Characterizing the reproduction number of epidemics with early   sub-exponential growth dynamics
  Early estimates of the transmission potential of emerging and re-emerging infections are increasingly used to inform public health authorities on the level of risk posed by outbreaks. Existing methods to estimate the reproduction number generally assume exponential growth in case incidence in the first few disease generations, before susceptible depletion sets in. In reality, outbreaks can display sub-exponential (i.e., polynomial) growth in the first few disease generations, owing to clustering in contact patterns, spatial effects, inhomogeneous mixing, reactive behavior changes, or other mechanisms. Here, we introduce the generalized growth model to characterize the early growth profile of outbreaks and estimate the effective reproduction number, with no need for explicit assumptions about the shape of epidemic growth. We demonstrate this phenomenologic approach using analytical results and simulations from mechanistic models, and provide validation against a range of empirical disease datasets. Our results suggest that sub-exponential growth in the early phase of an epidemic is the rule rather the exception. For empirical outbreaks, the generalized-growth model consistently outperforms the exponential model for a variety of directly and indirectly transmitted diseases datasets with model estimates supporting sub-exponential growth dynamics. The rapid decline in effective reproduction number predicted by analytical results and observed in real and synthetic datasets within 3-5 disease generations contrasts with the expectation of invariant reproduction number in epidemics obeying exponential growth. Overall, our approach promotes a more reliable and data-driven characterization of the early epidemic phase, which is important for accurate estimation of the reproduction number and prediction of disease impact. 
Gerardo Chowell, C\'ecile Viboud, Lone Simonsen, Seyed Moghadas
q-bio.QM q-bio.PE