Abstract
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 —the average number of secondary cases caused by a primary case in an otherwise susceptible population. The modelling approaches and resulting estimates of 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 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 for the SARS-CoV-2 outbreak, showing that many estimates are overly confident. Our results emphasize the importance of propagating uncertainties in all components of , including the shape of the generation-interval distribution, in efforts to estimate at the outset of an epidemic.
Highlights
Since December 2019, a novel coronavirus (SARS-CoV-2) has been spreading globally [1]
These analyses focused on estimating the basic reproductive number R0—the average number of secondary cases generated by a primary case in a fully susceptible population [15,16]—in order to assess the pandemic potential of SARS-CoV-2
Comparing the estimates that include only some sources of uncertainty to the pooled estimate (R pool 1⁄4 3:0; 95% credible intervals (CI): 2.1–4.6; see ‘all’ in figure 2), we see that propagating error from the growth rate is absolutely crucial: uncertainty in the pooled estimates for both middle bars, which lack growth-rate uncertainty, is overly narrow
Summary
Since December 2019, a novel coronavirus (SARS-CoV-2) has been spreading globally [1]. As SARS-CoV-2 began to spread in parts of China outside Hubei province, as well as in other countries, many analyses of the outbreak were published as pre-prints [5,6,7,8,9,10] and in peer-reviewed journals [11,12,13,14] These analyses focused on estimating the basic reproductive number R0—the average number of secondary cases generated by a primary case in a fully susceptible population [15,16]—in order to assess the pandemic potential of SARS-CoV-2. Rapid dissemination of these early analyses played an important role in shaping the response to the outbreak [17]
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