Model-based reconstruction of an epidemic using multiple datasets: Understanding influenza A/H1N1 pandemic dynamics in Israel

Intensified surveillance during the 2009 A/H1N1 influenza pandemic in Israel resulted in large virological and serological datasets, presenting a unique opportunity for investigating the pandemic dynamics. We employ a conditional likelihood approach for fitting a disease transmission model to virological and serological data, conditional on clinical data. The model is used to reconstruct the temporal pattern of the pandemic in Israel in five age-groups and evaluate the factors that shaped it. We estimate the reproductive number at the beginning of the pandemic to be R = 1.4. We find that the combined effect of varying absolute humidity conditions and school vacations (SVs) is responsible for the infection pattern, characterized by three epidemic waves. Overall attack rate is estimated at 32% (28-35%) with a large variation among the age-groups: the highest attack rates within school children and the lowest within the elderly. This pattern of infection is explained by a combination of the age-group contact structure and increasing immunity with age. We assess that SVs increased the overall attack rates by prolonging the pandemic into the winter. Vaccinating school children would have been the optimal strategy for minimizing infection rates in all age-groups.