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. 2013 Oct 10;9(10):e1003264. doi: 10.1371/journal.pcbi.1003264

Table 2. Model parameters.

Parameter Value
Time step 1 week
Simulation time 2000 centuries
Host parameters
Maximal population size Inline graphic 4980 individuals
MHC diversity 1 locus with 14 alleles
Number of KIR loci 5
Bit string length 16 bitsa
Specificity Inline graphic (bit scale) 1–10 bits
Host mutation rate Inline graphic 0.00005 per allele per birth event
Infection b
Infection state Inline graphic 0 (susceptible), 1 (acute), 2 (chronic)
Probability of viral transmission during acute phase Inline graphic 0.85 per contact
Probability of viral transmission during chronic phase Inline graphic 0.15 per contact
Probability of clearing the wild-type virus Inline graphic 0.85
Probability of clearing the MHC downregulating virus Inline graphic 0.75
Probability of clearing the virus evolving decoy molecules Inline graphic 0
Immunity time Inline graphic 10 years
Acute infection time Inline graphic 4 weeks
Virus parameters
Inline graphic 0 (for Inline graphic), 0.1 (for Inline graphic), 0.06 (for Inline graphic)
Virus mutation rate Inline graphic 0.0001 per week
Initial conditions
Initial population size Inline graphic 4500 individuals
KIR initial diversity (SRI) 5 (1 allele per locus)
a

: The choice to use 16-bit strings represents a large enough theoretical repertoire of 65,536 sequences.

b

: The parameters used for the infection are chosen to maintain the epidemic. Changing the length of the acute phase or the probabilites of clearance do not affect our results on the evolution of the KIRs qualitively (results not shown).