The emergence of SARS-CoV-2 in Europe and the US
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Abstract
Accurate understanding of the global spread of emerging viruses is critically important for public health response and for anticipating and preventing future outbreaks. Here, we elucidate when, where and how the earliest sustained SARS-CoV-2 transmission networks became established in Europe and the United States (US). Our results refute prior findings erroneously linking cases in January 2020 with outbreaks that occurred weeks later. Instead, rapid interventions successfully prevented onward transmission of those early cases in Germany and Washington State. Other, later introductions of the virus from China to both Italy and Washington State founded the earliest sustained European and US transmission networks. Our analyses reveal an extended period of missed opportunity when intensive testing and contact tracing could have prevented SARS-CoV-2 from becoming established in the US and Europe.
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SciScore for 10.1101/2020.05.21.109322: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources BEAST .xml file example, FAVITES simulated phylogenies, and the GISAID accession numbers for all sequences used in the analysis are hosted at https://github.com/Worobeylab/SC2_outbreak Methods Supplementary Text Table S1 Figure S1 Materials and Methods: Supplementary Text: BEASTsuggested: (BEAST, RRID:SCR_010228)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Th…
SciScore for 10.1101/2020.05.21.109322: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources BEAST .xml file example, FAVITES simulated phylogenies, and the GISAID accession numbers for all sequences used in the analysis are hosted at https://github.com/Worobeylab/SC2_outbreak Methods Supplementary Text Table S1 Figure S1 Materials and Methods: Supplementary Text: BEASTsuggested: (BEAST, RRID:SCR_010228)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:This genetic similarity places limitations on some inferences such as calculating the ratio of imported cases to local transmissions in a given area. Yet we have shown that, precisely because of this slow rate, when as little as one mutation separates viruses, this difference can provide enough information for hypothesis testing when appropriate methods are employed. Bearing this in mind will put us in a better position to understand SARS-CoV-2 in the coming years.
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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