Characterizations of SARS-CoV-2 mutational profile, spike protein stability and viral transmission
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SciScore for 10.1101/2020.05.03.066266: (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 Identification of variable sites: We have aligned nucleotide and amino acid sequences of ORF1ab, ORF3a, ORF6, ORF7a, ORF8, ORF10, envelop (E), membrane (M), nucleocapsid (N) and surface glycoprotein (S) using MUSCLE multiple sequence alignment algorithm in MEGA-X [17]. MUSCLEsuggested: (MUSCLE, RRID:SCR_011812), Pangolin coronavirus (MT072864.1) and two SARS-CoV strains TW11 (AY502924.1) and GD01 (AY278489.2) were downloaded from NCBI (https://www.ncbi.nlm.nih.gov/protein). NCBIsuggested: (NCBI, RRID:SCR_006472)https://www.ncbi.nlm.nih.gov/proteinsuggested: (Protein Database, RRID:SCR_017486)SciScore for 10.1101/2020.05.03.066266: (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 Identification of variable sites: We have aligned nucleotide and amino acid sequences of ORF1ab, ORF3a, ORF6, ORF7a, ORF8, ORF10, envelop (E), membrane (M), nucleocapsid (N) and surface glycoprotein (S) using MUSCLE multiple sequence alignment algorithm in MEGA-X [17]. MUSCLEsuggested: (MUSCLE, RRID:SCR_011812), Pangolin coronavirus (MT072864.1) and two SARS-CoV strains TW11 (AY502924.1) and GD01 (AY278489.2) were downloaded from NCBI (https://www.ncbi.nlm.nih.gov/protein). NCBIsuggested: (NCBI, RRID:SCR_006472)https://www.ncbi.nlm.nih.gov/proteinsuggested: (Protein Database, RRID:SCR_017486)We used FoldX BuildModel function to construct the mutant 3D protein structures [23]. FoldXsuggested: (FoldX, RRID:SCR_008522)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).
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.
- No funding statement was detected.
- No protocol registration statement was detected.
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