Table 1.

Model parameters and initial conditions. Unless otherwise stated, the parameter values shown in this table are used for all simulations shown in the results section. For some scenarios, we vary parameters to investigate how results are affected. The density of uninfected cells was estimated by assuming a locally densely packed collection of cells, with each cell having a volume of about 20 μm³ [31–33].

symbol	meaning	value	comment/source
U0(t = 0)	uninfected target cells with no virions bound	1.25×108 per ml	see caption
Un(t = 0)	uninfected target cells with n virions bound	0
In(t = 0)	infected target cells with n virions bound	0
V(t = 0)	inoculum dose (infectious virions)	100 per ml	arbitrary choice
X(t = 0)	immune response	1	see text
p	production rate of cell-bound infectious virions	100 per day	[33–36]
d	death rate of infected cells	2 per day	12 h lifespan [22,37,38]
c	virion clearance rate	6 per day	4 h lifespan [22,31,35,39,40]
r	rate of clonal expansion of the immune response	1 per day	[41–45]
gu	rate at which virions are internalized and lead to production of progeny virus	4 per day	6 h eclipse phase [22,34,35,46,47]
gi	rate at which virions are internalized into infected cells	varied	see text
f	probability that an internalized virus causes infection	varied	see text
	rate for virion attachment to uninfected/infected cells	varied	see text
	rate of virion detachment from uninfected/infected cells	varied	see text
w1/w2	rate of virus or infected cell clearance by antibodies or CTLs	varied	see text