Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak
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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 R 0 —the average number of secondary cases caused by a primary case in an otherwise susceptible population. The modelling approaches and resulting estimates of R 0 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 R 0 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 R 0 for the SARS-CoV-2 outbreak, showing that many R 0 estimates are overly confident. Our results emphasize the importance of propagating uncertainties in all components of R 0 , including the shape of the generation-interval distribution, in efforts to estimate R 0 at the outset of an epidemic.
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SciScore for 10.1101/2020.01.30.20019877: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Five studies (Liu et al., 2020; Majumder and Mandl, 2020; Read et al., 2020a; Riou and Althaus, 2020a; Zhao et al., 2020) were uploaded to pre-print servers (bioRxiv, medRxiv, and SSRN); one report was posted on the web site of Imperial College London (Imai et al., 2020); and one report was posted on nextstrain.org (Bedford et al., 2020). bioRxivsuggested: (bioRxiv, RRID:SCR_003933)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to …SciScore for 10.1101/2020.01.30.20019877: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Five studies (Liu et al., 2020; Majumder and Mandl, 2020; Read et al., 2020a; Riou and Althaus, 2020a; Zhao et al., 2020) were uploaded to pre-print servers (bioRxiv, medRxiv, and SSRN); one report was posted on the web site of Imperial College London (Imai et al., 2020); and one report was posted on nextstrain.org (Bedford et al., 2020). bioRxivsuggested: (bioRxiv, RRID:SCR_003933)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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