But suppose each individual in one population is exposed to exactly the same risk factors as a corresponding individual in the other population. That means that traditional epidemiological data sets from these two populations would be identical. One population may have a core group which sustains transmission while the other may not. Black box era analytic methods, which conceptualize risk as an individual based phenomenon, cannot capture risk which is determined by how individuals are connected. The problem with ignoring risk factors which are characteristics of infected rather than susceptible individuals can be appreciated by considering the inadequacies of black box era approaches to measuring vaccine effects.
Vaccines stimulate immune responses that help control infection after the host takes up an agent .
A vaccine induced immune response may control some agents before they have any consequences for the individual or for the transmission of infection. On the other hand, it may only decrease the contagiousness of infection without eliminating infection. The black box paradigm doesn't recognize the effects of primary HIV infection for two reasons. First it is very difficult to ascertain exposure to someone with primary infection. Second, it is not just the infections directly caused by primary infection that generate its dominance of HIV transmission dynamics.