N

Number of shRNA transduced into HSC

2, 4, or 6

P

Proportion of transduced HSC

1%, 20%

Time  step

Timestep of each iteration

12 hours

eff

Efficacy of each shRNA inhibiting viral production and/or infection, dependent on resistance mutations. Inhibition per shRNA was (1eff).

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 longlived.

Mean value of 4 timesteps.

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
