Fig 1.
Schematic representation of multiscale HCV infection and mathematical model.
(A) Schematic representation of intracellular HCV life cycle and trade-off between viral replication and release of intracellular viral RNA. Viral RNA in cells is translated to produce S and NS proteins. Viral RNA is either amplified through the functions of NS proteins through replication or is assembled with S proteins and released as a progeny virus. If the balance between viral replication and release leans toward replication, intracellular viral RNAs will accumulate. In contrast, high rates of intracellular RNA release will create opportunities for transmission to new cells but will deplete viral RNA in the cell. (B) Modeling the intracellular virus life cycle. Intracellular viral RNA either replicates inside the cell at rate k, is degraded at rate μ, or assembles with viral proteins to be released within HCV virions at rate ρ. (C) Multiscale modeling of intracellular replication and intercellular infection. Target cells are infected by infectious viruses at rate β. HCV, hepatitis C virus; NS protein, nonstructural protein; S protein, structural protein.
Fig 2.
Dynamics of HCV JFH-1 and Jc1-n infection in cell culture.
Fitting of the mathematical model to the experimental data of HCV JFH-1 and Jc1-n infection in cell culture. Three different numbers of Huh-7 cells infected with either HCV JFH-1 or Jc1-n 1 day after inoculation were seeded (experiment A: 1,000, experiment B: 2,000, and experiment C: 4,000 cells per well) and chased to detect the following values at days 0, 1, 2, 3, and 4 post seeding (log10 scale): numbers of uninfected and infected cells, amount of intracellular and extracellular viral RNA (copies/well), and extracellular viral infectivity (ffu/well) (orange circle: JFH-1, green triangle: Jc1-n). The shadowed regions correspond to 95% posterior intervals and the solid curves give the best-fit solution (mean) for Eqs 2–6 to the time-course dataset. All data for each strain were fitted simultaneously. The underlying data for this figure can be found in S1 Data. ffu, focus formation unit.
Table 1.
Parameter values estimated from the cell culture infection experiment.
Fig 3.
Characterization of viral dynamics of HCV JFH-1 and Jc1-n.
The distributions of the rate constant for infection, βθ; the release rate of intracellular viral RNA, ρ; the converted fraction of infectious viral RNA, fθ; and the replication rate of intracellular viral RNA, k, inferred by MCMC computations are shown in (A), (B), (C) and (D), respectively, for HCV JFH-1 (orange) and Jc1-n (green). Parameters βθ and ρ for Jc1-n were significantly larger than for JFH-1, whereas there was no significant difference in fθ between the two strains as assessed by repeated bootstrap t test. JFH-1 and Jc1-n stains had identical viral RNA replication rates. The distributions of accumulation rates of intracellular viral RNA, k−μ−ρ, and the Malthusian parameter, M, calculated from all accepted MCMC parameter estimates are shown in (E) and (F), respectively, for HCV JFH-1 (orange) and Jc1-n (green). These indices were significantly larger for JFH-1 than for Jc1-n as assessed by the repeated bootstrap t test. The underlying data for this Figure can be found in S2 Data. HCV, hepatitis C virus; MCMC, Markov chain Monte Carlo.
Fig 4.
Different strategies adopted by JFH-1 and Jc1-n for viral proliferation.
(A) Schematic representation of the fate of replicated intracellular viral RNA. Viral RNA is used either for driving RNA replication in cells or for producing progeny viruses for release outside cells or is degraded. (B) Percentage of replicated intracellular HCV JFH-1 and Jc1-n viral RNA that remains inside cells, is released outside cells, and is degraded. (C) Change in the Malthusian parameter (Eq 7) with various release rates of intracellular viral RNA. The orange and green curves show Malthusian parameters calculated using 100 parameter sets sampled from MCMC parameter estimates as functions of ρ for JFH-1 and Jc1-n, respectively. The gray vertical lines are the corresponding release rates estimated from the actual experimental data. (D) Change in the cumulative number of newly infected cells with the various release rates (Eq 8). (Left panels) The orange and green curves represent the cumulative numbers of newly infected cells until 3, 5, 7, 9, and 11 days post infection calculated using the means of estimated parameters as a function of ρ for JFH-1 and Jc1-n, respectively. The gray vertical line represents the mean release rate estimated from the experimental data. (Right panels) Enlarged views of the gray zones in left panels. Finely calculated cumulative numbers of newly infected cells are shown. The underlying data for this figure can be found in S3 Data. HCV, hepatitis C virus; MCMC, Markov chain Monte Carlo.