Genomic characterization and phylogenetic analysis of SARS‐COV‐2 in Italy

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1. 

   ScreenIT

   Jun 5, 2020

   SciScore for 10.1101/2020.03.15.20032870: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Written informed consent for any other medical procedures/interventions performed for routine treatment purposes was collected for each patient.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   After isolating the virus in Vero cells, SARS-CoV-2 RNA was extracted from the culture supernatant after 24 hours, and the full genome was obtained by amplifying 26 fragments using previously published specific primers 3.	Vero suggested: None
   Software and Algorithms
   Sentences	Resources
   The results …

   SciScore for 10.1101/2020.03.15.20032870: (What is this?)

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

   Table 1: Rigor

   Institutional Review Board Statement	Consent: Written informed consent for any other medical procedures/interventions performed for routine treatment purposes was collected for each patient.
   Randomization	not detected.
   Blinding	not detected.
   Power Analysis	not detected.
   Sex as a biological variable	not detected.
   Cell Line Authentication	not detected.

   Table 2: Resources

   Experimental Models: Cell Lines
   Sentences	Resources
   After isolating the virus in Vero cells, SARS-CoV-2 RNA was extracted from the culture supernatant after 24 hours, and the full genome was obtained by amplifying 26 fragments using previously published specific primers 3.	Vero suggested: None
   Software and Algorithms
   Sentences	Resources
   The results were mapped and aligned to the reference genome obtained from Gisaid (https://www.gisaid.org/, accession ID: EPI_ISL_412973) using Geneious software, v. 9.1.5 (http://www.geneious.com) 4.	Geneious suggested: (Geneious, RRID:SCR_010519)
   In order to investigate the temporal signal of the data set, a root-to-tip regression analysis was performed by using TempEst 5.	TempEst suggested: (TempEst, RRID:SCR_017304)
   The Hasegawa-Kishino-Yano model with a proportion of invariant sites (HKY+I) was selected as the simplest evolutionary model by means of JmodelTest, v. 2.1.7 (3), and the phylogenetic analysis was made using a Bayesian Markov Chain Monte Carlo (MCMC) method implemented in BEAST, v.1.8.4 6.	JmodelTest suggested: (jModelTest, RRID:SCR_015244) BEAST suggested: (BEAST, RRID:SCR_010228)
   All of the genes were tested for selection pressure using Datamonkey (https://www.datamonkey.org/).	Datamonkey suggested: (DataMonkey, RRID:SCR_010278)

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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: 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
2. Version published to 10.1002/jmv.25794

   Apr 10, 2020
3. 

   Version published to 10.1101/2020.03.15.20032870v1 on medRxiv

   Mar 20, 2020