Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

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1. Version published to 10.1016/j.cell.2021.03.052

   May 1, 2021
2. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2021.02.06.21251159: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Ethical statement: Helix data analyzed and presented here were obtained through IRB protocol WIRB#20203438, which grants a waiver of consent for a limited dataset for the purposes of public health under section 164.512(b) of the Privacy Rule (45 CFR § 164.512(b)). IRB: This work was also evaluated and approved by the Institutional Review Board at The Scripps Research Institute under IRB protocol IRB-15-6664.
   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
   The Helix COVID-19 Test is based on the Thermo Fisher TaqPath™ COVID-19 …

   SciScore for 10.1101/2021.02.06.21251159: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Ethical statement: Helix data analyzed and presented here were obtained through IRB protocol WIRB#20203438, which grants a waiver of consent for a limited dataset for the purposes of public health under section 164.512(b) of the Privacy Rule (45 CFR § 164.512(b)). IRB: This work was also evaluated and approved by the Institutional Review Board at The Scripps Research Institute under IRB protocol IRB-15-6664.
   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
   The Helix COVID-19 Test is based on the Thermo Fisher TaqPath™ COVID-19 Combo Kit, which targets three SARS-CoV-2 viral regions (N gene, S gene, and ORF1ab).	Thermo Fisher TaqPath™ suggested: None
   During the Amplify cDNA step, the annealing temperature was reduced from 65°C to 63°C.	Amplify suggested: (Amplify, RRID:SCR_002956)
   To measure cross-reactivity, the kmer reference list incorporated the NCBI database of 100,000 genomes for human and animal pathogens in addition to the SARS-CoV-2 reference.	NCBI suggested: (NCBI, RRID:SCR_006472)
   These libraries were individually sequenced on MinION R9 flow cells.	MinION suggested: (MinION, RRID:SCR_017985)
   We used a relatively uninformative conditional reference prior on the overall clock rate (Ferreira and Suchard, 2008), an exponentially growing population prior over the unknown tree and the BEAGLE library to improve computational performance (Ayres et al., 2019).	BEAGLE suggested: (BEAGLE, RRID:SCR_001789)

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   Results from OddPub: Thank you for sharing your code and data.

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   Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

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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 10.1101/2021.02.06.21251159 on medRxiv

   Feb 7, 2021