Table 1.

Parameter values for the multi-scale model. (The standard deviation of the random effects as estimated by a nonlinear mixed-effect model are provided in brackets () as described in [31].)

model	parameter	description	value and units
viral	log10β	viral infectivity	7.23 (0.2) virions−1 d−1
	δ	infected cell death rate	3.13 (0.02) d−1 cells−k
	k	innate immunity killing exponent	0.08 (0.02) unitless
	log10π	viral load corresponding to 50% infectiousness	2.59 (0.05) d−1
	m	viral load corresponding to 50% infectiousness	3.21 (0.33) d−1 cells−1
	log10ω	acquired immune recruitment rate	−4.55 (0.01) d−1 cells−1
	r	acquired immunity saturation exponent	10 unitless
	δE	acquired immune removal rate	1 d−1
	q	precursor maturation rate	2.4 × 10−5 d−1
	c	viral clearance rate	15 d−1
	T(0), I(0), M1(0), M2(0), E(0)	host-cell initial conditions	107, 1, 0, 0, 0 cells ml−1
	V(0)	virus initial conditions	${\displaystyle \frac{\pi I(0)}{c}}$ copies ml−1
	$\vartheta \hspace{0.17em}$	virus load scalar for additional variability simulations	1 unitless
transmission	λ	viral load corresponding to 50% contagiousness/infectiousness	107 copies ml−1
	α	hill slope modulating contagiousness/infectiousness	107 copies ml−1
	τ	average time delay for a newly infected person to begin producing virus	0.5 days
contacts	θ	average daily contact rate for Re = 1.0	2.3 d−1
		average daily contact rate for Re = 1.2	3.1 d−1
		average daily contact rate for Re = 1.4	3.5 d−1
		average daily contact rate for Re = 1.6	3.75 d−1
		average daily contact rate for Re = 1.8	4.0 d−1
		average daily contact rate for Re = 2.0	5.0 d−1
		average daily contact rate for Re = 2.2	5.5 d−1
	ρ	dispersion parameter	40