Table 1.
Feature comparison of plus-strand RNA viruses.
DMV: double-membrane vesicles, ER: endoplasmic reticulum, NS: non-structural, S: structural.
Fig 1.
Schematic illustration of the plus-strand RNA life cycle.
① Virus (V) enters the cell via receptor-mediated endocytosis (ke). ② The viral genome (RP) is released (kf). Virus within the endosome (VE) degrades with rate constant μVE. ③ Ribosomes (Ribo) bind at the viral genome and form (k1) a translation initiation complex (TC) that degrades with rate constant μTC. ④ The viral genome (RP) is translated (k2) into a polyprotein (PP) that ⑤ is subsequently cleaved (kc) into structural and non-structural viral proteins, PS and PN, respectively. To measure translation activity, luciferase (L) is integrated into the viral genome and produced with RNA translation. Viral proteins degrade with rate constant μP; luciferase degrades with rate constant μL. ⑥ Non-structural proteins and freshly translated viral RNA form (kPin) replicase complexes (RC) that are associated with replication organelles (ROs) and ⑦ serve as a template for the minus-strand synthesis (k4m) leading to double-stranded RNA (RDS).⑧ Viral non-structural proteins, such as the RdRp, within the replication organelle () bind to double-stranded RNA, forming (k5) a minus-strand replication intermediate complex (RIDS) that ⑨ initiates the plus-strand RNA synthesis (k4p) giving rise to multiple copies of viral plus-strand RNA (
). All species within the replication organelle degrade with the same rate constant μRO. ⑩ The viral genome can remain within the replication organelle, where it undergoes multiple rounds of genome replication (k3), ⑪ it can be exported (kPout) out of the replication organelle into the cytoplasm starting with the translation cycle again, or ⑫ the plus-strand RNA genome (
) is packaged together with structural proteins (PS) into virions (VR) that are released from the cell (kp) and ⑬ may re-infect the same cell or infect naïve cells (kre). Extracellular infectious viral species (V and VR) degrade with rate constant μV.
Table 2.
Parameter values and 95% confidence intervals in ().
Note that parameter values marked with * were fixed due to previous assumptions and calculations. Furthermore, confidence intervals marked with + hit the set estimation boundary; ± calculated from the data; # experimentally measured for Zika virus; ǂ experimentally measured for poliovirus.
Fig 2.
Best fit of the model to the data with standard deviation (left panel) and model prediction of plus-strand RNA allocation between the cytoplasm and replication organelle (RO) (right panel). For parameter values, see Table 2. [LEFT: green: (+)RNA = , red: (-)RNA =
, blue: A) Virus = Vtot = VR, B) and C) Virus = Vtot = (V+VR), yellow: Luc = L; RIGHT: yellow: RNA in cytoplasm =
, purple: RNA within replication organelle (RO) =
; Infectious virus was measured in PFU/mL, (+) and (-)RNA were measured in molecules/mL or relative RNA concentration, luciferase was measured in relative light unit (RLU)].
Fig 3.
Uncertainty analysis of the best-fit model.
For parameter values and 95% confidence intervals, see Table 2. The best fit is shown in Fig 2.
Fig 4.
Infectious virus concentration with parameter adjustments.
A) HCV concentration with estimated parameters (solid), the number of ribosomes taken from CVB3 (dashed), and the RNA synthesis rate taken from CVB3 (dotted). B) CVB3 concentration with estimated parameters (solid), the number of ribosomes taken from HCV (dashed), and the RNA synthesis rate taken from HCV (dotted).
Fig 5.
Replicase complexes over time.
Dynamics of replicase complexes for A) hepatitis C and dengue virus, B) coxsackievirus B3. The dashed grey line represents the carrying capacity or the maximum number of formed replicase complexes.
Fig 6.
Global sensitivity profile for the model species plus-strand RNA throughout infection (CVB3 = 10 hours, HCV = DENV = 72 hours).
Fig 7.
Effects of drug interventions applied to two different time points: at infection beginning (left) and in steady state (right). A successful drug treatment leads to more than 99% viral eradication (light yellow), while an ineffective drug treatment leads to 100% remaining virus (black).
Fig 8.
Combined drug effect on A) vRNA synthesis and formation of translation complex (TC), B) vRNA synthesis and translation, and C) viral RNA synthesis and polyprotein cleavage. Initiation of treatment was in steady state (100 h pi). A successful drug treatment leads to more than 99% viral eradication (light yellow), while an ineffective drug treatment leads to 100% remaining virus (black).
Fig 9.
Relative virus decay under combination therapy that clears HCV, DENV, and CVB3 infections.
A combined drug effect on A) vRNA synthesis and formation of translation complex (TC), B) vRNA synthesis and translation, and C) viral RNA synthesis and polyprotein cleavage. Initiation of treatment was in steady state (100 h pi). The drug efficacy constant (εA and εB) were chosen as minimal efficacies to clear all three viruses. For comparability, virus-specific concentrations in steady state have been normalized to their virus-specific pre-treatment steady-state concentration. A successful drug treatment leads to more than 99% viral eradication (light yellow), while an ineffective drug treatment leads to 100% remaining virus (black).