Measurability of the epidemic reproduction number in data-driven contact networks

Liu, Quan-Hui; Ajelli, Marco; Aleta, Alberto; Merler, Stefano; Moreno, Yamir; Vespignani, Alessandro

2009 H1N1 influenza pandemic At the beginning of each simulation, for each node i of age a i , we determine whether it is initially susceptible or removed by sampling from a Bernoulli distribution with probability P (a i ), where P (a) is the fraction of seropositive individual of age a as observed before the 2009 H1N1 pandemic in Italy [5] . Simulations are initialized with one infectious individual and no further introductions of index cases is assumed. One of the most striking features of the 2009 H1N1 influenza pandemic, observed in several studies focusing on different countries around the globe, was the presence of an age-specific susceptibility to infection, which was remarkably higher for young individuals (mainly corresponding to school-age individuals) [4, 5, 6, 7, 8, 9, 10] . In our model we use the estimates of age-specific susceptibility rates specific for the Italian population [5] : As direct estimates of the layer-specific transmission rates, we estimated them on the basis of agespecific seroprevalence data collected in Italy after the end of the 2009 H1N1 influenza pandemic [5] . Since the per-contact transmission probability p and the four layer-specific transmission rates w l are multiplying factors in Equation (1) (and thus cannot be estimated simultaneously), we fixed p = 1 and estimated w h , w s , w w , and w c .