Current drugs are effective in suppressing the virus but do not lead to cure. Achieving HBV cure is early stages for hepatitis B since current treatment options focus on removing circulating HBV DNA but are not effective in removing the HBV surface- and e- antigens that allow patients’ immune response to fight the virus.

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Why does this matter? What are their functions?

Recent clinical studies showed promising results in the use of an RNA interference-based (RNAi) treatment to address this short coming of the existing treatment. By mathematically modeling available HBV kinetic data under RNAi treatment, we were able to provide insights into HBV-host dynamics and estimate RNAi efficacy in reducing circulating virus, s and e antigens (Scientific Reports). Further research in this area could aid in the development of 2nd generation RNAi-based therapies.

Two significant pieces of collaborative research with Prof. Chayama at Hiroshima University revealed and further explored the multiphasic nature of HBV. The first piece of research (Hepatology) uncovered and characterized the surprising multiphasic nature of HBV infection. This finding is especially significant because it demonstrated that the virus progresses through distinct kinetic phases even in the absence of an adaptive immune response.

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Building upon these empirical findings, a subsequent study published in PLOS Computational Biology (2023) introduced a theoretical perspective to explain the mechanisms underlying this phenomenon. It employed an agent-based model (ABM) to reproduce the complex, multiphasic HBV infection kinetics observed in humanized uPA-SCID mice. This modeling approach introduces a key conceptual advance: it simulates the cyclic nature of the HBV lifecycle, accounting for asynchronous infection among hepatocytes and the gradual amplification of virion release. The model successfully fits experimental data by predicting an initial slow production rate, approximately one virion per 20 hours, that accelerates over several days to a steady-state rate of four virions per hour per cell.

These findings suggest that the intracellular production cycles, rather than immune pressure, are central to generating the observed multiphasic patterns. By explicitly modeling viral replication as a series of discrete production cycles, this work provides a powerful theoretical framework for understanding early HBV infection dynamics in the absence of adaptive immunity.  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.

Tracking virus kinetics via the blood/serum is very common and data is abundant from patients, whereas the dynamics of the virus at the cellular level (in the liver) is still in the early stages of data collection. Collaboration with Prof. Chayama of Hiroshima University resulted in a deeper understanding of the mode of action of interferon-α-based treatments. However, this research is important beyond showing differences in the efficacy of these treatments (Journal of Virology). The ability to compare the results simultaneously of the viral kinetics in the blood as well as “inside” the liver at the cellular level is an important contribution to the study of HBV. The richer data gathered through chimeric mice with humanized livers results in a more accurate model. This liver-based cellular data is necessary to build a strong foundational knowledge for more advanced research

In two letters published in Hepatology and Journal of Viral Hepatitis, Dahari Lab and partners underscored some interesting data in the search for better treatments and ultimately a cure for HBV. Specifically, the Lab identified two areas of interest. One is HBV pgRNA as additional new marker in the blood when trying to understand the status of HBV infection in patients (Hepatology). Current markers such as HBV DNA in the blood stream, have proven to be limited in their indication of covalently closed circular DNA (cccDNA) clearance for HBV. The research on HBV RNA kinetics suggests this marker may be more reliable in understanding the viral levels present.

The second is nucleos(t)ide analogue (NA) therapy (Journal of Viral Hepatitis). Using mathematical modeling it is possible to gain a clearer understanding of the NA mode of actions, especially as it relates to the interplay with pgRNA kinetics. Further study of HBV pgRNA kinetics during NA treatment in patients could yield significant data that informs more effective therapies for clearing the virus.

A third research study (Antiviral Research) with a broader scope, characterizes pgRNA as well as a broader set of variables and markers during 24-week monotherapy with tenofovir disoproxil fumarate (TDF). The HBV life cycle is complicated and the marker pgRNA as well as the other HBV markers included in this study, may give us a greater insight into how to potentially interrupt this cycle and develop better therapies. Our research in this area is ongoing as we collect richer data sets to build more detailed mathematical models on the molecular level to examine the HBV-host dynamics during NA monotherapy.

Data on HBV kinetics at the molecular level remain limited, yet such insights are crucial for advancing foundational science in HBV treatment. Few mathematical models currently capture the extracellular and intracellular dynamics of HBV in primary human hepatocytes (PHHs) during early infection and therapy. To address this gap, this study (JHEP Reports) developed a tri-compartment model that elucidates the relationships among cccDNA accumulation in the nucleus, intracellular HBV DNA synthesis in the cytoplasm, and extracellular viral kinetics. PHH-based modeling, integrating human cell data with computational analysis, provides an efficient and cost-effective alternative to patient- or chimeric-mouse-based studies.

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The model confirmed that Entecavir (ETV) – a clinically approved oral antiviral – effectively blocks HBV DNA replication and slows the nuclear accumulation of cccDNA, a stable ring-shaped viral DNA form. Simulations further predicted that HBV recycling to the nucleus halts once cccDNA reaches its maximal threshold and that viral secretion is dynamically regulated by intracellular HBV concentration. Even when administered at inoculation, ETV did not fully prevent infection but reduced intracellular HBV DNA by 97% over 12 days and delayed cccDNA buildup by 44%. Overall, these findings show that while ETV markedly suppresses viral replication and cccDNA formation, additional mechanisms maintain cccDNA homeostasis, offering new insights into early HBV infection and potential therapeutic strategies.

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 Not much is known about HBsAg clearance and production (turnover). The partnership with Replicor allowed us, through mathematical modeling, to better estimate/understand this phenomenon (Scientific Reports 2020). Current approved treatments for HBV mainly suppress the virus, while the Replicor treatment uses NAPs to directly suppress HBsAg production. For the first time, this suppression made it possible to study HBsAg turnover during antiviral treatment and to report a median serum HBsAg half-life (t1/2) that was estimated as 1.3 [0.9–1.8] days corresponding to a pretreatment production and clearance of ~10^8 [10^7.7 - 10^8.3 ].

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The current research suggests that this treatment results in rapid viral and HBsAg clearance as well as the appearance of anti-HBs (immune response) restoring and supporting the patient’s own immune response. Further modeling efforts to refine the understanding of the modes of action of NAPs against HBV is ongoing.

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Data and insights on HBV kinetics at the molecular (cellular) level are still in the early stages but are essential to building strong foundational science in the treatment of HBV. There are very limited data-driven mathematical models for understanding extracellular and intracellular HBV kinetics in cell cultures (PHHs) during early infection and treatment. This research (JHEP Reports 2025)  developed and utilized a tri-compartment mathematical model to better understand HBV dynamics during infection and treatment in PHHs. The model provides novel insights into the interrelationships and dynamics of three variables: cccDNA accumulation in the nucleus, intracellular HBV DNA production in the cytoplasm, and extracellular HBV DNA kinetics. PHH-based research—combining human hepatocytes with modeling data—serves as an effective and accessible complement to in vivo patient and chimeric mouse studies.

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Using this PHH-based modeling framework, the study captured multiphasic HBV kinetics and characterized early viral dynamics under different treatment conditions. Frequent measurements of extracellular (exHBV), intracellular (inHBV), and nuclear cccDNA levels over 12 days post-inoculation revealed that while untreated and Myr-preS1-treated cultures exhibited similar multiphasic exHBV and inHBV kinetics, entecavir (ETV) treatment markedly reduced and delayed cccDNA accumulation, reaching a plateau approximately five days later than untreated controls. Mathematical modeling further predicted that intracellular HBV recycling to the nucleus ceases once cccDNA reaches a maximum threshold and that HBV secretion is dynamically regulated by intracellular HBV concentration. Even when administered at inoculation, ETV did not completely prevent infection but gradually inhibited intracellular HBV DNA accumulation by 97% over 12 days, resulting in a 44% slower cccDNA buildup. Collectively, these findings demonstrate that while replication inhibitors substantially suppress viral replication and delay cccDNA formation, additional regulatory mechanisms govern cccDNA homeostasis, providing new insight into early HBV infection dynamics and antiviral response.

Understanding how the adaptive immune response influences hepatitis B virus (HBV) infection is essential for advancing therapeutic development. This study (Bulletin of Mathematical Biology 2024) combines experimental and mathematical modeling approaches to characterize HBV dynamics in mice engrafted with human hepatocytes (HEP) alone or with both human hepatocytes and components of a human immune system (HEP/HIS).

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We developed several within-host HBV models that differed in how they included adaptive immune responses such as cytolytic killing and non-cytolytic mechanisms of cure and viral suppression. Each model was tested against experimental data measuring serum HBV DNA and HBsAg levels. The model without immune activity reproduced the high viral loads seen in HEP mice, while those including immune responses matched the reduced viral levels observed in HEP/HIS mice.

Results showed that non-cytolytic mechanisms—either by suppressing viral production or making infected cells resistant to reinfection—best explained viral control. In contrast, cytolytic killing predicted excessive hepatocyte loss that was not supported by the data.

Overall, these findings indicate that non-cytolytic immune processes play a major role in controlling HBV during early infection in HEP/HIS mice and demonstrate how combining experimental data with modeling can clarify HBV–host interaction