Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak

Park, Sang Woo; Bolker, Benjamin M.; Champredon, David; Earn, David J. D.; Li, Michael; Weitz, Joshua S.; Grenfell, Bryan T.; Dushoff, Jonathan

A novel coronavirus (SARS-CoV-2) emerged as a global threat in December 2019. As the epidemic progresses, disease modellers continue to focus on estimating the basic reproductive number [Formula: see text] —the average number of secondary cases caused by a primary case in an otherwise susceptible population. The modelling approaches and resulting estimates of [Formula: see text] during the beginning of the outbreak vary widely, despite relying on similar data sources. Here, we present a statistical framework for comparing and combining different estimates of [Formula: see text] across a wide range of models by decomposing the basic reproductive number into three key quantities: the exponential growth rate, the mean generation interval and the generation-interval dispersion. We apply our framework to early estimates of [Formula: see text] for the SARS-CoV-2 outbreak, showing that many [Formula: see text] estimates are overly confident. Our results emphasize the importance of propagating uncertainties in all components of [Formula: see text] , including the shape of the generation-interval distribution, in efforts to estimate [Formula: see text] at the outset of an epidemic.