Table 2. Parameter fits for innate/adaptive/minimal immune mixed effects models.

These values represent the mean and standard deviation of the priors that maximize the likelihood as calculated by monolix. All parameters are assumed to be log-normally distributed, constraining all parameters to be positive. In some cases the standard deviation is greater than the mean, because the lognormal distribution can be highly skewed. (gen/ml) refers to viral genomes per ml of blood. Parameter distributions for all models are show in Online Resource 1 Figures 2–5

Parameter	Description	Innate		Adaptive		Minimal
		Mean	S.D.	Mean	S.D.	Mean	S.D
r (1/day)	Viral growth rate	1.69	0.48	1.83	0.46	1.60	0.47
k (1/day)	Max killing rate	4.18	0.46	4.11	0.56	3.68	0.66
s (1/day)	Immune growth/activation rate	0.17	0.01	0.52	0.02
ϕ (gen/ml)	V req’d for 50% max activation	25.2	9.67	23.6	7.67	11.2	3.90
ψ	R/X req’d for 50% max killing	0.37	0.01	3.78	0.22
V0 (gen/ml)	Viral load at t = 0	0.10	0.08	0.10	0.08	0.10	0.04
n	Hill exponent in killing term	27.9	48.4	6.97	10.38
m	Hill exponent in activation term	3.67	9.22	1.62	0.16
td (days)	Time before immune response					2.90	0.26