Accounting for Imported Cases in Estimating the Time-Varying Reproductive Number of Coronavirus Disease 2019 in Hong Kong
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Abstract
Estimating the time-varying reproductive number, Rt, is critical for monitoring transmissibility of an infectious disease. The impact of imported cases on the estimation is rarely explored. We developed a model to estimate separately the Rt for local cases and imported cases, accounting for imperfect contact tracing of cases. We applied this framework to data on coronavirus disease 2019 outbreaks in Hong Kong. The estimated Rt for local cases rose above 1 in late March 2020, which was undetected by other commonly used methods. When imported cases account for a considerable proportion of all cases, their impact on estimating Rt is critical.
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SciScore for 10.1101/2021.02.09.21251416: (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
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study has some limitations. First, we did not account for incomplete observations. Mild or asymptomatic cases would likely be undetected. Also, testing availability and criteria would also be likely changing over time. If the proportion of undetected cases were constant over the outbreak, the Rt would still be unbiased [17]. Further …
SciScore for 10.1101/2021.02.09.21251416: (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
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Our study has some limitations. First, we did not account for incomplete observations. Mild or asymptomatic cases would likely be undetected. Also, testing availability and criteria would also be likely changing over time. If the proportion of undetected cases were constant over the outbreak, the Rt would still be unbiased [17]. Further investigation would be necessary to develop method to account for the changing proportion of undetected cases. Finally, rapid changes in the parameters could affect the estimated Rt, such as the sudden change for the delay distribution from infection to confirmation caused by overwhelmed healthcare systems, changing case definition during the epidemic [19], or superspreading events during the outbreaks [20]. In conclusion, we developed methodology to estimate separately the Rt for local and imported cases, to account for the potential differential infectiousness between them, due to control measures targeting inbound travelers. We compared the developed framework with the two current approaches to account for imported cases and illustrate the importance of properly accounting for the differential infectiousness in the estimation of Rt. Accurate estimation of Rt allows situational awareness of transmission and control in the community.
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.
Results from scite Reference Check: We found no unreliable references.
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