Table 3 Parameter descriptions
Parameters | Definition | Values |
|---|---|---|
N | Number of shRNA transduced into HSC | 2, 4, or 6 |
P | Proportion of transduced HSC | 1%, 20% |
Time - step | Time-step of each iteration | 12 hours |
eff | Efficacy of each shRNA inhibiting viral production and/or infection, dependent on resistance mutations. Inhibition per shRNA was (1-eff). | 0.8, 0.5, 0 |
fitness | Fitness of viral strain relative to wild type | 0.5, 0.9, 0.99 |
lifespan | Lifespan of newly infected cell. Determined from Poisson distribution. Cells with a lifespan of 0 are considered long-lived. | Mean value of 4 time-steps. |
P.neigh | Probability a dead cell is replaced by an uninfected neighbour, provided one exists. Alternatively it is replaced by a new cell generated from HSC. | 0.99 |
P.mut | Probability of mutation per nt per reverse transcription | 3.4 × 10-5 |
P.inf | Probability of infection relative to total neighbouring viral production and cell transduction | 0.0667 |