. 2011 Dec 1;7(12):e1002289. doi: 10.1371/journal.pcbi.1002289

Table 2. Definitions of the model parameters and a description of the parameter values used in our simulations.

Symbol	Description	Value used in simulation	Interpretation of parameter
μ	Population death rate	1/50 years⁻¹	Uninfected hosts have an average life expectancy of 50 years. This estimate is based upon a population in Southern Africa [36].
B	Population birth rate		The population size is constant in the absence of infection.
γ	Proportion of newborns who receive the vaccine at birth.	0 for the first 50 years of the epidemic and 1 beyond year 50.	No hosts receive the vaccine between years 0 and 50. Beyond year 50 all newborns receive the vaccine. Note that in addition we have assumed that all other hosts receive the vaccine at year 50.
	Proportion of hosts in the population with host type h	In Figure 7 different proportions are compared: 0.1^k0.9^n-k, 0.3^k0.7^n-k and 0.5^k0.5^n-k, where is the number of epitopes for which the host is HLA matched. In the remaining figures the proportion is 0.2^k0.8^n-k	Recognition of each epitope is assumed to be independent. In Figure 7 different percentages of the population recognising each epitope are considered: 10%, 30% and 50%. In the remaining figures 20% of the population recognise each epitope.
	Rate of escape at epitope i in unvaccinated HLA matched hosts.	In Figure 3 different escape rates (the same rate at each epitope) are compared: 1/3 years⁻¹, 1/30 years⁻¹ and 0 years⁻¹. In Figure 5 rates ranging from 0 years⁻¹ to 1/1000 years⁻¹ are considered. In the remaining figures the rate at each epitope is 1/8 years⁻¹ [22].	The reciprocal of the rate of escape is equal to the average time between infection and escape.
	Rate of escape at epitope i in vaccinated HLA matched hosts.		At each epitope escape occurs at the same rate in vaccinated and unvaccinated hosts.
	Rate of reversion at epitope i in HLA mismatched hosts.	In Figure 4 different reversion rates (the same at each epitope) are compared: 1/3 years⁻¹, 1/30 years⁻¹ and 0 years⁻¹. In Figure 5 rates ranging from 0 years⁻¹ to 1/1000 years⁻¹ are considered. In the remaining figures the rate at each epitope is 1/36 years⁻¹ [22].	The reciprocal of the rate of reversion is equal to the average time between infection and reversion.
	Disease-related death rate of unvaccinated or unsuccessfully vaccinated hosts	(1/10-µ) years⁻¹	The average life expectancy in the absence of vaccine-induced protection (1/(µ+α)) is 10 years [37]. This estimate assumes that infected unvaccinated hosts do not receive treatment.
	Disease-related death rate of successfully vaccinated hosts.	0 years⁻¹	Successfully vaccinated hosts have the same life expectancy as uninfected hosts.
	Transmission rate per partnership with an unvaccinated or unsuccessfully vaccinated host	0.2/c	In an unvaccinated population this yields a basic reproduction number of 2 [33].
	Transmission rate per partnership with a successfully vaccinated hosts.	In Figure 2 different values are considered: 0.008/c and 0.1/c. In the remaining figures: 0.008/c	In Figure 2 successfully vaccinated hosts are 25 times or 2 times less infectious compared to unvaccinated or unsuccessfully vaccinated hosts. In the remaining figures they are 25 times less infectious.
c	Rate of partner exchange	See above	See above.
r	Fraction of vaccinated hosts resistant to infection	0	No hosts are resistant to infection
n	Number of epitopes in the vaccine	In Figure 6 different number of epitopes are considered: 1, 3 and 5. In the remaining simulations there are 5 epitopes.	This is the number of epitopes that the vaccine is capable of inducing CTL responses to.