Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin

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1. 

   ScreenIT

   Aug 4, 2020

   SciScore for 10.1101/2020.01.22.914952: (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

   Antibodies
   Sentences	Resources
   And the virus were detected using SL-CoV Rp3 NP antibody followed by Cy3-conjugated mouse anti-rabbit IgG.	Rp3 NP suggested: None
   An anti-Human IgG-HRP conjugated monoclonal antibody (Kyab Biotech Co., Ltd, Wuhan, China) was used at a dilution of 1:40000.	anti-Human IgG-HRP suggested: None
   ACE2 expression was detected using mouse anti-S tag monoclonal antibody followed by FITC-labelled goat anti-mouse IgG H&L (Abcam, ab96879).	anti-S suggested: (Abcam Cat# ab96879, RRID:AB_10687475) anti-mouse IgG suggested: (Abcam Cat# ab96879, RRID:AB_10687475)
   Viral replication was detected using rabbit antibody against the …

   SciScore for 10.1101/2020.01.22.914952: (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

   Antibodies
   Sentences	Resources
   And the virus were detected using SL-CoV Rp3 NP antibody followed by Cy3-conjugated mouse anti-rabbit IgG.	Rp3 NP suggested: None
   An anti-Human IgG-HRP conjugated monoclonal antibody (Kyab Biotech Co., Ltd, Wuhan, China) was used at a dilution of 1:40000.	anti-Human IgG-HRP suggested: None
   ACE2 expression was detected using mouse anti-S tag monoclonal antibody followed by FITC-labelled goat anti-mouse IgG H&L (Abcam, ab96879).	anti-S suggested: (Abcam Cat# ab96879, RRID:AB_10687475) anti-mouse IgG suggested: (Abcam Cat# ab96879, RRID:AB_10687475)
   Viral replication was detected using rabbit antibody against the Rp3 NP protein (made in house, 1:100) followed by cyanin 3-conjugated goat anti-rabbit IgG (1:50, Abcam, ab6939).	Rp3 NP protein suggested: None anti-rabbit IgG suggested: (Abcam Cat# ab6939, RRID:AB_955021)
   Experimental Models: Cell Lines
   Sentences	Resources
   The following cells were used for virus isolation in this study: Vero, Vero E6, and Huh7 that were cultured in DMEM +10% FBS.	Huh7 suggested: CLS Cat# 300156/p7178_HuH7, RRID:CVCL_0336)
   HeLa cells transiently expressing ACE2 were prepared by a lipofectamine 3000 system (Thermo Fisher Scientific) in 96-well plate, with mock-transfected cells as controls.	HeLa suggested: None
   nCoV-2019 grown from Vero E6 cells was used for infection at multiplicity of infection 0.05.	Vero E6 suggested: RRID:CVCL_XD71)
   Experimental Models: Organisms/Strains
   Sentences	Resources
   The following cells were used for virus isolation in this study: Vero, Vero E6, and Huh7 that were cultured in DMEM +10% FBS.	Vero suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)
   Software and Algorithms
   Sentences	Resources
   The raw NGS reads were firstly processed by Cutadapt (v1.18) with minimum read length of 30bp.	Cutadapt suggested: (cutadapt, RRID:SCR_011841)
   BWA (v0.7.12-r1039) was utilized to align reads to local database with a filter hits parameter at 0.8 FMM value and minimum alignment score at 30.	BWA suggested: (BWA, RRID:SCR_010910)
   NGS reads were assembled into genomes using Geneious (v11.0.3) and MEGAHIT (v1.2.9).	Geneious suggested: (Geneious, RRID:SCR_010519)
   Sequence alignment and editing were conducted using ClustalW and GeneDoc.	ClustalW suggested: (ClustalW, RRID:SCR_017277)
   Maximum Likelihood phylogenetic trees based on nucleotide sequences of full-length ORF1b and S genes were constructed using the Jukes-Cantor model with bootstrap values determined by 1000 replicates in the MEGA6 software package.	MEGA6 suggested: (MEGA Software, RRID:SCR_000667)

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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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2. 

   Version published to 10.1101/2020.01.22.914952 on bioRxiv

   Jan 23, 2020