Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

Article activity feed

1. 

   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.03.25.20043828: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	Consent: No data that was only released on GISAID was used without consent from the authors (see Acknowledgements).
   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
   A total of 24 ng of the low titer group was loaded onto a MinION R9.4.1 flow cell and sequenced for a total of 5.5 hours and generated 2.1 million reads.	MinION suggested: (MinION, RRID:SCR_017985)
   The RAMPART software from the ARTIC Network was used to monitor the sequencing run to estimate the depth of coverage across the genome for each barcoded sample in both runs …

   SciScore for 10.1101/2020.03.25.20043828: (What is this?)

   Please note, not all rigor criteria are appropriate for all manuscripts.

   Table 1: Rigor

   Institutional Review Board Statement	Consent: No data that was only released on GISAID was used without consent from the authors (see Acknowledgements).
   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
   A total of 24 ng of the low titer group was loaded onto a MinION R9.4.1 flow cell and sequenced for a total of 5.5 hours and generated 2.1 million reads.	MinION suggested: (MinION, RRID:SCR_017985)
   The RAMPART software from the ARTIC Network was used to monitor the sequencing run to estimate the depth of coverage across the genome for each barcoded sample in both runs https://github.com/artic-network/rampart).	RAMPART suggested: (Rampart, RRID:SCR_016742)
   Data and Code Availability: The SARS-CoV-2 sequences generated here can be found using the NCBI BioProject: (PRJNA614976) and GISAID (EPI_ISL_416416-416424).	NCBI BioProject suggested: (NCBI BioProject, RRID:SCR_004801)

   ---

   Results from OddPub: Thank you for sharing your data.

   ---

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

   Our estimates of domestic importation risk are likely conservative despite some important limitations in our air travel analysis. Because we do not have access to current airline data, we could not exactly quantify the impact of government restrictions on international travel. In addition, even without explicit government restrictions, general social distancing and work-from-home guidelines are reducing all airline travel. We did not account for these decreases in either our international or domestic travel data. While such variations may lower our domestic risk estimates, we also did not account for the large volumes of regional automobile and rail travel, especially along the corridor that connects Massachusetts, New York, New Jersey, Pennsylvania, and Washington D.C. to Connecticut. As such, the interconnectedness and large volumes of daily travel within the U.S. indicate that domestic spread of SARS-CoV-2 has become and will likely continue to be the primary source of new infections. We argue that, though simplistic, our model demonstrates the urgent need to focus control efforts in the U.S. on preventing further domestic virus spread. In China, local outbreak dynamics were highly correlated with travel between Wuhan and the outbreak dynamics therein during the early months of the epidemic (Kraemer et al., 2020). Similarly, if interstate introductions are not curtailed in the U.S. with improved surveillance measures, more robust diagnostic capabilities, and proper clinica...

   ---

   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.

   ---

   Read the original source
2. Version published to 10.1016/j.cell.2020.04.021

   May 1, 2020
3. 

   Version published to 10.1101/2020.03.25.20043828v1 on medRxiv

   Mar 26, 2020