Estimation of COVID-19 transmission rates in California and the U.S. with reporting delays
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Abstract
We estimated time-varying reproduction numbers of COVID-19 transmission in counties and regions of California and in states of the United States, using the Wallinga-Teunis method of estimations applied to publicly available data. The serial interval distribution assumed incorporates wide uncertainty in delays from symptom onset to case reporting. This assumption contributes smoothing and a small but meaningful increase in numerical estimates of reproduction numbers due to the likely existence of secondary cases not yet reported. Transmission in many areas of the U.S. may not yet be controlled, including areas in which case counts appear to be stable or slowly declining.
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SciScore for 10.1101/2020.05.14.20101162: (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 analysis includes several limitations. Use of the Wallinga-Teunis estimator conventionally assumes complete reporting. Changes in reporting over time (such as inclusion of probable cases, or those resulting from increased or decreased testing) will yield biased estimates of Rt, as would changes in reporting delays over time. Some …
SciScore for 10.1101/2020.05.14.20101162: (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 analysis includes several limitations. Use of the Wallinga-Teunis estimator conventionally assumes complete reporting. Changes in reporting over time (such as inclusion of probable cases, or those resulting from increased or decreased testing) will yield biased estimates of Rt, as would changes in reporting delays over time. Some jurisdictions have begun to report probable cases together with confirmed cases; such a change in the middle of a case series would yield an upward bias in the estimated Rt. Our estimates suggest that while control measures such as sheltering in place and social distancing appear to be helpful in reducing transmission, COVID-19 transmission continues to be a serious concern, as few states in the U.S. appear to have actually achieved subcriticality.
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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