith about 300 million persons infected worldwide and 800,000 deaths annually, chronic infection with hepatitis B virus (HBV) is a major public health burden with high endemic areas around the world. Current treatment options focus on removing circulating HBV DNA but are suboptimal in removing hepatitis B s- and e-antigens. ARC-520, a RNA interference drug, had induced substantial hepatitis B s- and e- antigen reductions in animals and patients receiving therapy. We study the effect of ARC-520 on hepatitis B s- and e-antigen decline by developing mathematical models for the dynamics of intracellular and serum viral replication, and compare it to patient HBV DNA, hepatitis B s- and e-antigen data from a clinical trial with one ARC-520 injection and daily nucleoside analogue therapy. We examine biological parameters describing the different phases of HBV DNA, s-antigen and e-antigen decline and rebound after treatment initiation, and estimate treatment effectiveness. Such approach can inform the RNA interference drug therapy.

immunology↗