Table 1. Parameters of the models.

Parameter	Type	Meaning	Value and confidence interval (if applicable)
${\mathrm{\Delta }}_{tclean}$	Fixed	Time to washing (h)	$2$
$L_0$	Fixed	Initial resource concentration (unit)	$1$
${\mathrm{\Delta }}_{tcyt}$	Fixed	Time from cell infection to cytokine generation (h)	$5$
$C_{initial}$	Fixed	Initial number of healthy cells (pcs)	30,000
$V_{initial}$	Fixed	Initial number of virions (pcs)	3,000
$N_V$	Fixed	The number of points in time for free virion measurements (pcs)	$3$
$N_{RNA}$	Fixed	The number of points in time for viral RNA measurements (pcs)	$4$
${\tau }_1$	Fixed	Time corresponding to the first measurement of infected cells (h)	$2$
${\gamma }_{{\tau }_1}$	Fixed	The fraction of infected cells for WT at the moment ${\tau }_1$ (%)	$6$
${\beta }_{cyt}$	Global	Intensity of cytokine entry ( ${(\text{pcs}\cdot \text{h})}^{-1}$)	1.18025e−08 [1.1241e−08 to 1.3663e−08]
$n_{l2V}$	Global	Resources used to produce a single virion (fraction of the relative unit)	$0.000067$
			[0.00006–0.000073]
$p_{Vir}$	Global	Virion generation intensity ( ${(\text{pcs}\cdot \text{h})}^{-1}$)	$316245$ [80672.2– $\mathrm{\infty }$]
${\mathrm{\Delta }}_{tRNAdouble}$	Global	Time required to double viral RNA in an infected cell (h)	$30$ [25.9151– $\mathrm{\infty }$]
$k$	Global	Reduction of infection intensity for infected and resistant cells (times)	$115$ [99.3414–154.112]
${\mathrm{\Delta }}_{tlatent}$	Global	Time from cell infection to virus generation (h)	$7.36095$ [7.36095–7.36095]
$Nor{m}_V$	Global	Normalization coefficient for the number of virions	$2.1$
$Nor{m}_{RNA}$	Global	Normalization coefficient for the concentration of viral RNA	$2.73$
$\beta$	Local	Intensity of cell infection ( ${(\text{pcs}\cdot \text{h})}^{-1}$)	WT 3.476e−08 [3.15e−08 to 3.65e−08]	Delta 2.046e−08 [1.77e−08 to 2.15e−08]
$p_c$	Local	Cytokine generation intensity ( ${(\text{pcs}\cdot \text{h})}^{-1}$)	WT 106,422 [96,527–123,197]	Delta 150,453 [136,465–201,622]
$R_0$	Internal	Internal cell parameter updating frequency ( ${\text{h}}^{-1}$)	$100$
${\mathrm{\Delta }}_{DE}$	Internal	Step in numerical solution of the system of equations (h)	${10}^{-3}$
${\mathrm{\Delta }}_h$	Internal	Step in evaluation of the function $p$ (h)	${10}^{-5}$
${\alpha }_i,i=1,\dots N_V$	Internal	Weights for penalties in the error functional	$1,1,1$
${\alpha }_j^{\prime }$, $j=1,\dots ,N_{RNA}$	Internal	Weights for penalties in the error functional	$10,1,1,1$
${\theta }_{{\tau }_1}$	Internal	Weight for penalty in the error functional	5.10−7