Table 1 Estimates for the parameters of the mathematical ODE-model describing HIV-1 infection kinetics within the different environments
Parameter | Description | Unit | Suspension | 3D Collagen | |
|---|---|---|---|---|---|
Loose | Dense | ||||
λ CD8 | Proliferation of CD8 cells after adaptation phase | day−1 | 1.13 [0.74, 1.74] | 0.58 [0.24, 1.01] | 0.29 [0.12, 0.56] |
λ CD4 | Proliferation of CD4 cells after adaptation phase | day−1 | 0.60 [0.36, 1.02] | 0.78 [0.36, 1.29] | 0.59 [0.32, 0.89] |
T C | Max. capacity for CD3 T cells | ×105 cells well−1 | 3.11 [2.72, 3.56] | 3.53 [2.80, 4.52] | 4.28 [3.15, 6.37] |
δ CD8 | Net-death rate of CD8 cells during adaptation phase | day−1 | 0.07 [0, 0.19] | 0.11 [0, 0.23] | 0.08 [0, 0.19] |
δ CD4 | Net-death rate of CD4 cells during adaptation phase | day−1 | 0.03 [0, 0.11] | 0.23 [0.05, 0.39] | 0.25 [0.09, 0.38] |
I 0 | Initial fraction of non-productively infected cells in T20x2 experiment | 1 | 0.17 [0.10, 0.23] | ||
ρ | Viral production rate | ×104 RT (cell × day)−1 | 1.02 [0.80, 1.38] | 0.48 [0.37, 0.66] | 0.43 [0.32, 0.61] |
δ I | Death rate of infected cells | day−1 | 0.42 [0.40, 0.44] | 0.48 [0.46, 0.50] | 0.52 [0.51, 0.56] |
κ V | Viral diffusion rate from culture to supernatant | day−1 | 0.72 [0.55, 0.95] | 0.13 [0.10, 0.17] | 0.15 [0.11, 0.19] |
I 0 | Initial fraction of non-productively infected cells in WT experiment | ×10−2 | 3.3 [1.7, 4.8] | ||
V 0 | Initial fraction of infectious virus in WT experiment | 1 | 4.4 × 10−8 [0, fi = 10−3] | ||
T ref,0 | Initial fraction of refractory cells in WT experiment | 1 | 0.10 [0.0074, 0.12] | ||
β f | Cell-free infection rate | ×10−5 (RT × day)−1 | 2.3 [0, 3.0] | ||
β c | Cell-to-cell infection rate | ×10−5 (cell × day)−1 | 1 × 10−6 [0, 7.0] | 4.3 [3.6, 5.4] | 1.7 [1.4, 2.6] |
λ r | Proliferation rate of refractory cells | day−1 | 0.22 [0.16, 0.29] | 0.78 [0.77, λCD4 = 0.78] | 0.49 [0.45, 0.52] |
