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Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release

Carolin Zitzmann,Lars Kaderali,Alan S. Perelson

Abstract

Hepatitis C virus (HCV) causes acute hepatitis C and can lead to life-threatening complications if it becomes chronic. The HCV genome is a single plus strand of RNA. Its intracellular replication is a spatiotemporally coordinated process of RNA translation upon cell infection, RNA synthesis within a replication compartment, and virus particle production. While HCV is mainly transmitted via mature infectious virus particles, it has also been suggested that HCV-infected cells can secrete HCV RNA carrying exosomes that can infect cells in a receptor independent manner. In order to gain insight into these two routes of transmission, we developed a series of intracellular HCV replication models that include HCV RNA secretion and/or virus assembly and release. Fitting our models to in vitro data, in which cells were infected with HCV, suggests that initially most secreted HCV RNA derives from intracellular cytosolic plus-strand RNA, but subsequently secreted HCV RNA derives equally from the cytoplasm and the replication compartments. Furthermore, our model fits to the data suggest that the rate of virus assembly and release is limited by host cell resources. Including the effects of direct acting antivirals in our models, we found that in spite of decreasing intracellular HCV RNA and extracellular virus concentration, low level HCV RNA secretion may continue as long as intracellular RNA is available. This may possibly explain the presence of detectable levels of plasma HCV RNA at the end of treatment even in patients that ultimately attain a sustained virologic response.

Introduction

Hepatitis C virus (HCV) causes an acute infection that is cleared in some individuals, but which if it becomes chronic can cause liver cirrhosis and hepatocellular carcinoma. Approximately 70 million people worldwide live with chronic hepatitis C, with 400,000 related deaths annually. Hepatitis C can be cured with combinations of direct acting antivirals that inhibit viral replication and which can achieve cure rates above 95%. HCV is a Hepacivirus belonging to the family Flaviviridae and has a single plus-strand RNA genome. A common feature of all plus-strand RNA viruses including HCV is their ability to rearrange intracellular host membranes to generate so-called replication compartments (RCs) or “replication factories”. In HCV, these RCs derived from the rough endoplasmic reticulum represent a distinct environment for efficient viral genome replication and antiviral immune response protection.

Methods

Intracellular HCV replication and HCV RNA secretion models (SM models)

The intracellular HCV replication model of [30] contains four different HCV RNA species: plus-strand HCV RNA used for translation (T), plus-strand HCV RNA in the RC (R) used for replication, minus-strand HCV RNA (C) in the RC, which may be in the form of replication complexes, used for replication, and secreted HCV RNA (S) (Fig 1A). Here the secretion of intracellular RNA can be due to the RNA being in either exosomes or viral particles or both. We will simply refer to this as secretion of RNA containing particles. The plus-strand RNA in the cytoplasm that can be used for translation, T, may be transferred into the RC at rate σ. This plus-strand RNA in the RC, R, can now be used for the synthesis of minus-strand RNA containing replication complexes, C, which in turn can produce more plus-strand RNA, R, at rate α. As in prior models [30,31], due to limited availability of host factors, the minus-strand RNA synthesis follows a logistic growth law, with maximum rate r, which slows as the number of negative strands approaches the RCs carrying capacity Cmax. Newly synthesized plus-strand RNA, R, is transferred back to the site of vRNA translation at rate θ in order to produce more viral proteins. The HCV RNA species located at the site of translation degrade with rate μT. As in Quintela et al. [30], we assume that the HCV RNA species within the RC (R and C) degrade with the same rate μR.

Discussion

Modeling HCV dynamics has a rich history and has been used for studying viral pathogenesis and spread, as well as the effects of antiviral treatment [20,44,46–50]. Some models have included intracellular events that occur during HCV replication and viral spread [20,30,31,51–53], but there is still a lack of detailed knowledge about these processes. The secretion of HCV RNA in the form of exosomes is currently not well understood, but experimental studies have shown that HCV RNA carrying exosomes derived from infected cells are able to infect naïve cells as well as stimulate type I interferon responses from plasmacytoid dendritic cells. Quintela et al. introduced a mathematical model of intracellular HCV RNA replication that takes HCV RNA secretion into account. However, all plus-strand RNA species within their model can potentially be secreted and the model did not distinguish between secretion in exosomes from that in viral particles. In the present study, we distinguish these two routes of secretion.

Citation: Zitzmann C, Kaderali L, Perelson AS (2020) Mathematical modeling of hepatitis C RNA replication, exosome secretion and virus release. PLoS Comput Biol 16(11): e1008421. https://doi.org/10.1371/journal.pcbi.1008421.

Editor: Kathryn Miller-Jensen, Yale University, UNITED STATES

Received: June 23, 2020; Accepted: October 6, 2020; Published: November 5, 2020

Data Availability:

All relevant data are within the manuscript and its Supporting Information files.

Funding:

Portions of this work were done under the auspices of the U.S. Department of Energy under contract 89233218CNA000001 and was supported by NIH grants R01-OD011095 (ASP), R01-AI028433 (ASP) and R01-AI 078881 (ASP). Parts of this work were supported by the BMBF through the ERASysAPP project SysVirDrug 031A602A (LK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests:

The authors have declared that no competing interests exist.

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