Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus)
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly pathogenic virus that has caused the global COVID-19 pandemic. Tracing the evolution and transmission of the virus is crucial to respond to and control the pandemic through appropriate intervention strategies. This paper reports and analyses genomic mutations in the coding regions of SARS-CoV-2 and their probable protein secondary structure and solvent accessibility changes, which are predicted using deep learning models. Prediction results suggest that mutation D614G in the virus spike protein, which has attracted much attention from researchers, is unlikely to make changes in protein secondary structure and relative solvent accessibility. Based on 6324 viral genome sequences, we create a spreadsheet dataset of point mutations that can facilitate the investigation of SARS-CoV-2 in many perspectives, especially in tracing the evolution and worldwide spread of the virus. Our analysis results also show that coding genes E, M, ORF6, ORF7a, ORF7b and ORF10 are most stable, potentially suitable to be targeted for vaccine and drug development.
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SciScore for 10.1101/2020.07.10.171769: (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 The number of available sequences is thus different from one protein to another (see column “Avai Num” in Table 1). Num”suggested: (National University of Malaysia; Selangor; Malaysia, RRID:SCR_004724)Specifically, we use the Python Bio.pairwise2.align.globalms function (https://biopython.org/docs/dev/api/Bio.pairwise2.html) where a match is given 2 points, a mismatch is deducted 0.5 points, 2 points are deducted when opening a gap, and 1 point is deducted when extending it. Pythonsuggested: (IPython, RRID:SCR_001658)Results from OddPub: Thank you for sharing your data.
Results from Limitatio…SciScore for 10.1101/2020.07.10.171769: (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 The number of available sequences is thus different from one protein to another (see column “Avai Num” in Table 1). Num”suggested: (National University of Malaysia; Selangor; Malaysia, RRID:SCR_004724)Specifically, we use the Python Bio.pairwise2.align.globalms function (https://biopython.org/docs/dev/api/Bio.pairwise2.html) where a match is given 2 points, a mismatch is deducted 0.5 points, 2 points are deducted when opening a gap, and 1 point is deducted when extending it. Pythonsuggested: (IPython, RRID:SCR_001658)Results from OddPub: Thank you for sharing your 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.
- No funding statement was detected.
- No protocol registration statement was detected.
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