Mechanistic dynamics of Hepatitis C virus replication in single liver cells

Infection with hepatitis C virus (HCV) causes chronic liver diseases. Strong biological evidence suggests intracellular spatial dependence is a crucial factor in the process the virus uses to replicate its RNA genome. For HCV, replication is believed to occur in specialized compartments within virus-infected cells, termed replication complexes. Replication complexes are derived from altered regions of an interconnected intracellular membrane network called the Endoplasmic Reticulum (ER).

The HCV-encoded NS5A protein is an essential component of HCV replication and probably contributes many functions that the virus is dependent upon to replicate its RNA and assemble its progeny. Research has revealed a substantial spatial facet of NS5A function and particular biophysical characteristics of the protein arise from its anchoring to the 3D embedded curved 2D ER manifold. To facilitate discovery of novel anti-HCV treatments, it is necessary to understand the dynamics of virus replication within human liver cells. Computational virology is a relatively new field and aims to describe the physics underpinning virus replication using mathematical formulae. An approach such as this may reveal areas of the virus life cycle amenable to novel antiviral intervention that conventional biology may miss e.g. spatial dependence of virus-encoded factors within specific intracellular regions. Exploring the biophysics of viral replication mechanism through cross-discipline work, i.e., application of physics-based solutions to understand biology-based data is a highly interesting aim. We used data derived from 3D confocal microscopy of HCV-infected human hepatoma cells labeled for the ER membrane in order to reconstruct 3D geometries of single hepatocytes using NeuRA2. On top of these geometries, we developed a model using (surface) partial differential equations (sPDE) of viral RNA replication dynamics with particular emphasis upon RNA movement, viral protein production, cleavage and movement, and viral RNA replication within the membranous web. In particular, we present the estimation of the biophysical meaningful NS5A diffusion constant based on the comparison of experimental FRAP time series data and simulation data. Advanced simulations within biophysical applications ask for advanced algorithms and implementations which are running efficiently on massively parallel high performance computers. The arising sPDEs on the ER surface are solved using the simulation platform UG4 within a Finite Volume framework combined with multigrid techniques. The application of modern scientific computing technology to our advanced biophysical concepts for solving challenging real-life problems paves new ways for computational virology.

Corresponding author: Knodel, Markus M.

E-Mail: [e-mail]