Fig. 2

Schematic of infection dynamics of a single genotype from an individual in a longitudinal cohort study. a Samples are collected at times τ^j, and are either negative (x^j = 0) or positive (x^j = 1). In this example the samples after the period of prophylaxis can be encoded as 01100110. Examples of possible times for the acquisition T_inf and clearance T_clear of two infections are shown. b The exact values of T_inf and T_clear are unknown and hence are treated as parameters whose distributions are estimated via data augmentation. The green region denotes the probability that the first infection is present at that time. The orange region denotes the probability that the second infection of the same genotype is present at that time