Mutational analysis unveils the temporal and spatial distribution of G614 genotype of SARS-CoV-2in different Indian states and its association with case fatality rate of COVID-19
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Abstract
Pan genomic analysis of the global SARS-CoV-2 isolates has resulted in the identification of several regions of increased genetic variation but there is absence of research on its association with the clinical outcome. The present study fills the vacuum and does mutational analysis of genomic sequence of Indian SARS-CoV-2 isolates. Results reveal the existence of non-synonymous G614 spike protein mutation in 61.45% of the total study genome along with three other mutations. Further, temporal variation in the frequencies of G614 genotype in the country is observed. The examination of the probable association of G614 genotype with COVID-19 severity shows that CFR G614 genotype in India is positively and strongly correlated. It appears that the clinical outcome of the COVID-19 cases in India are significantly and adversely affected by the increasing trend in the G614 genotype; which needs to be addressed combining both laboratory experiments and epidemiological investigations.
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SciScore for 10.1101/2020.07.27.222562: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources It has been ascertained that all the retrieved sequences were mapped to reference genome of SARS-CoV-2deposited from Wuhan, China (GenBank Accession No. NC_045512.2) using Geneious Pro (V.8.0.5). Geneioussuggested: (Geneious, RRID:SCR_010519)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 …SciScore for 10.1101/2020.07.27.222562: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources It has been ascertained that all the retrieved sequences were mapped to reference genome of SARS-CoV-2deposited from Wuhan, China (GenBank Accession No. NC_045512.2) using Geneious Pro (V.8.0.5). Geneioussuggested: (Geneious, RRID:SCR_010519)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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SciScore for 10.1101/2020.07.27.222562: (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 It has been ascertained that all the retrieved sequences were mapped to reference genome of SARS-CoV2deposited from Wuhan, China (GenBank Accession No. NC_045512.2) using Geneious Pro (V.8.0.5). Geneioussuggested: (Geneious, SCR_010519)Data from additional tools added to each annotation on a weekly basis.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. …
SciScore for 10.1101/2020.07.27.222562: (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 It has been ascertained that all the retrieved sequences were mapped to reference genome of SARS-CoV2deposited from Wuhan, China (GenBank Accession No. NC_045512.2) using Geneious Pro (V.8.0.5). Geneioussuggested: (Geneious, SCR_010519)Data from additional tools added to each annotation on a weekly basis.
About SciScore
SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore is not a substitute for expert review. SciScore checks for the presence and correctness of RRIDs (research resource identifiers) in the manuscript, and detects sentences that appear to be missing RRIDs. SciScore also checks to make sure that rigor criteria are addressed by authors. It does this by detecting sentences that discuss criteria such as blinding or power analysis. SciScore does not guarantee that the rigor criteria that it detects are appropriate for the particular study. Instead it assists authors, editors, and reviewers by drawing attention to sections of the manuscript that contain or should contain various rigor criteria and key resources. For details on the results shown here, including references cited, please follow this link.
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