Table 1. Virtual patient-specific parameter values.

Seven parameters in the model were deemed patient-specific and were drawn from a normal distribution with mean the parameter value obtained either through fitting or from the literature (S1 Table). The standard deviation (Std Dev) for each normal distribution was informed by values in the literature (see Materials and methods and Supplementary Information Sections S6.1). Initial parameter sampling and new parameters generated through the simulated annealing optimization, were bounded within the interval range noted. All other parameters in the model were fixed to their original value (S1 Table).

Param	Units	Description	Mean	Ref	Std Dev	Ref	Range
$p_{M_{\mathrm{\Phi }I},L}$	1/day	Monocyte to macrophage differentiation by IL-6	1.7	[55]	2.2	[7]	[0, 9.9]
$p_{L,M_{\Phi I}}$	pg/ml/day	IL-6 production by inflammatory macrophages	1872	[56]	2.2	[7]	[1863, 1880]
pF,I	pg/ml/day	IFN production by infected cells	2.82	[57]	1.9	[53]	[0, 12.2]
pM,I	1/day	Monocyte recruitment rate by infected cells	0.22	[58]	0.08	[59]	[0, 0.63]
${\eta }_{F,M_{\Phi I}}$	109cells/ml	IFN by infected cells	0.0012	[57]	10−5	[60]	[0, 4.7 × 10−4]
ϵF,I	pg/ml	IFN production of CD8+ T cells	0.004	[61]	10−5	[54]	[0, 5.34 × 10−4]
pF,M	pg/ml/day	IFN production by monocytes	3.56	[62,63]	0.013	[62]	[3.4, 3.6]