The origin and early spread of SARS-CoV-2 in Europe

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1. Version published to 10.1073/pnas.2012008118

   Feb 10, 2021
2. 

   ScreenIT

   Jun 14, 2020

   SciScore for 10.1101/2020.06.10.20127738: (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
   Parameter inference: For inferences, we used the implementation of the multi-type birth-death model in the bdmm package (19, 20) in the BEAST2 software (21).	BEAST2 suggested: (BEAST2, RRID:SCR_017307)

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   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).

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   Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:

   Estimates for the reproductive number fall roughly within the range of previous estimates (29), though we mention a …

   SciScore for 10.1101/2020.06.10.20127738: (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
   Parameter inference: For inferences, we used the implementation of the multi-type birth-death model in the bdmm package (19, 20) in the BEAST2 software (21).	BEAST2 suggested: (BEAST2, RRID:SCR_017307)

   ---

   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:

   Estimates for the reproductive number fall roughly within the range of previous estimates (29), though we mention a particular caveat with respect to the reproductive number in Hubei below. Unsurprisingly, prevalence estimates in early March generally exceed confirmed case counts by a factor of 1-3 (Figure S4). Our inferences of epidemiological parameters do not challenge the idea that the early reproductive number in different outbreaks is difficult to estimate precisely, but not hugely variable, and that there is substantial under-reporting in line-list data (30). Finally, we estimated the rate of new cases arising from migration compared with the rate of new cases arising from within-region transmission in the regions analyzed. The magnitudes of these rates are quite uncertain due to uncertainty in the inferred migration and transmission rates (Figure S11) and under-reporting in case counts, which we implicitly assume to be constant in time and between demes. However, the temporal trends suggested by these data are still compelling and robust towards different prior assumptions. We see that under sustained risk of case migration from Hubei, isolated cases were confirmed throughout Europe beginning in late January 2020 but did not immediately cause large outbreaks. Shortly after the first evidence of sustained within-region transmission in Italy, outbreaks in the rest of Europe also took hold (Figure 2). Our results based on the multi-type birth-death model take into accoun...

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   Results from TrialIdentifier: No clinical trial numbers were referenced.

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   Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

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   Results from JetFighter: We did not find any issues relating to colormaps.

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   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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3. 

   Version published to 10.1101/2020.06.10.20127738 on medRxiv

   Jun 12, 2020