Table 2. Sensitivity analyses of key infection properties.

For each pathogen, we show the three most important parameters with the associated partial rank correlation coefficient (PRCC) and its 95% confidence interval. Notations for parameter values are in Tables 1 and 3. Peak of infected cells is a measure of the size of the infection, peak of free-virion (or elementary bodies, EBs) load is how much progeny is released for re-seeding the infection or transmission, and day of peak is a measure for how quickly the infection grows. For effects on protection by epithelial parameters we tested: ν, μ, ρ_b, ρ_p, ζ, and ζ_u.

Uninfected Epithelium
Total number of cells	ρb: 0.72 [0.68, 0.74]	Δq: 0.66 [0.61, 0.70]	ν: -0.45 [-0.50, -0.39]
Time to homeostasis	Δq: 0.62 [0.58, 0.67]	ρp: -0.60 [-0.66, -0.55]	ν: -0.41 [-0.45, -0.35]
wart-associated HPV
effects of epithelial parameters
Peak of infected cells	ρb: 0.98 [0.98, 0.99]	ν: -0.94 [-0.95, -0.93]	μ: -0.73 [-0.77, -0.69]
Peak of free-virion load	ζ: -0.96 [-0.97, -0.96]	ρb: 0.94 [0.94, 0.95]	ν: -0.85 [-0.87, -0.83]
Duration of infection	ζ: 0.96 [0.95, 0.97]	ρb: -0.93 [-0.94, -0.92]	ρp: -0.85 [-0.87, -0.82]
Day of peak	ζ: 0.95 [0.95, 0.96]	ρb: -0.93 [-0.94, -0.92]	ρp: -0.88 [-0.90, -0.86]
effects of infection parameters
Peak of infected cells	ρa: 1.00 [0.99, 1.00]	κ: -0.84 [-0.85, -0.83]	θ: -0.02 [-0.09, 0.05]
Peak of free-virion load	θ: 0.92 [0.91, 0.93]	ρa: 0.88 [0.87, 0.90]	β: 0.05 [-0.002, 0.11]
Duration of infection	κ: -0.96 [-0.97, -0.96]	β: 0.71 [0.67, 0.73]	θ: 0.71 [0.68, 0.75]
Day of peak	κ: -0.99 [-1.00, -0.99]	β: -0.49 [-0.55, -0.42]	θ: -0.49 [-0.55, -0.41]
HR-HPV
effects of epithelial parameters
Peak of infected cells	ρb: 0.98 [0.97, 0.98]	ν: -0.94 [-0.94, -0.93]	ζ: -0.91 [-0.92, -0.89]
Peak of free-virion load	ζ: -0.97 [-0.97, -0.97]	ρb: 0.95 [0.95, 0.96]	ν: -0.87 [-0.86, -0.85]
Duration of infection	ζ: 0.97 [0.96, 0.97]	ρb: -0.95 [-0.96, -0.94]	νp: 0.86 [0.84, 0.88]
Day of peak	ζ: 0.97 [0.96, 0.97]	ρb: -0.95 [-0.96, -0.94]	νp: 0.86 [0.84, 0.88]
effects of infection parameters
Peak of infected cells	ab: 0.93 [0.92, 0.94]	ρa: 0.91 [0.90, 0.92]	ap: 0.24 [0.17, 0.31]
Peak of free-virion load	θ: 0.87 [0.86, 0.89]	ρa: 0.80 [0.78, 0.83]	ab: 0.77 [0.75, 0.81]
Duration of infection	κ: -0.95 [-0.95, -0.94]	θ: 0.68 [0.64, 0.71]	β: 0.66 [0.62, 0.70]
Day of peak	ap: -0.99 [-0.99, -0.99]	κ: -0.94 [-0.95, -0.94]	ρa: -0.15 [-0.22, -0.09]
Chlamydia
effects of epithelial parameters
Peak of infected cells	ρp: 0.95 [0.94, 0.96]	ν: -0.94 [-0.94, -0.93]	ζu: -0.91 [-0.92, -0.90]
Peak of EBs	ζu: -0.97 [-0.97, -0.96]	ρp: 0.91 [0.90, 0.92]	ν: -0.89 [-0.91, -0.87]
Duration of infection	ζu: -0.94 [-0.95, -0.93]	ρb: 0.92 [0.91, 0.93]	ν: -0.87 [-0.89, -0.86]
Day of peak	ζu: 0.94 [0.93, 0.95]	ν: 0.93 [0.92, 0.94]	ρp: -0.91 [-0.92, -0.89]
effects of infection parameters
Peak of infected cells	βu: 0.68 [0.64, 0.71]	βp: 0.53 [0.50, 0.58]	βb: 0.28 [0.22, 0.36]
Peak of EBs	βu: 0.79 [0.76, 0.81]	ηu: -0.68 [-0.73, -0.65]	βp: -0.61 [-0.66, -0.57]
Duration of infection	βp: 0.85 [0.84, 0.87]	f: -0.65 [-0.69, -0.61]	ηu: 0.37 [0.32, 0.42]
Day of peak	βu: -0.82 [-0.84, -0.80]	βp: -0.79 [-0.82, -0.77]	ηu: -0.33 [-0.40, -0.26]