Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

Article activity feed

1. 

   ScreenIT

   Mar 1, 2021

   SciScore for 10.1101/2020.04.01.20047076: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   n=4) sequencing platforms, and (ii) using version 1 of the ARTIC COVID-19 multiplex PCR primers (https://artic.network/ncov-2019), followed by nanopore sequencing on an ONT MinION (n=45).	MinION suggested: (MinION, RRID:SCR_017985)
   Both the concentration and the quality of all isolated RNA samples were measured and checked with the Agilent Bioanalyzer 2100 and Qubit.	Agilent Bioanalyzer suggested: None
   The mapping of cleaned reads was performed against GenBank reference strain MN908947.3 using Bowtie2 (Langmead and Salzberg, 2012).	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   Consensus …

   SciScore for 10.1101/2020.04.01.20047076: (What is this?)

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

   Table 1: Rigor

   NIH rigor criteria are not applicable to paper type.

   Table 2: Resources

   Software and Algorithms
   Sentences	Resources
   n=4) sequencing platforms, and (ii) using version 1 of the ARTIC COVID-19 multiplex PCR primers (https://artic.network/ncov-2019), followed by nanopore sequencing on an ONT MinION (n=45).	MinION suggested: (MinION, RRID:SCR_017985)
   Both the concentration and the quality of all isolated RNA samples were measured and checked with the Agilent Bioanalyzer 2100 and Qubit.	Agilent Bioanalyzer suggested: None
   The mapping of cleaned reads was performed against GenBank reference strain MN908947.3 using Bowtie2 (Langmead and Salzberg, 2012).	Bowtie2 suggested: (Bowtie 2, RRID:SCR_016368)
   Consensus sequences were generated using samtools 1.2 (Li et al., 2009).	samtools suggested: (SAMTOOLS, RRID:SCR_002105)
   Sequences were aligned using MAFFT v7.4 (Katoh and Standley, 2013) and manually inspected in Geneious v11.0.3 (https://www.geneious.com).	MAFFT suggested: (MAFFT, RRID:SCR_011811) Geneious suggested: (Geneious, RRID:SCR_010519)
   The ML phylogeny was estimated with PhyML (Guindon et al., 2010) using the HKY+Γ4 substitution model (Hasegawa et al., 1985) with gamma-distributed rate variation (Yang, 1994).	PhyML suggested: (PhyML, RRID:SCR_014629)
   The Bayesian coalescent tree analysis was undertaken in the BEAST (Ayres et al., 2012; Suchard et al., 2018) framework, also using the HKY+Γ4 substitution model with gamma-distributed rate variation with an exponential population growth tree prior and a strict molecular clock.	BEAST suggested: (BEAST, RRID:SCR_010228)

   ---

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

   ---

   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.

   ---

   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.2020.04.023

   May 1, 2020
3. 

   Version published to 10.1101/2020.04.01.20047076v1 on medRxiv

   Apr 4, 2020