Table 1 Parameter values and derived quantities for the in vitro experiment
Parameter name | Symbol | Unit | SHIV-KS661 | SHIV-#64 | ||
|---|---|---|---|---|---|---|
Value | 95% CI | Value | 95% CI | |||
Calculated parameters for the continuous approximation of cell and virus harvest | ||||||
Harvest rate of target and infected cells | μ | day-1 | 0.057 | ― | 0.057 | ― |
Harvest rate of total and infectious virus | c | day-1 | 1.93 | ― | 1.93 | ― |
Fitted parameters from separate experiments | ||||||
Rate of virion infectivity loss | c 50 | day-1 | 0.869 | 0.598–1.141 | 0.992 | 0.866–1.117 |
Degradation rate of virion RNA | c RNA | day−1 | 0.091 | 0.029–0.152 | 0.160 | 0.051–0.269 |
Parameters obtained from simultaneous fit to full in vitro dataset | ||||||
Rate constant for infections | β 50 | (TCID50/ml・day)−1 | 1.49 × 105 | 7.97 × 10−6–2.46 × 105 | 1.47 × 104 | 8.86 × 10−5–2.36 × 104 |
Death rate of target cells | d | day−1 | 6.95 × 10−3 | 3.89 × 104–5.15 × 102 | 2.47 × 10−3 | 1.09 × 103–5.75 × 103 |
Death rate of infected cells | δ | day−1 | 1.48 | 1.20–1.81 | 1.56 | 1.23–1.96 |
Production rate of total virus | p RNA | RNA copies・day−1 | 3.74 × 104 | 1.94 × 104–6.35 × 104 | 4.15 × 104 | 2.67 × 104–6.07 × 104 |
Production rate of infectious virus | p 50 | TCID50・day−1 | 0.322 | 0.164–0.593 | 0.028 | 0.0156–0.0426 |
Quantities derived from fitted values | ||||||
Viral burst size (total) | p RNA /δ | RNA copies | 2.52 × 104 | 1.39 × 104–4.08 × 104 | 2.65 × 104 | 2.03 × 104–3.43 × 104 |
Viral burst size (infectious) | p 50/ δ | TCID50 | 0.215 | 0.127–0.351 | 0.018 | 0.0104–0.0280 |
Malthusian coefficient | M | ― | 3.08 | 2.82–3.52 | 2.59 | 2.37–2.80 |
Basic reproductive number (without removal) | R 0 | ― | 19.6 | 16.5–23.6 | 13.4 | 11.4–15.7 |
Basic reproductive number (with removal) | R *0 | ― | 6.25 | 5.29–7.51 | 4.84 | 4.13–5.62 |