SARS Coronavirus-2 variant tracing within the first Coronavirus Disease 19 clusters in northern Germany

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1. Version published to 10.1016/j.cmi.2020.09.034

   Jan 1, 2021
2. 

   ScreenIT

   Jun 17, 2020

   SciScore for 10.1101/2020.06.11.20127332: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The local ethics committee of the City of Hamburg approved the study (PV7306).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Patient 1, a male laboratory worker in his late 40s, with type II diabetes and high BMI.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Cell culture and virus isolation: Vero E6 cells (ATCC® CRL-1586) were propagated in DMEM containing 3% FCS, 1% Penicillin/ Streptomycin, 1 % L-Glutamine, 1 % Sodium pyruvate, 1 % non-essential amino acids (Gibco/ Thermo Fisher, Waltham, USA) under standard culture conditions.	Vero E6 suggested…

   SciScore for 10.1101/2020.06.11.20127332: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	IRB: The local ethics committee of the City of Hamburg approved the study (PV7306).
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	Patient 1, a male laboratory worker in his late 40s, with type II diabetes and high BMI.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   Cell culture and virus isolation: Vero E6 cells (ATCC® CRL-1586) were propagated in DMEM containing 3% FCS, 1% Penicillin/ Streptomycin, 1 % L-Glutamine, 1 % Sodium pyruvate, 1 % non-essential amino acids (Gibco/ Thermo Fisher, Waltham, USA) under standard culture conditions.	Vero E6 suggested: None
   Software and Algorithms
   Sentences	Resources
   MiSeq v2 kit (Illumina)	MiSeq suggested: (A5-miseq, RRID:SCR_012148)
   Only high confidence variants present in > 33% of reads within at least one individual sample were included and annotated using ANNOVAR (22).	ANNOVAR suggested: (ANNOVAR, RRID:SCR_012821)
   Data were clustered by hclust clustering method ward.D2.	hclust suggested: (HCLUST, RRID:SCR_009154)

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   Results from OddPub: Thank you for sharing your 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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   Read the original source
3. 

   Version published to 10.1101/2020.06.11.20127332v1 on medRxiv

   Jun 16, 2020